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1. Addario C. et al. Different alcohol exposures induce selective alterations on the expression of dynorphin and nociceptin systems related genes in rat brain // Addict. Biol. 2013. Vol. 18, № 3. P. 425–433.

In the amoeboid spermatozoa from Caenorhabditis elegans, motility acquisition is preceded by substantial rearrangement of the plasma membrane. The current genetic model posits a multicomponent complex of membrane and cytoplasmic proteins responsible for pseudopod extension. This model can be translated into a physiological context through the involvement of cholesterol-enriched signaling platforms. We show that discrete cholesterol-enriched microdomains are present in C. elegans spermatids. These microdomains redistributed towards the cell body upon pseudopod extension resulting in a phospholipid-enriched pseudopod. Cholesterol saturation in the spermatids prevented pseudopod extension and motility acquisition, whereas cholesterol depletion increased the rate of in vitro pseudopod extension. This work suggests that plasma membrane cholesterol plays an important role in regulating the membrane dynamics that precede pseudopod extension and motility acquisition. (C) 2012 Elsevier Inc. All rights reserved.

http://dx.doi.org//10.1016/j.bbrc.2012.09.071

2. Androjna C. et al. Pulsed Electromagnetic Field Treatment Enhances Healing Callus Biomechanical Properties in an Animal Model of Osteoporotic Fracture // Bioelectromagnetics. 2014. Vol. 35, № 6. P. 396–405.

Delayed bone healing has been noted in osteoporosis patients and in the ovariectomized (OVX) rat model of estrogen-depletion osteopenia. Pulsed electromagnetic field (PEMF) devices are clinically approved as an adjunct to cervical fusion surgery in patients at high risk for non-fusion and for the treatment of fracture non-unions. These bone growth stimulating devices also accelerate the healing of fresh fracture repair in skeletally mature normal rats but have not been tested for efficacy to accelerate and/or enhance the delayed bone repair process in OVX rats. The current study tested the hypothesis that daily PEMF treatments would improve the fracture healing response in skeletally mature OVX rats. By 6 weeks of healing, PEMF treatments resulted in improved hard callus elastic modulus across fibula fractures normalizing the healing process in OVX rats with respect to this mechanical property. Radiographic evidence showed an improved hard callus bridging across fibula fractures in OVX rats treated with PEMF as compared to sham treatments. These findings provide a scientific rationale for investigating whether PEMF might improve bone-healing responses in at-risk osteoporotic patients. (C) 2014 Wiley Periodicals, Inc.

http://dx.doi.org//10.1002/bem.21855

3. U07870
Astle W.J. et al. The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease // Cell. 2016. Vol. 167, № 5. P. 1415–+.

Many common variants have been associated with hematological traits, but identification of causal genes and pathways has proven challenging. We performed a genome-wide association analysis in the UK Biobank and INTERVAL studies, testing 29.5 million genetic variants for association with 36 red cell, white cell, and platelet properties in 173,480 European-ancestry participants. This effort yielded hundreds of low frequency (<5%) and rare (<1%) variants with a strong impact on blood cell phenotypes. Our data highlight general properties of the allelic architecture of complex traits, including the proportion of the heritable component of each blood trait explained by the polygenic signal across different genome regulatory domains. Finally, through Mendelian randomization, we provide evidence of shared genetic pathways linking blood cell indices with complex pathologies, including autoimmune diseases, schizophrenia, and coronary heart disease and evidence suggesting previously reported population associations between blood cell indices and cardiovascular disease may be non-causal.

http://dx.doi.org//10.1016/j.cell.2016.10.042

4. Basu U., Guan L.L., Moore S.S. Functional Genomics Approach for Identification of Molecular Processes Underlying Neurodegenerative Disorders in Prion Diseases // Curr. Genomics. 2012. Vol. 13, № 5. P. 369–378.

Prion diseases or transmissible spongiform encephalopathies (TSEs) are infectious neurodegenerative disorders leading to death. These include Cresutzfeldt-Jakob disease (CJD), familial, sporadic and variant CJD and kuru in humans; and animal TSEs include scrapie in sheep, bovine spongiform encephalopathy (BSE) in cattle, chronic wasting disease (CWD) of mule deer and elk, and transmissible mink encephalopathy. All these TSEs share common pathological features such as accumulation of mis-folded prion proteins in the central nervous system leading to cellular dysfunction and cell death. It is important to characterize the molecular pathways and events leading to prion induced neurodegeneration. Here we discuss the impact of the functional genomics approaches including microarrays, subtractive hybridization and microRNA profiling in elucidating transcriptional cascades at different stages of disease. Many of these transcriptional changes have been observed in multiple neurodegenerative diseases which may aid in identification of biomarkers for disease. A comprehensive characterization of expression profiles implicated in neurodegenerative disorders will undoubtedly advance our understanding on neuropathology and dysfunction during prion disease and other neurodegenerative disorders. We also present an outlook on the future work which may focus on analysis of structural genetic variation, genome and transcriptome sequencing using next generation sequencing with an integrated approach on animal and human TSE related studies.

5. U07870
Berry J.A. et al. Sleep Facilitates Memory by Blocking Dopamine Neuron-Mediated Forgetting // Cell. 2015. Vol. 161, № 7. P. 1656–1667.

The development of major depression requires both genetic and environmental factors. A brain proteomic investigation on the genetic model of Flinders sensitive and resistant line (FSL-FRL) rats was performed. Maternal separation (MS) was also applied to identify protein networks affected by stress exposure, since early-life trauma is considered an important antecedent of depression. Hippocampus (HIP) and prefrontal/frontal cortex proteins were extracted and separated by 2-Dimensional (2-D) gel electrophoresis. After image analysis, significantly modulated proteins in the different conditions analysed were identified by mass spectrometry. The expression of proteins involved in energy metabolism, cellular localization and transport, cytoskeleton organization and apoptosis differed in the two lines. Maternal separation differently affected the genetic backgrounds, by modulating cytoskeleton and neuron morphogenesis proteins in FSL; energy metabolism, cellular localization, neuron differentiation and intracellular transport in FRL. The present work shows that different mechanisms could be involved in the pathophysiology of depression and the vulnerability to stress, suggesting possible new cellular pathways and key markers for the study of affective disorders. (C) 2011 IBRO. Published by Elsevier Ltd. All rights reserved.

http://dx.doi.org//10.1016/j.neuroscience.2010.12.043

6. U15400
Betteken M.I., Rocha E.R., Smith C.J. Dps and DpsL Mediate Survival In Vitro and In Vivo during the Prolonged Oxidative Stress Response in Bacteroides fragilis // J. Bacteriol. 2015. Vol. 197, № 20. P. 3329–3338.

Bacteroides fragilis is a Gram-negative anaerobe and member of the human intestinal tract microbiome, where it plays many beneficial roles. However, translocation of the organism to the peritoneal cavity can lead to peritonitis, intra-abdominal abscess formation, bacteremia, and sepsis. During translocation, B. fragilis is exposed to increased oxidative stress from the oxygenated tissues of the peritoneal cavity and the immune response. In order to survive, B. fragilis mounts a robust oxidative stress response consisting of an acute and a prolonged oxidative stress (POST) response. This report demonstrates that the ability to induce high levels of resistance to tert-butyl hydroperoxide (tBOOH) after extended exposure to air can be linked to the POST response. Disk diffusion assays comparing the wild type to a Delta dps mutant and a Delta dps Delta bfr mutant showed greater sensitivity of the mutants to tBOOH after exposure to air, suggesting that Dps and DpsL play a role in the resistance phenotype. Complementation studies with dps or bfr (encoding DpsL) restored tBOOH resistance, suggesting a role for both of these ferritin-family proteins in the response. Additionally, cultures treated with the iron chelator dipyridyl were not killed by tBOOH, indicating Dps and DpsL function by sequestering iron to prevent cellular damage. An in vivo animal model showed that the Delta dps Delta bfr mutant was attenuated, indicating that management of iron is important for survival within the abscess. Together, these data demonstrate a role for Dps and DpsL in the POST response which mediates survival in vitro and in vivo. IMPORTANCE B. fragilis is the anaerobe most frequently isolated from extraintestinal opportunistic infections, but there is a paucity of information about the factors that allow this organism to survive outside its normal intestinal environment. This report demonstrates that the iron storage proteins Dps and DpsL protect against oxidative stress and that they contribute to survival both in vitro and in vivo. Additionally, this work demonstrates an important role for the POST response in B. fragilis survival and provides insight into the complex regulation of this response.

http://dx.doi.org//10.1128/JB.00342-15

7. U12116
Blechingberg J., Holm I.E., Nielsen A.L. Characterization and expression analysis in the developing embryonic brain of the porcine FET family: FUS, EWS, and TAF15 // Gene. 2012. Vol. 493, № 1. P. 27–35.

The FET protein family consists of FUS (TLS), EWS (EWSIU), and TAF15. The FET proteins bind DNA and RNA and are involved in transcriptional regulation and RNA processing. Translocations involving the FET genes have been identified in human sarcomas, and mutations in the FUS and TAF15 genes are associated with Amyotrophic lateral Sclerosis. We here describe the characterization of the porcine FET proteins and an expression analysis during embryonic brain development. The FET proteins are well conserved between pig and human. FET protein mutations associated with Amyotrophic Lateral Sclerosis affect evolutionary conserved amino acids. In cultured cells the porcine FET proteins have a nuclear localization with some specific cytoplasmic aggregation of TAF15 in neuronal progenitor cells. Immunohistochemical analyses supported a predominant nuclear localization, but also faint cytoplasmic localization. The FET proteins have similar expression profiles throughout the development of the embryonic porcine brain and most cell types appeared positive for expression. Quantitative RT-PCR analyses showed that the FET mRNA expression decreased during embryonic development of hippocampus and for FUS and EWS during embryonic development of cortex. FET mRNA expression was relatively constant in brain stem, basal ganglia, and cerebellum. Overall the FET protein localization and mRNA and protein expression analyses were concordant with previous analysis from the human brain. The presented results indicate that the porcine brain could be an alternative model for the future examination of the normal functions as well as neurological disease associated functions of the FET proteins. (C) 2011 Elsevier B.V. All rights reserved.

http://dx.doi.org//10.1016/j.gene.2011.11.038

8. U07870
Chan C.-H. et al. Pharmacological Inactivation of Skp2 SCF Ubiquitin Ligase Restricts Cancer Stem Cell Traits and Cancer Progression // Cell. 2013. Vol. 154, № 3. P. 556–568.

Skp2 E3 ligase is overexpressed in numerous human cancers and plays a critical role in cell-cycle progression, senescence, metabolism, cancer progression, and metastasis. In the present study, we identified a specific Skp2 inhibitor using high-throughput in silico screening of large and diverse chemical libraries. This Skp2 inhibitor selectively suppresses Skp2 E3 ligase activity, but not activity of other SCF complexes. It also phenocopies the effects observed upon genetic Skp2 deficiency, such as suppressing survival and Akt-mediated glycolysis and triggering p53-independent cellular senescence. Strikingly, we discovered a critical function of Skp2 in positively regulating cancer stem cell populations and self-renewal ability through genetic and pharmacological approaches. Notably, Skp2 inhibitor exhibits potent antitumor activities in multiple animal models and cooperates with chemotherapeutic agents to reduce cancer cell survival. Our study thus provides pharmacological evidence that Skp2 is a promising target for restricting cancer stem cell and cancer progression.

http://dx.doi.org//10.1016/j.cell.2013.06.048

9. U07870
Chan C.K.F. et al. Identification and Specification of the Mouse Skeletal Stem Cell // Cell. 2015. Vol. 160, № 1–2. P. 285–298.

How are skeletal tissues derived from skeletal stem cells? Here, we map bone, cartilage, and stromal development from a population of highly pure, postnatal skeletal stem cells (mouse skeletal stem cells, mSSCs) to their downstream progenitors of bone, cartilage, and stromal tissue. We then investigated the transcriptome of the stem/progenitor cells for unique gene-expression patterns that would indicate potential regulators of mSSC lineage commitment. We demonstrate that mSSC niche factors can be potent inducers of osteogenesis, and several specific combinations of recombinant mSSC niche factors can activate mSSC genetic programs in situ, even in nonskeletal tissues, resulting in de novo formation of cartilage or bone and bone marrow stroma. Inducing mSSC formation with soluble factors and subsequently regulating the mSSC niche to specify its differentiation toward bone, cartilage, or stromal cells could represent a paradigm shift in the therapeutic regeneration of skeletal tissues.

http://dx.doi.org//10.1016/j.cell.2014.12.002

10. 09646906
Chen G. et al. Genome-wide association study identifies novel loci association with fasting insulin and insulin resistance in African Americans // Hum. Mol. Genet. 2012. Vol. 21, № 20. P. 4530–4536.

Insulin resistance (IR) is a key determinant of type 2 diabetes (T2D) and other metabolic disorders. This genome-wide association study (GWAS) was designed to shed light on the genetic basis of fasting insulin (FI) and IR in 927 non-diabetic African Americans. 5 396 838 single-nucleotide polymorphisms (SNPs) were tested for associations with FI or IR with adjustments for age, sex, body mass index, hypertension status and first two principal components. Genotyped SNPs (n 12) with P 5 10(6) in African Americans were carried forward for de novo genotyping in 570 non-diabetic West Africans. We replicated SNPs in or near SC4MOL and TCERG1L in West Africans. The meta-analysis of 1497 African Americans and West Africans yielded genome-wide significant associations for SNPs in the SC4MOL gene: rs17046216 (P 1.7 10(8) and 2.9 10(8) for FI and IR, respectively); and near the TCERG1L gene with rs7077836 as the top scoring (P 7.5 10(9) and 4.9 10(10) for FI and IR, respectively). In silico replication in the MAGIC study (n 37 037) showed weak but significant association (adjusted P-value of 0.0097) for rs34602777 in the MYO5A gene. In addition, we replicated previous GWAS findings for IR and FI in Europeans for GCKR, and for variants in four T2D loci (FTO, IRS1, KLF14 and PPARG) which exert their action via IR. In summary, variants in/near SC4MOL, and TCERG1L were associated with FI and IR in this cohort of African Americans and were replicated in West Africans. SC4MOL is under-expressed in an animal model of T2D and plays a key role in lipid biosynthesis, with implications for the regulation of energy metabolism, obesity and dyslipidemia. TCERG1L is associated with plasma adiponectin, a key modulator of obesity, inflammation, IR and diabetes.

http://dx.doi.org//10.1093/hmg/dds282

11. Cheviron Z.A. et al. Functional Genomics of Adaptation to Hypoxic Cold-Stress in High-Altitude Deer Mice: Transcriptomic Plasticity and Thermogenic Performance // Evolution. 2014. Vol. 68, № 1. P. 48–62.

In species that are distributed across steep environmental gradients, adaptive variation in physiological performance may be attributable to transcriptional plasticity in underlying regulatory networks. Here we report the results of common-garden experiments that were designed to elucidate the role of regulatory plasticity in evolutionary adaptation to hypoxic cold-stress in deer mice (Peromyscus maniculatus). We integrated genomic transcriptional profiles with measures of metabolic enzyme activities and whole-animal thermogenic performance under hypoxia in highland (4350 m) and lowland (430 m) mice from three experimental groups: (1) wild-caught mice that were sampled at their native elevations; (2) wild-caught/lab-reared mice that were deacclimated to low-elevation conditions in a common-garden lab environment; and (3) the F-1 progeny of deacclimated mice that were maintained under the same low-elevation common-garden conditions. In each experimental group, highland mice exhibited greater thermogenic capacities than lowland mice, and this enhanced performance was associated with upregulation of transcriptional modules that influence several hierarchical steps in the O-2 cascade, including tissue O-2 diffusion (angiogenesis) and tissue O-2 utilization (metabolic fuel use and cellular oxidative capacity). Most of these performance-related transcriptomic changes occurred over physiological and developmental timescales, suggesting that regulatory plasticity makes important contributions to fitness-related physiological performance in highland deer mice.

http://dx.doi.org//10.1111/evo.12257

12. Cirera S. et al. Expression studies of six human obesity-related genes in seven tissues from divergent pig breeds // Anim. Genet. 2014. Vol. 45, № 1. P. 59–66.

Obesity has reached epidemic proportions globally and has become the cause of several major health risks worldwide. Presently, more than 100 loci have been related to obesity and metabolic traits in humans by genome-wide association studies. The complex genetic architecture behind obesity has triggered a need for the development of better animal models than rodents. The pig has emerged as a very promising biomedical model to study human obesity traits. In this study, we have characterized the expression patterns of six obesity-related genes, leptin (LEP), leptin receptor (LEPR), melanocortin 4 receptor (MC4R), fat mass and obesity associated (FTO), neuronal growth regulator 1 (NEGR)1 and adiponectin (ADIPOQ), in seven obesity-relevant tissues (liver; muscle; pancreas; hypothalamus; and retroperitoneal, subcutaneous and mesenteric adipose tissues) in two pig breeds (production pigs and Gottingen minipigs) that deviate phenotypically and genetically from each other with respect to obesity traits. We observe significant differential expression for LEP, LEPR and ADIPOQ in muscle and in all three adipose tissues. Interestingly, in pancreas, LEP expression is only detected in the fat minipigs. FTO shows significant differential expression in all tissues analyzed, and NEGR1 shows significant differential expression in muscle, pancreas, hypothalamus and subcutaneous adipose tissue. The MC4R transcript can be detected only in hypothalamus. In general, the expression profiles of the investigated genes are in accordance with those observed in human studies. Our study shows that both the differences between the investigated breeds and the phenotypic state with respect to obesity/leanness play a large role for differential expression of the obesity-related genes.

http://dx.doi.org//10.1111/age.12082

13. U07870
Dillon C.P. et al. RIPK1 Blocks Early Postnatal Lethality Mediated by Caspase-8 and RIPK3 // Cell. 2014. Vol. 157, № 5. P. 1189–1202.

Receptor-interacting protein kinase (RIPK)-1 is involved in RIPK3-dependent and -independent signaling pathways leading to cell death and/or inflammation. Genetic ablation of ripk1 causes postnatal lethality, which was not prevented by deletion of ripk3, caspase-8, or fadd. However, animals that lack RIPK1, RIPK3, and either caspase-8 or FADD survived weaning and matured normally. RIPK1 functions in vitro to limit caspase-8-dependent, TNFR-induced apoptosis, and animals lacking RIPK1, RIPK3, and TNFR1 survive to adulthood. The role of RIPK3 in promoting lethality in ripk1(-/-) mice suggests that RIPK3 activation is inhibited by RIPK1 postbirth. Whereas TNFR-induced RIPK3-dependent necroptosis requires RIPK1, cells lacking RIPK1 were sensitized to necroptosis triggered by poly I: C or interferons. Disruption of TLR (TRIF) or type I interferon (IFNAR) signaling delayed lethality in ripk1(-/-)tnfr1(-/-) mice. These results clarify the complex roles for RIPK1 in postnatal life and provide insights into the regulation of FADD-caspase-8 and RIPK3-MLKL signaling by RIPK1.

http://dx.doi.org//10.1016/j.cell.2014.04.018

14. U07870
Dixit A. et al. Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens // Cell. 2016. Vol. 167, № 7. P. 1853–+.

Genetic screens help infer gene function in mammalian cells, but it has remained difficult to assay complex phenotypes-such as transcriptional profiles-at scale. Here, we develop Perturb-seq, combining single-cell RNA sequencing (RNA-seq) and clustered regularly interspaced short palindromic repeats (CRISPR)-based perturbations to perform many such assays in a pool. We demonstrate Perturb-seq by analyzing 200,000 cells in immune cells and cell lines, focusing on transcription factors regulating the response of dendritic cells to lipopolysaccharide (LPS). Perturb-seq accurately identifies individual gene targets, gene signatures, and cell states affected by individual perturbations and their genetic interactions. We posit new functions for regulators of differentiation, the anti-viral response, and mitochondrial function during immune activation. By decomposing many high content measurements into the effects of perturbations, their interactions, and diverse cell metadata, Perturb-seq dramatically increases the scope of pooled genomic assays.

http://dx.doi.org//10.1016/j.cell.2016.11.038

15. Dixon S.J. et al. Human Haploid Cell Genetics Reveals Roles for Lipid Metabolism Genes in Nonapoptotic Cell Death // ACS Chem. Biol. 2015. Vol. 10, № 7. P. 1604–1609.

Little is known about the regulation of nonapoptotic cell death. Using massive insertional mutagenesis of haploid KBM7 cells we identified nine genes involved in small-molecule-induced nonapoptotic cell death, including mediators of fatty acid metabolism (ACSL4) and lipid remodeling (LPCAT3) in ferroptosis. One novel compound, CIL56, triggered cell death dependent upon the rate-limiting de novo lipid synthetic enzyme ACC1. These results provide insight into the genetic regulation of cell death and highlight the central role of lipid metabolism in nonapoptotic cell death.

http://dx.doi.org//10.1021/acschembio.5b00245

16. U49676
Doitsidou M. et al. A combinatorial regulatory signature controls terminal differentiation of the dopaminergic nervous system in C. elegans // Genes Dev. 2013. Vol. 27, № 12. P. 1391–1405.

Terminal differentiation programs in the nervous system are encoded by cis-regulatory elements that control the expression of terminal features of individual neuron types. We decoded the regulatory information that controls the expression of five enzymes and transporters that define the terminal identity of all eight dopaminergic neurons in the nervous system of the Caenorhabditis elegans hermaphrodite. We show that the tightly coordinated, robust expression of these dopaminergic enzymes and transporters ("dopamine pathway'') is ensured through a combinatorial cis-regulatory signature that is shared by all dopamine pathway genes. This signature is composed of an Ets domain-binding site, recognized by the previously described AST-1 Ets domain factor, and two distinct types of homeodomain-binding sites that act in a partially redundant manner. Through genetic screens, we identified the sole C. elegans Distalless/Dlx ortholog, ceh-43, as a factor that acts through one of the homeodomain sites to control both induction and maintenance of terminal dopaminergic fate. The second type of homeodomain site is a Pbx-type site, which is recognized in a partially redundant and neuron subtype-specific manner by two Pbx factors, ceh-20 and ceh-40, revealing novel roles of Pbx factors in the context of terminal neuron differentiation. Taken together, we revealed a specific regulatory signature and cognate, terminal selector-type transcription factors that define the entire dopaminergic nervous system of an animal. Dopaminergic neurons in the mouse olfactory bulb express a similar combinatorial transcription factor collective of Ets/Dlx/Pbx factors, suggesting deep phylogenetic conservation of dopaminergic regulatory programs.

http://dx.doi.org//10.1101/gad.217224.113

17. 09646906
El Wakil A. et al. Dkk3 is a component of the genetic circuitry regulating aldosterone biosynthesis in the adrenal cortex // Hum. Mol. Genet. 2012. Vol. 21, № 22. P. 4922–4929.

Primary aldosteronism (PA, autonomous aldosterone production from the adrenal cortex) causes the most common form of secondary arterial hypertension (HT), which is also the most common curable form of HT. Recent studies have highlighted an important role of mutations in genes encoding potassium channels in the pathogenesis of PA, both in human disease and in animal models. Here, we have exploited the unique features of the hyperaldosteronemic phenotype of Kcnk3 null mice, which is dependent on sexual hormones, to identify genes whose expression is modulated in the adrenal gland according to the dynamic hyperaldosteronemic phenotype of those animals. Genetic inactivation of one of the genes identified by our strategy, dickkopf-3 (Dkk3), whose expression is increased by calcium influx into adrenocortical cells, in the Kcnk3 null background results in the extension of the low-renin, potassium-rich diet insensitive hyperaldosteronemic phenotype to the male sex. Compound Kcnk3/Dkk3 animals display an increased expression of Cyp11b2, the rate-limiting enzyme for aldosterone biosyntheis in the adrenal zona glomerulosa (ZG). Our data show that Dkk3 can act as a modifier gene in a mouse model for altered potassium channel function and suggest its potential involvement in human PA syndromes.

http://dx.doi.org//10.1093/hmg/dds333

18. 09646906
Eschbach J. et al. PGC-1 is a male-specific disease modifier of human and experimental amyotrophic lateral sclerosis // Hum. Mol. Genet. 2013. Vol. 22, № 17. P. 3477–3484.

Amyotrophic lateral sclerosis (ALS) is a devastating, adult-onset neurodegenerative disorder of the upper and lower motor systems. It leads to paresis, muscle wasting and inevitably to death, typically within 35 years. However, disease onset and survival vary considerably ranging in extreme cases from a few months to several decades. The genetic and environmental factors underlying this variability are of great interest as potential therapeutic targets. In ALS, men are affected more often and have an earlier age of onset than women. This gender difference is recapitulated in transgenic rodent models, but no underlying mechanism has been elucidated. Here we report that SNPs in the brain-specific promoter region of the transcriptional co-activator PGC-1, a master regulator of metabolism, modulate age of onset and survival in two large and independent ALS populations and this occurs in a strictly male-specific manner. In complementary animal studies, we show that deficiency of full-length (FL) Pgc-1 leads to a significantly earlier age of onset and a borderline shortened survival in male, but not in female ALS-transgenic mice. In the animal model, FL Pgc-1-loss is associated with reduced mRNA levels of the trophic factor Vegf-A in males, but not in females. In summary, we indentify PGC-1 as a novel and clinically relevant disease modifier of human and experimental ALS and report a sex-dependent effect of PGC-1 in this neurodegenerative disorder.

http://dx.doi.org//10.1093/hmg/ddt202

19. 01433334
Feith D.J., Pegg A.E., Fong L.Y.Y. Targeted expression of ornithine decarboxylase antizyme prevents upper aerodigestive tract carcinogenesis in p53-deficient mice // Carcinogenesis. 2013. Vol. 34, № 3. P. 570–576.

Upper aerodigestive tract (UADT) cancers of the oral cavity and esophagus are a significant global health burden, and there is an urgent need to develop relevant animal models to identify chemopreventive and therapeutic strategies to combat these diseases. Antizyme (AZ) is a multifunctional negative regulator of cellular polyamine levels, and here, we evaluate the susceptibility of keratin 5 (K5)-AZ transgenic mice to tumor models that combine chemical carcinogenesis with dietary and genetic risk factors known to influence human susceptibility to UADT cancer and promote UADT carcinogenesis in mice. First, p53(/-) and K5-AZ/p53(/-) (AZ/p53(/-)) mice were placed on a zinc-deficient (ZD) or zinc-sufficient (ZS) diet and chronically exposed to 4-nitroquinoline 1-oxide. Tongue tumor incidence, multiplicity and size were substantially reduced in both ZD and ZS AZ/p53(/-) mice compared with p53(/-). AZ expression also reduced progression to carcinoma in situ or invasive carcinoma and decreased expression of the squamous cell carcinoma biomarkers K14, cyclooxygenase-2 and metallothionein. Next, AZ-expressing p53(/-) and p53 null mice were placed on the ZD diet and treated with a single dose of N-nitrosomethylbenzylamine. Regardless of p53 status, forestomach (FST) tumor incidence, multiplicity and size were greatly reduced with AZ expression, which was also associated with a significant decrease in FST epithelial thickness along with reduced proliferation marker K6 and increased differentiation marker loricrin. These studies demonstrate the powerful tumor suppressive effects of targeted AZ expression in two distinct and unique mouse models and validate the polyamine metabolic pathway as a target for chemoprevention of UADT cancers.

http://dx.doi.org//10.1093/carcin/bgs377

20. U004533
Fraire-Zamora J.J., Tran T., Cardullo R.A. Cholesterol-enriched microdomains regulate pseudopod extension in the MSP-based cytoskeleton of amoeboid sperm // Biochem. Biophys. Res. Commun. 2012. Vol. 427, № 3. P. 478–484.

In the amoeboid spermatozoa from Caenorhabditis elegans, motility acquisition is preceded by substantial rearrangement of the plasma membrane. The current genetic model posits a multicomponent complex of membrane and cytoplasmic proteins responsible for pseudopod extension. This model can be translated into a physiological context through the involvement of cholesterol-enriched signaling platforms. We show that discrete cholesterol-enriched microdomains are present in C. elegans spermatids. These microdomains redistributed towards the cell body upon pseudopod extension resulting in a phospholipid-enriched pseudopod. Cholesterol saturation in the spermatids prevented pseudopod extension and motility acquisition, whereas cholesterol depletion increased the rate of in vitro pseudopod extension. This work suggests that plasma membrane cholesterol plays an important role in regulating the membrane dynamics that precede pseudopod extension and motility acquisition. (C) 2012 Elsevier Inc. All rights reserved.

http://dx.doi.org/10.1016/j.bbrc.2012.09.071

21. U12116
Galetto C.D. et al. Isolation and nucleotide sequence analysis of the of Rhinella arenarum beta-catenin: An mRNA and protein expression study during the larval stages of the digestive tract development // Gene. 2012. Vol. 511, № 2. P. 256–264.

beta-catenin interacts with several proteins mediating key biological processes, such as cadherin-mediated cell-cell adhesion as well as signal transduction. This work was done to establish the molecular basis and regulation of the formation pattern of cadherin/beta-catenin-mediated adherens junctions, using an animal model of unknown gene sequence, the toad Rhinella arenarum. A Rhinella arenarum beta-catenin homolog was isolated from larval tissue, their sequence compared and analyzed with those of eight other vertebrates using bioinformatics tools. The mRNA and protein expression levels of beta-catenin were determined during the development of Rhinella arenarum digestive tract both by Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR) and immunohistochemistry-morphometry respectively. Using Xenopus laevis frog specific primers, a fragment 539 bp of Rhinella arenarum toad beta-catenin cDNA was obtained and sequenced. The resulting putative sequence of 177 amino acids showed high similarity at the amino acid level (97%) when compared to other six vertebrates (Xenopus laevis, Xenopus tropicalis, Mus musculus, Rattus norvegicus, Bos taurus and Homo sapiens), with sequences and structural domains characteristic of catenins. Subsequently, using primers specifically designed for Rhinella arenarum nucleotide sequence, beta-catenin-mRNA increasing levels were found during the Rhinella arenarum metamorphosis. Finally, increasing beta-catenin protein expression during development has confirmed the specificity the detection of Rhinella arenarum beta-catenin. Summarizing, we have isolated and sequenced a beta-catenin-homologue sequence from the Rhinella arenarum toad, which is highly conserved between species, and following we have detected beta-catenin mRNA and protein levels during their digestive tract development. (C) 2012 Elsevier B.V. All rights reserved.

http://dx.doi.org//10.1016/j.gene.2012.09.030

22. Garcia-Fuster M.J. et al. The melanin-concentrating hormone (MCH) system in an animal model of depression-like behavior // Eur. Neuropsychopharmacol. 2012. Vol. 22, № 8. P. 607–613.

Selective breeding for divergence in locomotion in a novel environment (bHR, bred High-Responder; bLR, bred Low-Responder) correlates with stress-reactivity, spontaneous anxiety-like behaviors and predicts vulnerability in a rodent model of depression. Identifying genetic factors that may account for such vulnerability are key determinants not only for the illness outcome but also for the development of better-tailored treatment options. Melanin-concentrating hormone (MCH) is a neuropeptide that exhibits some of the hallmarks of a regulator of affective states. The aim of this study was to ascertain the role of the MCH system in depression-like behaviors in bHR vs. bLR rats. bLR rats showed a 44% increase in hypothalamic pMCH mRNA and a 14% decrease in hippocampal CA1 MCH1R mRNA when compared to bHR rats. Interestingly, the amount of time that rats spent immobile in the FST (depressive-like behavior) correlated positively with the amount of hypothalamic pMCH mRNA and negatively with that of hippocampal CA1 MCH1R. The results indicate that the bLR bHR is a useful rat model to investigate individual basal genetic differences that participate in the monitoring of emotional responsiveness (i.e., depression- and anxiety-like behaviors). They also point to the MCH system (i.e., chronically higher pMCH expression and consequently receptor down-regulation) as a candidate biomarker for the severity of depressive-like behavior. The data indicate that MCH1R participates in the modulation of depression-like behavior through a process that involves the CA1 region of the hippocampus, supporting the possible use of MCH1R antagonists in the treatment of depression. (C) 2011 Elsevier B.V. and ECNP. All rights reserved.

http://dx.doi.org//10.1016/j.euroneuro.2011.12.001

23. U07870
Gonzales K.A.U. et al. Deterministic Restriction on Pluripotent State Dissolution by Cell-Cycle Pathways // Cell. 2015. Vol. 162, № 3. P. 564–579.

During differentiation, human embryonic stem cells (hESCs) shut down the regulatory network conferring pluripotency in a process we designated pluripotent state dissolution (PSD). In a high-throughput RNAi screen using an inclusive set of differentiation conditions, we identify centrally important and context-dependent processes regulating PSD in hESCs, including histone acetylation, chromatin remodeling, RNA splicing, and signaling pathways. Strikingly, we detected a strong and specific enrichment of cell-cycle genes involved in DNA replication and G2 phase progression. Genetic and chemical perturbation studies demonstrate that the S and G2 phases attenuate PSD because they possess an intrinsic propensity toward the pluripotent state that is independent of G1 phase. Our data therefore functionally establish that pluripotency control is hardwired to the cell-cycle machinery, where S and G2 phase-specific pathways deterministically restrict PSD, whereas the absence of such pathways in G1 phase potentially permits the initiation of differentiation.

http://dx.doi.org//10.1016/j.cell.2015.07.001

24. Guo D. et al. Low-level expression of human ACAT2 gene in monocytic cells is regulated by the C/EBP transcription factors // Acta Biochim. Biophys. Sin. 2016. Vol. 48, № 11. P. 980–989.

Acyl-coenzyme A: cholesterol acyltransferases (ACATs) are the exclusive intracellular enzymes that catalyze the formation of cholesteryl/steryl esters (CE/SE). In our previous work, we found that the high-level expression of human ACAT2 gene with the CpG hypomethylation of its whole promoter was synergistically regulated by two transcription factors Cdx2 and HNF1 alpha in the intestine and fetal liver. Here, we first observed that the specific CpG-hypomethylated promoter was correlated with the low expression of human ACAT2 gene in monocytic cell line THP-1. Then, two CCAAT/enhancer binding protein (C/EBP) elements within the activation domain in the specific CpG-hypomethylation promoter region were identified, and the expression of ACAT2 in THP-1 cells was evidently decreased when the C/EBP transcription factors were knock-downed using RNAi technology. Furthermore, ChIP assay confirmed that C/EBPs directly bind to their elements for low-level expression of human ACAT2 gene in THP-1 cells. Significantly, the increased expressions of ACAT2 and C/EBPs were also found in macrophages differentiated from both ATRA-treated THP-1 cells and cultured human blood monocytes. These results demonstrate that the low-level expression of human ACAT2 gene with specific CpG-hypomethylated promoter is regulated by the C/EBP transcription factors in monocytic cells, and imply that the lowly expressed ACAT2 catalyzes the synthesis of certain CE/SE that are assembled into lipoproteins for the secretion.

http://dx.doi.org//10.1093/abbs/gmw091

25. U16687
Hansen C.H.F. et al. Mode of Delivery Shapes Gut Colonization Pattern and Modulates Regulatory Immunity in Mice // J. Immunol. 2014. Vol. 193, № 3. P. 1213–1222.

Delivery mode has been associated with long-term changes in gut microbiota composition and more recently also with changes in the immune system. This has further been suggested to link Cesarean section (C-section) with an increased risk for development of immune-mediated diseases such as type 1 diabetes. In this study, we demonstrate that both C-section and cross-fostering with a genetically distinct strain influence the gut microbiota composition and immune key markers in mice. Gut microbiota profiling by denaturing gradient gel electrophoresis and 454/FLX-based 16S rRNA gene amplicon sequencing revealed that mice born by C-section had a distinct bacterial profile at weaning characterized by higher abundance of Bacteroides and Lachnospiraceae, and less Rikenellaceae and Ruminococcus. No clustering according to delivery method as determined by principal component analysis of denaturing gradient gel electrophoresis profiles was evident in adult mice. However, the adult C-section-born mice had lower proportions of Foxp3(+) regulatory T cells, tolerogenic CD103(+) dendritic cells, and less Il10 gene expression in mesenteric lymph nodes and spleens. This demonstrates long-term systemic effect on the regulatory immune system that was also evident in NOD mice, a model of type 1 diabetes, born by C-section. However, no effect of delivery mode was seen on diabetes incidence or insulitis development. In conclusion, the first exposure to microorganisms seems to be crucial for the early life gut microbiota and priming of regulatory immune system in mice, and mode of delivery strongly influences this.

http://dx.doi.org//10.4049/jimmunol.1400085

26. Herrera-Perez Z., Gretz N., Dweep H. A Comprehensive Review on the Genetic Regulation of Cisplatin-induced Nephrotoxicity // Curr. Genomics. 2016. Vol. 17, № 3. P. 279–293.

Cisplatin (CDDP) is a well-known antineoplastic drug which has been extensively utilized over the last decades in the treatment of numerous kinds of tumors. However, CDDP induces a wide range of toxicities in a dose-dependent manner, among which nephrotoxicity is of particular importance. Still, the mechanism of CDDP-induced renal damage is not completely understood; moreover, the knowledge about the role of microRNAs (miRNAs) in the nephrotoxic response is still unknown. miRNAs are known to interact with the representative members of a diverse range of regulatory pathways (including postnatal development, proliferation, inflammation and fibrosis) and pathological conditions, including kidney diseases: polycystic kidney diseases (PKDs), diabetic nephropathy (DN), kidney cancer, and drug-induced kidney injury. In this review, we shed light on the following important aspects: (i) information on genes/proteins and their interactions with previously known pathways engaged with CDDP-induced nephrotoxicity, (ii) information on newly discovered biomarkers, especially, miRNAs for detecting CDDP-induced nephrotoxicity and (iii) information to improve our understanding on CDDP. This information will not only help the researchers belonging to nephrotoxicity field, but also supply an indisputable help for oncologists to better understand and manage the side effects induced by CDDP during cancer treatment. Moreover, we provide up-to-date information about different in vivo and in vitro models that have been utilized over the last decades to study CDDP-induced renal injury. Taken together, this review offers a comprehensive network on genes, miRNAs, pathways and animal models which will serve as a useful resource to understand the molecular mechanism of CDDP-induced nephrotoxicity.

http://dx.doi.org//10.2174/1389202917666160202220555

27. Honjo K. et al. Plasminogen activator inhibitor-1 regulates macrophage-dependent postoperative adhesion by enhancing EGF-HER1 signaling in mice // Faseb J. 2017. Vol. 31, № 6. P. 2625–2637.

Adhesive small bowel obstruction remains a common problem for surgeons. After surgery, platelet aggregation contributes to coagulation cascade and fibrin clot formation. With clotting, fibrin degradation is simultaneously enhanced, driven by tissue plasminogen activator-mediated cleavage of plasminogen to form plasmin. The aim of this study was to investigate the cellular events and proteolytic responses that surround plasminogen activator inhibitor (PAI-1; Serpine1) inhibition of postoperative adhesion. Peritoneal adhesion was induced by gauze deposition in the abdominal cavity in C57BL/6 mice and those that were deficient in fibrinolytic factors, such as Plat(-/-) and Serpine1(-/-) . In addition, C57BL/6 mice were treated with the novel PAI-1 inhibitor, TM5275. Some animals were treated with clodronate to deplete macrophages. Epidermal growth factor (EGF) experiments were performed to understand the role of macrophages and how EGF contributes to adhesion. In the early phase of adhesive small bowel obstruction, increased PAI-1 activity was observed in the peritoneal cavity. Genetic and pharmacologic PAI-1 inhibition prevented progression of adhesion and increased circulating plasmin. Whereas Serpine1(-/-) mice showed intra-abdominal bleeding, mice that were treated with TM5275 did not. Mechanistically, PAI-1, in combination with tissue plasminogen activator, served as a chemoattractant for macrophages that, in turn, secreted EGF and up-regulated the receptor, HER1, on peritoneal mesothelial cells, which led to PAI-1 secretion, further fueling the vicious cycle of impaired fibrinolysis at the adhesive site. Controlled inhibition of PAI-1 not only enhanced activation of the fibrinolytic system, but also prevented recruitment of EGF-secreting macrophages. Pharmacologic PAI-1 inhibition ameliorated adhesion formation in a macrophage-dependent manner.

http://dx.doi.org//10.1096/fj.201600871RR

28. U12116
Hou Y. et al. Estrogen regulates iron homeostasis through governing hepatic hepcidin expression via an estrogen response element // Gene. 2012. Vol. 511, № 2. P. 398–403.

Iron is essential for the human being, involving in oxygen transport, energy metabolism and DNA synthesis. Iron homeostasis is tightly governed by the hepcidin-ferroportin axis, of which hepcidin is the master regulator. Excess iron is associated with various diseases including osteopenia and osteoporosis, which are closely related to the alternation of the endogenous estrogen level. To verify the biological effect of estrogen on iron metabolism, we established a mouse model of estrogen deficiency by ovariectomy. We demonstrated that the hemoglobin content and serum iron level decreased, whereas the tissue iron level in liver and spleen increased in the ovariectomized mice. Moreover, the transcription of hepatic hepcidin was elevated in ovariectomized mice compared to the control mice. We further demonstrated that there was an estrogen response element (ERE) in the promoter region of the hepcidin gene. The assay using the luciferase reporter system confirmed the existence of a functional ERE in the hepcidin promoter, as the estradiol treatment reduced hepcidin expression in cells transfected with ERE-intact construct, with no response to estradiol in cells transfected with ERE-devoid construct. In conclusion, estrogen greatly contributes to iron homeostasis by regulating hepatic hepcidin expression directly through a functional ERE in the promoter region of hepcidin gene. These findings might help build a better understanding towards the etiology of postmenopausal osteoporosis accompanied by excess tissue iron (such as iron retention of osteoclasts in bone) under estrogen deficiency. (C) 2012 Elsevier B.V. All rights reserved.

http://dx.doi.org/10.1016/j.gene.2012.09.060

29. U07870
Irie N. et al. SOX17 Is a Critical Specifier of Human Primordial Germ Cell Fate // Cell. 2015. Vol. 160, № 1–2. P. 253–268.

Specification of primordial germ cells (PGCs) marks the beginning of the totipotent state. However, without a tractable experimental model, the mechanism of human PGC (hPGC) specification remains unclear. Here, we demonstrate specification of hPGC-like cells (hPGCLCs) from germline competent pluripotent stem cells. The characteristics of hPGCLCs are consistent with the embryonic hPGCs and a germline seminoma that share a CD38 cell-surface marker, which collectively defines likely progression of the early human germline. Remarkably, SOX17 is the key regulator of hPGC-like fate, whereas BLIMP1 represses endodermal and other somatic genes during specification of hPGCLCs. Notable mechanistic differences between mouse and human PGC specification could be attributed to their divergent embryonic development and pluripotent states, which might affect other early cell-fate decisions. We have established a foundation for future studies on resetting of the epigenome in hPGCLCs and hPGCs for totipotency and the transmission of genetic and epigenetic information.

http://dx.doi.org//10.1016/j.cell.2014.12.013

30. U04533
Jang G.H. et al. Functional characterization of genetic variations in the MDR3 promoter // Biochem. Biophys. Res. Commun. 2013. Vol. 430, № 4. P. 1312–1318.

Multidrug resistance 3 (MDR3) is present on the canalicular membrane of the hepatocyte and plays an important role in protecting the liver from bile acids. In this study, we characterized the transcriptional effects of four common haplotypes and four polymorphic variants in the promoter region of MDR3 that were identified in 126 DNA samples from Koreans. We measured the luciferase activities of the four MDR3 promoter haplotypes using in vitro reporter assays. Among them, two haplotypes showed a significant decrease in reporter activity compared to the reference. One of the mechanisms by which these haplotypes might decrease MDR3 transcriptional activity was determined: one of the polymorphisms that are present in haplotype 3, g.-1584C>T, was associated with a significant reduction in the promoter activity of MDR3, and the transcription factor NF-Y was predicted to bind to the promoter in the region of g.-1584C>T. Electrophoretic mobility shift assays showed that the g.-1584C allele exhibited greater binding to NF-Y than did the g.-1584T allele. Through the measurement of promoter activity after the overexpression of NF-Y, we found that NF-Y can act as a transcriptional activator of MDR3. These data suggest that the reduced transcriptional activity of g.-1584C>T results from a reduction in the binding affinity of the activator NF-Y to the MDR3 promoter region. Our study suggests that two common haplotypes of MDR3 can regulate the transcriptional rate of MDR3 and that NF-Y may be one of the transcriptional factors involved in this regulation. (C) 2012 Elsevier Ltd. All rights reserved.

http://dx.doi.org//10.1016/j.bbrc.2012.12.041

31. U07870
Jonas K. et al. Proteotoxic Stress Induces a Cell-Cycle Arrest by Stimulating Lon to Degrade the Replication Initiator DnaA // Cell. 2013. Vol. 154, № 3. P. 623–636.

The decision to initiate DNA replication is a critical step in the cell cycle of all organisms. Cells often delay replication in the face of stressful conditions, but the underlying mechanisms remain incompletely defined. Here, we demonstrate in Caulobacter crescentus that proteotoxic stress induces a cell-cycle arrest by triggering the degradation of DnaA, the conserved replication initiator. A depletion of available Hsp70 chaperone, DnaK, either through genetic manipulation or heat shock, induces synthesis of the Lon protease, which can directly degrade DnaA. Unexpectedly, we find that unfolded proteins, which accumulate following a loss of DnaK, also allosterically activate Lon to degrade DnaA, thereby ensuring a cell-cycle arrest. Our work reveals a mechanism for regulating DNA replication under adverse growth conditions. Additionally, our data indicate that unfolded proteins can actively and directly alter substrate recognition by cellular proteases.

http://dx.doi.org//10.1016/j.cell.2013.06.034

32. U15400
Kalivoda K.A., Steenbergen S.M., Vimr E.R. Control of the Escherichia coli Sialoregulon by Transcriptional Repressor NanR // J. Bacteriol. 2013. Vol. 195, № 20. P. 4689–4701.

NanR, one of >8,500 GntR superfamily helix-turn-helix transcriptional regulators, controls expression of the genes required for catabolism of sialic acids in Escherichia coli. It is predicted to do the same in related bacteria harboring orthologs of nanR. The sialic acids are a family of over 40 naturally occurring nine-carbon keto-sugar acids found mainly in the animal lineage, which includes starfish to humans in the deuterostome lineage. Sialic acids function in development, immunity, protein localization and stability, and homeostasis. They also serve as microbial carbon and nitrogen sources and ligands for cell recognition during host colonization. The importance of microbial sialic acid metabolism for host-microbe interactions has made it a target for therapeutic development. Exploiting this target depends on understanding sialometabolic pathways in a wide range of evolutionarily distinct bacteria. Here, we show by transcriptome, genetic, and biochemical analyses that the most common sialic acid, N-acetylneuraminate, induces the nanATEK-yhcH, yjhATS (nanCMS), and yjhBC operons by directly inactivating NanR, converting the predominantly dimeric form of the repressor to an inactive monomer of approximately 30-kDa. Additionally, other results identify critical amino acid residues and nucleotides in the regulator and operator, respectively. The combined results better define how sialic acids, acting through NanR, affect the metabolic flux of an important group of host-derived metabolites. Thus, E. coli serves as a valuable model for understanding sialocatabolic pathways in bacteria.

http://dx.doi.org//10.1128/JB.00692-13

33. U004533
Kumari S. et al. Influence of membrane cholesterol in the molecular evolution and functional regulation of TRPV4 // Biochem. Biophys. Res. Commun. 2015. Vol. 456, № 1. P. 312–319.

TRPV4 is involved in several physiological and sensory functions as well as with several diseases and genetic disorders, though the molecular mechanisms for these are unclear. In this work we have analyzed molecular evolution and structure-function relationship of TRPV4 using sequences from different species. TRPV4 has evolved during early vertebrate origin (450 million years). Synteny analysis confirms that TRPV4 has coevolved with two enzymes involved in sterol biosynthesis, namely MVK and GLTP. Cholesterol-recognizing motifs are present within highly conserved TM4-Loop4-TM5 region of TRPV4. TRPV4 is present in lipid raft where it co-localizes with Caveolin1 and Filipin. TM4-Loop4-TM5 region as well as Loop4 alone can physically interact with cholesterol, its precursor mevalonate and derivatives such as stigmasterol and aldosterone. Mobility of TRPV4-GFP depends on membrane cholesterol level. Molecular evolution of TRPV4 shared striking parallelism with the cholesterol bio-synthesis pathways at the genetic, molecular and metabolic levels. We conclude that interaction with sterols and cholesterol-dependent membrane dynamics have influence on TRPV4 function. These results may have importance on TRPV4-medaited cellular functions and pathophysiology. (C) 2014 Elsevier Inc. All rights reserved.

http://dx.doi.org/10.1016/j.bbrc.2014.11.077

34. U15400
Lasaro M. et al. Escherichia coli Isolate for Studying Colonization of the Mouse Intestine and Its Application to Two-Component Signaling Knockouts // J. Bacteriol. 2014. Vol. 196, № 9. P. 1723–1732.

The biology of Escherichia coli in its primary niche, the animal intestinal tract, is remarkably unexplored. Studies with the streptomycin-treated mouse model have produced important insights into the metabolic requirements for Escherichia coli to colonize mice. However, we still know relatively little about the physiology of this bacterium growing in the complex environment of an intestine that is permissive for the growth of competing flora. We have developed a system for studying colonization using an E. coli strain, MP1, isolated from a mouse. MP1 is genetically tractable and does not require continuous antibiotic treatment for stable colonization. As an application of this system, we separately knocked out each two-component system response regulator in MP1 and performed competitions against the wild-type strain. We found that only three response regulators, ArcA, CpxR, and RcsB, produce strong colonization defects, suggesting that in addition to anaerobiosis, adaptation to cell envelope stress is a critical requirement for E. coli colonization of the mouse intestine. We also show that the response regulator OmpR, which had previously been hypothesized to be important for adaptation between in vivo and ex vivo environments, is not required for MP1 colonization due to the presence of a third major porin.

http://dx.doi.org//10.1128/JB.01296-13

35. Leu Y.-W. et al. Early life ethanol exposure causes long-lasting disturbances in rat mesenchymal stem cells via epigenetic modifications // Biochem. Biophys. Res. Commun. 2014. Vol. 453, № 3. P. 338–344.

Fetal alcohol syndrome (FAS) is a birth defect due to maternal alcohol consumption during pregnancy. Because mesenchymal stem cells (MSCs) are the main somatic stem cells in adults and may contribute to tissue homeostasis and repair in adulthood, we investigated whether early life ethanol exposure affects MSCs and contributes to the propensity for disease onset in later life. Using a rodent model of FAS, we found that ethanol exposure (5.25 g/kg/day) from postnatal days 4 to 9 in rat pups (mimic of human third trimester) caused long-term anomalies in bone marrow-derived MSCs. MSCs isolated from ethanol-exposed animals were prone to neural induction but resistant to osteogenic and adipogenic inductions compared to their age-matched controls. The altered differentiation may contribute to the severe trabecular bone loss seen in ethanol-exposed animals at 3 months of age as well as overt growth retardation. Expression of alkaline phosphatase, osteocalcin, aP2, and PPAR gamma were substantially inhibited, but BDNF was up-regulated in MSCs isolated from ethanol-exposed 3 month-old animals. Several signaling pathways were distorted in ethanol-exposed MSCs via altered trimethylation at histone 3 lysine 27. These results demonstrate that early life ethanol exposure can have long-term impacts in rat MSCs by both genetic and epigenetic mechanisms. (C) 2014 Elsevier Inc. All rights reserved.

http://dx.doi.org//10.1016/j.bbrc.2014.09.083

36. U07870
Li J. et al. Artemisinins Target GABA(A) Receptor Signaling and Impair alpha Cell Identity // Cell. 2017. Vol. 168, № 1–2. P. 86–+.

Type 1 diabetes is characterized by the destruction of pancreatic beta cells, and generating new insulin-producing cells from other cell types is a major aim of regenerative medicine. One promising approach is transdifferentiation of developmentally related pancreatic cell types, including glucagon-producing a cells. In a genetic model, loss of the master regulatory transcription factor Arx is sufficient to induce the conversion of a cells to functional beta-like cells. Here, we identify artemisinins as small molecules that functionally repress Arx by causing its translocation to the cytoplasm. We show that the protein gephyrin is the mammalian target of these antimalarial drugs and that the mechanism of action of these molecules depends on the enhancement of GABA(A) receptor signaling. Our results in zebrafish, rodents, and primary human pancreatic islets identify gephyrin as a druggable target for the regeneration of pancreatic b cell mass from alpha cells.

http://dx.doi.org//10.1016/j.cell.2016.11.010

37. U62882
Liu P. et al. Morphology, mitochondrial development and adipogenic-related genes expression during adipocytes differentiation in grass carp (Ctenopharyngodon idellus) // Sci. Bull. 2015. Vol. 60, № 14. P. 1241–1251.

To investigate the differentiation mechanism of grass carp preadipocytes, a primary adipocytes culture system was established. Confluent preadipocytes were induced to differentiation, and the morphology and gene expression were evaluated at different stages. It was shown that preadipocytes were gradually filled with droplets and the cellular lipid content increased during the differentiation. Ultrastructure observation indicated that the number of mitochondria increased with adipocytes differentiation. Consistently, the mitochondrial protein content was elevated in the differentiating adipocytes. qRT-PCR showed that the expression level of lipogenesis-related genes such as peroxisome proliferator activator receptor gamma (PPAR gamma), lipoprotein lipase (LPL), fatty acid synthase (FAS) and stearoyl-CoA desaturase (SCD) increased during adipocytes differentiation. The mitochondrial relevant gene also elevated when adipocyte differentiation, such as PPAR coactivator-1 (PGC-1 alpha), PGC-1 beta and nuclear respiratory factor (NRF-1). However, the expression of carnitine palmitoyltransferase I alpha (CPT-1 alpha) gene decreased at the initial stage, but increased at the last stage of cell differentiation. These results indicated that the differentiation process of grass carp preadipocytes is similar to that of land animals, but the molecular mechanisms are not exactly the same. The findings revealed in this study provides new information to the study of fish adipocyte differentiation.

http://dx.doi.org//10.1007/s11434-015-0833-9

38. U07870
Man S.M. et al. Critical Role for the DNA Sensor AIM2 in Stem Cell Proliferation and Cancer // Cell. 2015. Vol. 162, № 1. P. 45–58.

Colorectal cancer is a leading cause of cancer-related deaths. Mutations in the innate immune sensor AIM2 are frequently identified in patients with colorectal cancer, but how AIM2 modulates colonic tumorigenesis is unknown. Here, we found that Aim2-deficient mice were hypersusceptible to colonic tumor development. Production of inflammasome-associated cytokines and other inflammatory mediators was largely intact in Aim2-deficient mice; however, intestinal stem cells were prone to uncontrolled proliferation. Aberrant Wnt signaling expanded a population of tumor-initiating stem cells in the absence of AIM2. Susceptibility of Aim2-deficient mice to colorectal tumorigenesis was enhanced by a dysbiotic gut microbiota, which was reduced by reciprocal exchange of gut microbiota with healthy wild-type mice. These findings uncover a synergy between a specific host genetic factor and gut microbiota in determining the susceptibility to colorectal cancer. Therapeutic modulation of AIM2 expression and microbiota has the potential to prevent colorectal cancer.

http://dx.doi.org//10.1016/j.cell.2015.06.001

39. U07870
Manavella P.A. et al. Fast-Forward Genetics Identifies Plant CPL Phosphatases as Regulators of miRNA Processing Factor HYL1 // Cell. 2012. Vol. 151, № 4. P. 859–870.

MicroRNAs (miRNAs) are processed from primary transcripts that contain partially self-complementary foldbacks. As in animals, the core microprocessor in plants is a Dicer protein, DICER-LIKE1 (DCL1). Processing accuracy and strand selection is greatly enhanced through the RNA binding protein HYPONASTIC LEAVES 1 (HYL1) and the zinc finger protein SERRATE (SE). We have combined a luciferase-based genetic screen with whole-genome sequencing for rapid identification of new regulators of miRNA biogenesis and action. Among the first six mutants analyzed were three alleles of C-TERMINAL DOMAIN PHOSPHATASE-LIKE 1 (CPL1)/FIERY2 (FRY2). In the miRNA processing complex, SE functions as a scaffold to mediate CPL1 interaction with HYL1, which needs to be dephosphorylated for optimal activity. In the absence of CPL1, HYL1 dephosphorylation and hence accurate processing and strand selection from miRNA duplexes are compromised. Our findings thus define a new regulatory step in plant miRNA biogenesis.

http://dx.doi.org//10.1016/j.cell.2012.09.039

40. U12116
Morinha F. et al. Detection and characterization of interleukin-6 gene variants in Canis familiaris: Association studies with periodontal disease // Gene. 2011. Vol. 485, № 2. P. 139–145.

Periodontal disease (PD) is the most common inflammatory disease of the oral cavity of domestic carnivores. In Human Medicine molecular genetics research showed that several genes play a role in the predisposition and progression of this complex disease, primarily through the regulation of inflammatory mediators, but the exactly mechanisms are poorly understood. This study aims to contribute to the characterization of the genetic basis of PD in the dog, a classically accepted model in Periodontology. We searched for genetic variations in the interleukin-6 (IL6) gene, in order to verify its association with PD in a case-control study including 25 dogs in the PD case group and 45 dogs in the control group. We indentified and characterized three new genetic variations in IL6 gene. No statistically significant differences were detected between the control and PD cases groups. Our results do not support an evidence for a major role contribution of these variants in the susceptibility to PD in the analyzed population. Nevertheless, the sequence variant I/5_g.105 G>A leads to an amino acid change (arginine to glutamine) and was predicted to be possibly damaging to the IL6 protein. A larger cohort and functional studies would be of extreme importance in a near future to understand the possible role of IL6 variants in this disease. (C) 2011 Elsevier B.V. All rights reserved.

http://dx.doi.org//10.1016/j.gene.2011.06.018

41. Nikonova E.V. et al. Transcriptional responses to loss or gain of function of the leucine-rich repeat kinase 2 (LRRK2) gene uncover biological processes modulated by LRRK2 activity // Hum. Mol. Genet. 2012. Vol. 21, № 1. P. 163–174.

Mutations in the leucine-rich repeat kinase 2 gene (LRRK2) are the most common genetic cause of Parkinson's disease (PD) and cause both autosomal dominant familial and sporadic PD. Currently, the physiological and pathogenic activities of LRRK2 are poorly understood. To decipher the biological functions of LRRK2, including the genes and pathways modulated by LRRK2 kinase activity in vivo, we assayed genome-wide mRNA expression in the brain and peripheral tissues from LRRK2 knockout (KO) and kinase hyperactive G2019S (G2019S) transgenic mice. Subtle but significant differences in mRNA expression were observed relative to wild-type (WT) controls in the cortex, striatum and kidney of KO animals, but only in the striatum in the G2019S model. In contrast, robust, consistent and highly significant differences were identified by the direct comparison of KO and G2019S profiles in the cortex, striatum, kidney and muscle, indicating opposite effects on mRNA expression by the two models relative to WT. Ribosomal and glycolytic biological functions were consistently and significantly up-regulated in LRRK2 G2019S compared with LRRK2 KO tissues. Genes involved in membrane-bound organelles, oxidative phosphorylation, mRNA processing and the endoplasmic reticulum were down-regulated in LRRK2 G2019S mice compared with KO. We confirmed the expression patterns of 35 LRRK2-regulated genes using quantitative reverse transcription polymerase chain reaction. These findings provide the first description of the transcriptional responses to genetically modified LRRK2 activity and provide preclinical target engagement and/or pharmacodynamic biomarker strategies for LRRK2 and may inform future therapeutic strategies for LRRK2-associated PD.

http://dx.doi.org//10.1093/hmg/ddr451

42. U07870
Nobile C.J. et al. A Recently Evolved Transcriptional Network Controls Biofilm Development in Candida albicans // Cell. 2012. Vol. 148, № 1–2. P. 126 -138

A biofilm is an organized, resilient group of microbes in which individual cells acquire properties, such as drug resistance, that are distinct from those observed in suspension cultures. Here, we describe and analyze the transcriptional network controlling biofilm formation in the pathogenic yeast Candida albicans, whose biofilms are a major source of medical device-associated infections. We have combined genetic screens, genome-wide approaches, and two in vivo animal models to describe a master circuit controlling biofilm formation, composed of six transcription regulators that form a tightly woven network with similar to 1,000 target genes. Evolutionary analysis indicates that the biofilm network has rapidly evolved: genes in the biofilm circuit are significantly weighted toward genes that arose relatively recently with ancient genes being underrepresented. This circuit provides a framework for understanding many aspects of biofilm formation by C. albicans in a mammalian host. It also provides insights into how complex cell behaviors can arise from the evolution of transcription circuits.

http://dx.doi.org//10.1016/j.cell.2011.10.048

43. U07870
Orru V. et al. Genetic Variants Regulating Immune Cell Levels in Health and Disease // Cell. 2013. Vol. 155, № 1. P. 242–256.

The complex network of specialized cells and molecules in the immune system has evolved to defend against pathogens, but inadvertent immune system attacks on "self'' result in autoimmune disease. Both genetic regulation of immune cell levels and their relationships with autoimmunity are largely undetermined. Here, we report genetic contributions to quantitative levels of 95 cell types encompassing 272 immune traits, in a cohort of 1,629 individuals from four clustered Sardinian villages. Wefirst estimated trait heritability, showing that it can be substantial, accounting for up to 87% of the variance (mean 41%). Next, by assessing similar to 8.2 million variants that we identified and confirmed in an extended set of 2,870 individuals, 23 independent variants at 13 loci associated with at least one trait. Notably, variants at three loci (HLA, IL2RA, and SH2B3/ATXN2) overlap with known autoimmune disease associations. These results connect specific cellular phenotypes to specific genetic variants, helping to explicate their involvement in disease.

http://dx.doi.org//10.1016/j.cell.2013.08.041

44. U07870
Parnas O. et al. A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks // Cell. 2015. Vol. 162, № 3. P. 675–686.

Finding the components of cellular circuits and determining their functions systematically remains a major challenge in mammalian cells. Here, we introduced genome-wide pooled CRISPR-Cas9 libraries into dendritic cells (DCs) to identify genes that control the induction of tumor necrosis factor (Tnf) by bacterial lipopolysaccharide (LPS), a key process in the host response to pathogens, mediated by the Tlr4 pathway. We found many of the known regulators of Tlr4 signaling, as well as dozens of previously unknown candidates that we validated. By measuring protein markers and mRNA profiles in DCs that are deficient in known or candidate genes, we classified the genes into three functional modules with distinct effects on the canonical responses to LPS and highlighted functions for the PAF complex and oligosaccharyltransferase (OST) complex. Our findings uncover new facets of innate immune circuits in primary cells and provide a genetic approach for dissection of mammalian cell circuits.

http://dx.doi.org//10.1016/j.cell.2015.06.059

45. U12116
Peng X.-E. et al. Two genetic variants in FABP1 and susceptibility to non-alcohol fatty liver disease in a Chinese population // Gene. 2012. Vol. 500, № 1. P. 54–58.

Liver fatty acid-binding protein (FABP1) serves as a key regulator of hepatic lipid metabolism, and polymorphisms within the FABP1 gene have been associated with several metabolic traits. To investigate the association between FABP1 polymorphisms and the risk of non-alcohol fatty liver disease (NAFLD) in a Chinese population, the genotypes and haplotypes of FABP1 (rs2241883 T/C and rs1545224G/A) were determined in 553 patients with NAFLD and 553 healthy controls. The results showed that individuals with at least one copy of the rs2241883 C allele (TC or CC genotype) had an elevated risk for developing NAFLD (odds ratio [OR] = 1.32, 95% CI: 1.01-1.71), and individuals with at least one copy of the rs1545224 A allele (GA or AA genotype) also had a significantly increased risk for NAFLD (OR = 1.52, 95% CI: 1.14-2.02). Cumulative effect analysis of the two SNPs revealed that individuals with two risk genotypes were at significantly higher risk of NAFLD than those without risk genotype, and a significant trend of increased risk with increasing numbers of risk genotype was observed. Stratification analysis showed that the rs2241883 C allele carriers had higher level of LDL-C and the rs1545224 A allele carriers had higher level of FPG than those without this allele. In addition, haplotype analysis revealed that the one composed of the rs1545224 A and rs2241883 C variants was significantly associated with an increased risk for NAFLD (OR = 1.34; 95% CI = 1.05-1.40) compared to the GT haplotype. Taken together, the present study suggests that genetic variations within FABP1 influence susceptibility to NAFLD independently or jointly. (c) 2012 Elsevier B.V. All rights reserved.

http://dx.doi.org/10.1016/j.gene.2012.03.050

46. Perez-Montarelo D. et al. Haplotypic diversity of porcine LEP and LEPR genes involved in growth and fatness regulation // J. Appl. Genetics. 2015. Vol. 56, № 4. P. 525–533.

The analysis of structural genetic variability in candidate genes can make it possible to analyse the selection footprint and deepen the understanding of the genetic basis of complex traits. The leptin (LEP) and its receptor (LEPR) porcine genes are involved in food intake and energy homeostasis, and polymorphisms associated to growth and fatness traits have been detected in both genes. The main objective of this study was to explore the genetic variability of the most polymorphic regions of both genes in a variety of pig populations and wild boars from diverse European and Asian origins. In total, 54 animals were included in the analyses, with a remarkable sampling of Spanish wild boars and Iberian pigs. The sequencing allowed the identification of 69 and 26 polymorphisms in LEP and LEPR genes, respectively. Neighbour-joining trees built for the 69 haplotypes identified in the LEP and the 24 haplotypes detected in the LEPR showed the known genetic divergence between European and Asian pig breeds. A high variability of the LEP was detected in the different analysed populations providing new data for the existence of two domestication centres in Asia. In comparison to the LEP gene, the LEPR showed a lower variability, especially in the Iberian breed that showed no variability. Moreover, results of the Hudson-Kreitman-Aguad, neutrality test support a possible selection event of the LEPR gene region in this breed, potentially related with its leptin resistance pattern and good adaptation to a traditional extensive production system with strong seasonal changes of feeding resources.

http://dx.doi.org//10.1007/s13353-015-0284-7

47. Provenzano G. et al. Mutant mouse models of autism spectrum disorders // Dis. Markers. 2012. Vol. 33, № 5. P. 225–239.

Autism spectrum disorders (ASDs) are a heterogeneous group of neurodevelopmental diseases characterized by a triad of specific behavioral traits: abnormal social interactions, communication deficits and stereotyped or repetitive behaviors. Several recent studies showed that ASDs have a strong genetic basis, contributing to the discovery of a number of ASD-associated genes. Due to the genetic complexity of these disorders, mouse strains with targeted deletion of ASD genes have become an essential tool to investigate the molecular and neurodevelopmental mechanisms underlying ASD. Here we will review the most relevant genetic mouse models developed by targeted inactivation of ASD-associated genes, and discuss their importance for the development of novel pharmacological therapies of these disorders.

http://dx.doi.org//10.3233/DMA-2012-0917

48. U07870
Puram R.V. et al. Core Circadian Clock Genes Regulate Leukemia Stem Cells in AML // Cell. 2016. Vol. 165, № 2. P. 303–316.

Leukemia stem cells (LSCs) have the capacity to self-renew and propagate disease upon serial transplantation in animal models, and elimination of this cell population is required for curative therapies. Here, we describe a series of pooled, in vivo RNAi screens to identify essential transcription factors (TFs) in a murine model of acute myeloid leukemia (AML) with genetically and phenotypically defined LSCs. These screens reveal the heterodimeric, circadian rhythm TFs Clock and Bmal1 as genes required for the growth of AML cells in vitro and in vivo. Disruption of canonical circadian pathway components produces anti-leukemic effects, including impaired proliferation, enhanced myeloid differentiation, and depletion of LSCs. We find that both normal and malignant hematopoietic cells harbor an intact clock with robust circadian oscillations, and genetic knockout models reveal a leukemiaspecific dependence on the pathway. Our findings establish a role for the core circadian clock genes in AML.

http://dx.doi.org//10.1016/j.cell.2016.03.015

49. U49676
Rosario M. et al. Neocortical dendritic complexity is controlled during development by NOMA-GAP-dependent inhibition of Cdc42 and activation of cofilin // Genes Dev. 2012. Vol. 26, № 15. P. 1743–1757.

Neocortical neurons have highly branched dendritic trees that are essential for their function. Indeed, defects in dendritic arborization are associated with human neurodevelopmental disorders. The molecular mechanisms regulating dendritic arbor complexity, however, are still poorly understood. Here, we uncover the molecular basis for the regulation of dendritic branching during cortical development. We show that during development, dendritic branching requires post-mitotic suppression of the RhoGTPase Cdc42. By generating genetically modified mice, we demonstrate that this is catalyzed in vivo by the novel Cdc42-GAP NOMA-GAP. Loss of NOMA-GAP leads to decreased neocortical volume, associated specifically with profound oversimplification of cortical dendritic arborization and hyperactivation of Cdc42. Remarkably, dendritic complexity and cortical thickness can be partially restored by genetic reduction of post-mitotic Cdc42 levels. Furthermore, we identify the actin regulator cofilin as a key regulator of dendritic complexity in vivo. Cofilin activation during late cortical development depends on NOMA-GAP expression and subsequent inhibition of Cdc42. Strikingly, in utero expression of active cofilin is sufficient to restore postnatal dendritic complexity in NOMA-GAP-deficient animals. Our findings define a novel cell-intrinsic mechanism to regulate dendritic branching and thus neuronal complexity in the cerebral cortex.

http://dx.doi.org//10.1101/gad.191593.112

50. U16687
Sarmiento J. et al. A Functional Polymorphism of Ptpn22 Is Associated with Type 1 Diabetes in the BioBreeding Rat // J. Immunol. 2015. Vol. 194, № 2. P. 615–629.

The R620W variant of PTPN22 is one of the major genetic risk factors for several autoimmune disorders including type 1 diabetes (T1D) in humans. In the BioBreeding T1D-prone (BBDP) rat, a single nucleotide polymorphism in Ptpn22 results in an A629T substitution immediately C-terminal to the aliphatic residues central to the Ptpn22-C-terminal Src kinase interaction. This variant exhibits a 50% decrease in C-terminal Src kinase binding affinity and contributes to T cell hyperresponsiveness. Examination of BBDP sublines congenic for the Iddm26.2 locus that includes Ptpn22 has not only shown an expansion of activated CD4(+)25(+) T lymphocytes in animals homozygous for the BBDP allele, consistent with enhanced TCR-mediated signaling, but also a decrease in their proportion of peripheral Foxp3(+) regulatory T cells. Furthermore, clinical assessment of both an F2(BBDP 3 ACI.1u.Lyp) cohort and Iddm26.2 congenic BBDP sublines has revealed an association of Ptpn22 with T1D. Specifically, in both cases, T1D risk is significantly greater in BBDP Ptpn22 homozygous and heterozygous animals. These findings are consistent with a role for rat Ptpn22 allelic variation within Iddm26.2 in the regulation of T cell responses, and subsequently the risk for development of T1D.

http://dx.doi.org//10.4049/jimmunol.1302689

51. U21083
Schoggins J.W. et al. A diverse range of gene products are effectors of the type I interferon antiviral response // Nature. 2011. Vol. 472, № 7344. P. 481-U545.

Nature | Letter Print Share/bookmark ????? A diverse range of gene products are effectors of the type I interferon antiviral response John W. Schoggins, Sam J. Wilson, Maryline Panis, Mary Y. Murphy, Christopher T. Jones, Paul Bieniasz & Charles M. Rice Affiliations Contributions Corresponding author Nature 472, 481–485 (28 April 2011) doi:10.1038/nature09907 Received 20 May 2010 Accepted 03 February 2011 Published online 10 April 2011 Corrigendum (July, 2015) Article tools PDF Citation Rights & permissions Article metrics The type I interferon response protects cells against invading viral pathogens. The cellular factors that mediate this defence are the products of interferon-stimulated genes (ISGs). Although hundreds of ISGs have been identified since their discovery more than 25 years ago1, 2, 3, only a few have been characterized with respect to antiviral activity. For most ISG products, little is known about their antiviral potential, their target specificity and their mechanisms of action. Using an overexpression screening approach, here we show that different viruses are targeted by unique sets of ISGs. We find that each viral species is susceptible to multiple antiviral genes, which together encompass a range of inhibitory activities. To conduct the screen, more than 380 human ISGs were tested for their ability to inhibit the replication of several important human and animal viruses, including hepatitis C virus, yellow fever virus, West Nile virus, chikungunya virus, Venezuelan equine encephalitis virus and human immunodeficiency virus type-1. Broadly acting effectors included IRF1, C6orf150 (also known as MB21D1), HPSE, RIG-I (also known as DDX58), MDA5 (also known as IFIH1) and IFITM3, whereas more targeted antiviral specificity was observed with DDX60, IFI44L, IFI6, IFITM2, MAP3K14, MOV10, NAMPT (also known as PBEF1), OASL, RTP4, TREX1 and UNC84B (also known as SUN2). Combined expression of pairs of ISGs showed additive antiviral effects similar to those of moderate type I interferon doses. Mechanistic studies uncovered a common theme of translational inhibition for numerous effectors. Several ISGs, including ADAR, FAM46C, LY6E and MCOLN2, enhanced the replication of certain viruses, highlighting another layer of complexity in the highly pleiotropic type I interferon system.

http://dx.doi.org//10.1038/nature09907

52. U04533
Shan J. et al. Genetic analysis of the SIRT1 gene promoter in ventricular septal defects // Biochem. Biophys. Res. Commun. 2012. Vol. 425, № 4. P. 741–745.

Mutations in cardiac transcription factor genes, such as GATA-4, NKX2-5 and TBX5 genes, have been associated to the patients with familial and isolated congenital heart disease (CHD). Little work has been done on the epigenetic causes for CHD. Sirtuis are highly conserved NAD-dependent class III deacetylases. In mammals, there are seven members of surtuin family, SIRT1-SIRT7. SIRT1, the closest to yeast Sir2, has deacetylase activity and ADP-ribosyltransferase activity. SIRT1 has been involved in many cellular processes and implicated in human diseases, such as obesity, type 2 diabetes, cancer and neurodegenerative diseases. We hypothesized that altered levels of SIRT1 gene expression, rather than mutations in SIRT1 gene, may contribute to the human diseases. In this study, we genetically analyze the SIRT1 gene promoter in patients with ventricular septal defects (VSD) (n = 333) and ethic-matched healthy controls (n = 348). In all, six single-nucleotide polymorphisms (SNPs) and twelve heterozygous sequence variants were identified. Four novel heterozygous variants, g.69643693A > G, g.69643963A > T, g.69643971G > A and g.69644366Ins, were found in six VSD patients, but in none of controls. Six SNPs and variants, g.69643707A > C (rs35706870), g.69643874C > A, g.69644209C > G, g.69644213G > A, g.69644268T > A and g.69644441G > A. were only identified in controls. The other SNPs and variants were found in both groups with similar frequencies. Therefore, the variants within the SIRT1 gene promoter identified in VSD patients may alter the transcriptional activities of SIRT1 gene promoter. Changed SIRT1 protein levels may contribute to the VSD etiology by affecting the activities of its substrates. (C) 2012 Elsevier Inc. All rights reserved.

http://dx.doi.org/10.1016/j.bbrc.2012.07.145

53. U07870
Singer M. et al. A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells // Cell. 2016. Vol. 166, № 6. P. 1500–+.

Reversing the dysfunctional T cell state that arises in cancer and chronic viral infections is the focus of therapeutic interventions; however, current therapies are effective in only some patients and some tumor types. To gain a deeper molecular understanding of the dysfunctional T cell state, we analyzed population and single-cell RNA profiles of CD8(+) tumor-infiltrating lymphocytes (TILs) and used genetic perturbations to identify a distinct gene module for T cell dysfunction that can be uncoupled from T cell activation. This distinct dysfunction module is downstream of intracellular metallothioneins that regulate zinc metabolism and can be identified at single-cell resolution. We further identify Gata-3, a zinc-finger transcription factor in the dysfunctional module, as a regulator of dysfunction, and we use CRISPR-Cas9 genome editing to show that it drives a dysfunctional phenotype in CD8(+) TILs. Our results open novel avenues for targeting dysfunctional T cell states while leaving activation programs intact.

http://dx.doi.org//10.1016/j.cell.2016.08.052

54. Skorobogata O. et al. Dynein-mediated trafficking negatively regulates LET-23 EGFR signaling // Mol. Biol. Cell. 2016. Vol. 27, № 23. P. 3771–3779.

Epidermal growth factor receptor (EGFR) signaling is essential for animal development, and increased signaling underlies many human cancers. Identifying the genes and cellular processes that regulate EGFR signaling in vivo will help to elucidate how this pathway can become inappropriately activated. Caenorhabditis elegans vulva development provides an in vivo model to genetically dissect EGFR signaling. Here we identified a mutation in dhc-1, the heavy chain of the cytoplasmic dynein minus end-directed microtubule motor, in a genetic screen for regulators of EGFR signaling. Despite the many cellular functions of dynein, DHC-1 is a strong negative regulator of EGFR signaling during vulva induction. DHC-1 is required in the signal-receiving cell and genetically functions upstream or in parallel to LET-23 EGFR. LET-23 EGFR accumulates in cytoplasmic foci in dhc-1 mutants, consistent with mammalian cell studies in which dynein is shown to regulate late endosome trafficking of EGFR with the Rab7 GTPase. However, we found different distributions of LET-23 EGFR foci in rab-7 versus dhc-1 mutants, suggesting that dynein functions at an earlier step of LET-23 EGFR trafficking to the lysosome than RAB-7. Our results demonstrate an in vivo role for dynein in limiting LET-23 EGFR signaling via endosomal trafficking.

http://dx.doi.org//10.1091/mbc.E15-11-0757

55. U07870
Steculorum S.M. et al. Hypothalamic UDP Increases in Obesity and Promotes Feeding via P2Y6-Dependent Activation of AgRP Neurons // Cell. 2015. Vol. 162, № 6. P. 1404–1417.

Activation of orexigenic AgRP-expressing neurons in the arcuate nucleus of the hypothalamus potently promotes feeding, thus defining new regulators of AgRP neuron activity could uncover potential novel targets for obesity treatment. Here, we demonstrate that AgRP neurons express the purinergic receptor 6 (P2Y6), which is activated by uridine-diphosphate (UDP). In vivo, UDP induces ERK phosphorylation and cFos expression in AgRP neurons and promotes action potential firing of these neurons in brain slice recordings. Consequently, central application of UDP promotes feeding, and this response is abrogated upon pharmacologic or genetic inhibition of P2Y6 as well as upon pharmacogenetic inhibition of AgRP neuron activity. In obese animals, hypothalamic UDP content is elevated as a consequence of increased circulating uridine concentrations. Collectively, these experiments reveal a potential regulatory pathway in obesity, where peripheral uridine increases hypothalamic UDP concentrations, which in turn can promote feeding via PY6-dependent activation of AgRP neurons.

http://dx.doi.org/10.1016/j.cell.2015.08.032

56. Subbanna S. et al. Ethanol Exposure Induces Neonatal Neurodegeneration by Enhancing CB1R Exon1 Histone H4K8 Acetylation and Up-regulating CB1R Function causing Neurobehavioral Abnormalities in Adult Mice // Int. J. Neuropsychopharmacol. 2015. Vol. 18, № 5.

Background: Ethanol exposure to rodents during postnatal day 7 (P7), which is comparable to the third trimester of human pregnancy, induces long-term potentiation and memory deficits. However, the molecular mechanisms underlying these deficits are still poorly understood. Methods: In the present study, we explored the potential role of epigenetic changes at cannabinoid type 1 (CB1R) exon1 and additional CB1R functions, which could promote memory deficits in animal models of fetal alcohol spectrum disorder. Results: We found that ethanol treatment of P7 mice enhances acetylation of H4 on lysine 8 (H4K8ace) at CB1R exon1, CB1R binding as well as the CB1R agonist-stimulated GTP gamma S binding in the hippocampus and neocortex, two brain regions that are vulnerable to ethanol at P7 and are important for memory formation and storage, respectively. We also found that ethanol inhibits cyclic adenosine monophosphate response element-binding protein (CREB) phosphorylation and activity-regulated cytoskeleton-associated protein (Arc) expression in neonatal and adult mice. The blockade or genetic deletion of CB1Rs prior to ethanol treatment at P7 rescued CREB phosphorylation and Arc expression. CB1R knockout mice exhibited neither ethanol-induced neurodegeneration nor inhibition of CREB phosphorylation or Arc expression. However, both neonatal and adult mice did exhibit enhanced CREB phosphorylation and Arc protein expression. P7 ethanol-treated adult mice exhibited impaired spatial and social recognition memory, which were prevented by the pharmacological blockade or deletion of CB1Rs at P7. Conclusions: Together, these findings suggest that P7 ethanol treatment induces CB1R expression through epigenetic modification of the CB1R gene, and that the enhanced CB1R function induces pCREB, Arc, spatial, and social memory deficits in adult mice.

http://dx.doi.org//10.1093/ijnp/pyu028

57. U12116
Tessier S.N., Storey K.B. Myocyte enhancer factor-2 and cardiac muscle gene expression during hibernation in thirteen-lined ground squirrels // Gene. 2012. Vol. 501, № 1. P. 8–16.

Many small mammals turn to hibernation to survive the winter, cycling through bouts of prolonged torpor where metabolic rate and body temperature fall to low levels. Remarkably, hypertrophy is promoted in cardiac muscle to support the stronger contractions needed in the cold. We proposed that altered expression of mRNA/protein levels of myocyte enhancer factor-2 (MEF2A, MEF2C) transcription factors and downstream targets (e.g., desmin, glucose transporter 4, and myomesin 1) would aid cardiac muscle of thirteen-lined ground squirrels (Ictidomys tridecemlineatus) in meeting challenges associated with hibernation. Gene and protein responses were compared over six conditions: control (euthermic animals in a 5 degrees C cold room), entrance into torpor, short and long torpors, arousal and interbout. Mef2a relative transcript levels were significantly elevated from controls contributing to increases in MEF2A protein levels throughout the torpor-arousal bout In addition, levels of phosphorylated, activated MEF2A (Thr312) correlated with increases in MEF2A-DNA binding. MEF2C transcript/protein levels were significantly elevated over controls at selected sampling points whereas phosphorylated/activated MEF2C (Ser387) levels rose during torpor and DNA binding was most prominent during entrance into torpor. Some gene targets of MEF2 action were also upregulated. Desmin transcript levels remained constant whereas enhanced protein expression occurred during entrance into torpor. Glut4 transcript levels were enhanced in arousal and protein expression was elevated over all five sampling points during torpor/arousal. Myomesin 1 transcript levels increased between early torpor and early arousal and protein levels increased during entrance and deep torpor. These data provide insights into the changes in gene/protein in expression that help to prepare cardiac muscle for hibernation. (C) 2012 Elsevier B.V. All rights reserved.

http://dx.doi.org//10.1016/j.gene.2012.04.004

58. Tsai S.-Y. et al. GAGA factor, a positive regulator of global gene expression, modulates transcriptional pausing and organization of upstream nucleosomes // Epigenetics Chromatin. 2016. Vol. 9. P. 32.

Background: Genome-wide studies in higher eukaryotes have revealed the presence of paused RNA polymerase II (RNA-Pol) at about 30-50 bp downstream of the transcription start site of genes involved in developmental control, cell proliferation and intercellular signaling. Promoter-proximal pausing is believed to represent a critical step in transcriptional regulation. GAGA sequence motifs have frequently been found in the upstream region of paused genes in Drosophila, implicating a prevalent binding factor, GAF, in transcriptional pausing. Results: Using newly isolated mutants that retain only similar to 3 % normal GAF level, we analyzed its impacts on transcriptional regulation in whole animals. We first examined the abundance of three major isoforms of RNA-Pol on Hsp70 during heat shock. By cytogenetic analyses on polytene chromosomes and chromatin immunoprecipitation (ChIP), we show that paused RNA-Pol of Hsp70 is substantially reduced in mutants. Conversely, a global increase in paused RNA-Pol is observed when GAF is over-expressed. Coupled analyses of transcriptome and GAF genomic distribution show that 269 genes enriched for upstream GAF binding are down-regulated in mutants. Interestingly, similar to 15 % of them encode transcriptional factors, which might control similar to 2000 additional genes down-regulated in mutants. Further examination of RNA-Pol distribution in GAF targets reveals that a positive correlation exists between promoter-proximal RNA-Pol density and GAF occupancy in WT, but not in mutants. Comparison of nucleosome profiles indicates that nucleosome occupancy is preferentially attenuated by GAF in the upstream region that strongly favors nucleosome assembly. Using a dominant eye phenotype caused by GAF over-expression, we detect significant genetic interactions between GAF and the nucleosome remodeler NURF, the pausing factor NELF, and BAB1 whose binding sites are enriched specifically in genes displaying GAF-dependent pausing. Conclusion: Our results provide direct evidence to support a critical role of GAF in global gene expression, transcriptional pausing and upstream nucleosome organization of a group of genes. By cooperating with factors acting at different levels, GAF orchestrates a series of events from local nucleosome displacement to paused transcription. The use of whole animals containing broad tissue types attests the physiological relevance of this regulatory network.

http://dx.doi.org//10.1186/s13072-016-0082-4

59. U07870
Ulirsch J.C. et al. Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits // Cell. 2016. Vol. 165, № 6. P. 1530–1545.

Genome-wide association studies (GWAS) have successfully identified thousands of associations between common genetic variants and human disease phenotypes, but the majority of these variants are non-coding, often requiring genetic fine-mapping, epigenomic profiling, and individual reporter assays to delineate potential causal variants. We employ a massively parallel reporter assay (MPRA) to simultaneously screen 2,756 variants in strong linkage disequilibrium with 75 sentinel variants associated with red blood cell traits. We show that this assay identifies elements with endogenous erythroid regulatory activity. Across 23 sentinel variants, we conservatively identified 32 MPRA functional variants (MFVs). We used targeted genome editing to demonstrate endogenous enhancer activity across 3 MFVs that predominantly affect the transcription of SMIM1, RBM38, and CD164. Functional follow-up of RBM38 delineates a key role for this gene in the alternative splicing program occurring during terminal erythropoiesis. Finally, we provide evidence for how common GWAS-nominated variants can disrupt cell-type-specific transcriptional regulatory pathways.

http://dx.doi.org//10.1016/j.cell.2016.04.048

60. U49676
Valenta T. et al. Probing transcription-specific outputs of beta-catenin in vivo // Genes Dev. 2011. Vol. 25, № 24. P. 2631–2643.

beta-Catenin, apart from playing a cell-adhesive role, is a key nuclear effector of Wnt signaling. Based on activity assays in Drosophila, we generated mouse strains where the endogenous beta-catenin protein is replaced by mutant forms, which retain the cell adhesion function but lack either or both of the N- and the C-terminal transcriptional outputs. The C-terminal activity is essential for mesoderm formation and proper gastrulation, whereas N-terminal outputs are required later during embryonic development. By combining the double-mutant beta-catenin with a conditional null allele and a Wnt1-Cre driver, we probed the role of Wnt/beta-catenin signaling in dorsal neural tube development. While loss of beta-catenin protein in the neural tube results in severe cell adhesion defects, the morphology of cells and tissues expressing the double-mutant form is normal. Surprisingly, Wnt/beta-catenin signaling activity only moderately regulates cell proliferation, but is crucial for maintaining neural progenitor identity and for neuronal differentiation in the dorsal spinal cord. Our model animals thus allow dissecting signaling and structural functions of beta-catenin in vivo and provide the first genetic tool to generate cells and tissues that entirely and exclusively lack canonical Wnt pathway activity.

http://dx.doi.org//10.1101/gad.181289.111

61. U07870
van der Veeken J. et al. Memory of Inflammation in Regulatory T Cells // Cell. 2016. Vol. 166, № 4. P. 977–990.

Eukaryotic cells can "remember'' transient encounters with a wide range of stimuli, inducing lasting states of altered responsiveness. Regulatory T (Treg) cells are a specialized lineage of suppressive CD4 T cells that act as critical negative regulators of inflammation in various biological contexts. Treg cells exposed to inflammatory conditions acquire strongly enhanced suppressive function. Using inducible genetic tracing, we analyzed the long-term stability of activation-induced transcriptional, epigenomic, and functional changes in Treg cells. We found that the inflammation-experienced Treg cell population reversed many activation-induced changes and lost its enhanced suppressive function over time. The "memory-less'' potentiation of Treg suppressor function may help avoid a state of generalized immunosuppression that could otherwise result from repeated activation.

http://dx.doi.org//10.1016/j.cell.2016.07.006

62. U07870
Watson E. et al. Interspecies Systems Biology Uncovers Metabolites Affecting C. elegans Gene Expression and Life History Traits // Cell. 2014. Vol. 156, № 4. P. 759–770.

Diet greatly influences gene expression and physiology. In mammals, elucidating the effects and mechanisms of individual nutrients is challenging due to the complexity of both the animal and its diet. Here, we used an interspecies systems biology approach with Caenorhabditis elegans and two of its bacterial diets, Escherichia coli and Comamonas aquatica, to identify metabolites that affect the animal's gene expression and physiology. We identify vitamin B12 as the major dilutable metabolite provided by Comamonas aq. that regulates gene expression, accelerates development, and reduces fertility but does not affect lifespan. We find that vitamin B12 has a dual role in the animal: it affects development and fertility via the methionine/S-Adenosylmethionine (SAM) cycle and breaks down the short-chain fatty acid propionic acid, preventing its toxic buildup. Our interspecies systems biology approach provides a paradigm for understanding complex interactions between diet and physiology.

http://dx.doi.org//10.1016/j.cell.2014.01.047

63. U12116
Xu R. et al. A genome-wide analysis of the RNA helicase gene family in Solanum lycopersicum // Gene. 2013. Vol. 513, № 1. P. 128–140.

Helicases belong to a class of molecular motor proteins that are found in yeast, animals, and plants. The helicase family is divided into three subfamilies, including the DEAD-box, DEAH-box and DExD/H-box helicases, which are classified based on variations within a common motif, known as motif II. The RNA helicases are involved in every step of RNA metabolism, including nuclear transcription, pre-mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay, and organellar gene expression. The RNA helicase protein family plays a crucial role in plant growth and development as well as in response to biotic and abiotic stresses. However, unlike Arabidopsis, no detailed information regarding the RNA helicase family is currently available for tomato (Solanum lycopersicum) due to a limited number of whole-genome sequences. In this study, we identified a total of 157 RNA helicase genes in the tomato genome. According to the structural features of the motif II region, we classified the tomato RNA helicase genes into DEAD-box, DEAH-box and DExD/H-box helicase genes. But there are 27 RNA helicases not belonging to this three subfamilies, we called that "other helicase". We mapped the 157 RNA helicase genes onto the tomato chromosomes, which range from chr01 to chr12. Microarray and expressed sequence tag data showed that many of these RNA helicase proteins may be involved in diverse biological processes and responses to various stresses. To our knowledge, this is the first report of a genome-wide analysis of the tomato RNA helicase gene family. This study provides valuable information for understanding the classification and putative functions of the RNA helicase gene family in Solanaceae. (c) 2012 Elsevier B.V. All rights reserved.

http://dx.doi.org//10.1016/j.gene.2012.10.053

64. Yan Z. et al. A Cis-acting Regulatory Variation of the Estrogen Receptor alpha (ESR1) Gene Is Associated with Hepatitis B Virus-Related Liver Cirrhosis // Hum. Mutat. 2011. Vol. 32, № 10. P. 1128–1136.

The hepatic fibrogenesis and sexual dimorphism of hepatitis B virus-related liver cirrhosis (HBV-LC) are related to estrogen and its receptors. Abnormal expression of estrogen receptor a (ESR1) is implicated in the development of cirrhosis in both animal models and humans. Here, we examine whether the ESR1 polymorphisms are related to HBV-LC risk among chronic HBV carriers, and we investigate the functional significance of positively associated polymorphisms. A total of 2,404 unrelated Chinese HBV carriers were recruited to conduct the two-stage designed case-control study. Two ESR1 haplotype tagging polymorphisms, c.30T>C (rs2077647) and c.453-397T>C (rs2234693), were genotyped in 1,285 patients with HBV-LC and in 1,119 asymptomatic HBV carriers. We observed a significantly increased susceptibility to HBV-LC associated with the c.30C allele (P = 4.2x10(-8)), c.453-397C allele (P = 2.0x10(-8)), and [c.30C; c.453-397C] haplotype (Dominant model, P = 8.85x10(-10), odds ratio = 1.50, 95% CI 1.32 similar to 1.71) compared with the T alleles and (c.30T; c.453-397T) haplotype of c.30T>C and c.453-397T>C polymorphisms, respectively. Functional analyses were conducted to verify the biological functions of the associated genetic variations and showed that the c.453-397T>C polymorphism is a novel c.453-397C allele-specific and c-myb-dependent enhancer-like cis-acting regulatory variation and could be part of the genetic variations underlying the susceptibility of individuals to HBV-LC. Hum Mutat 32:1128-1136, 2011. (C) 2011 Wiley-Liss, Inc.

http://dx.doi.org//10.1002/humu.21544

65. U04533
Yang J.W. et al. Expression of tyrosine hydroxylase is epigenetically regulated in neural stem cells // Biochem. Biophys. Res. Commun. 2011. Vol. 414, № 4. P. 712–718.

Tyrosine hydroxylase (TH) is the first and rate-limiting enzyme in the biosynthesis of catecholamines, and its expression is regulated in a developmental stage- and cell type-specific manner. Our previous work suggested that the genetic elements responsible for cell type-specific expression of TH were in the repressor region of the TH promoter between -2187 and -1232 bp. To investigate the molecular mechanisms underlying the specificity of TH expression, the DNA methylation patterns of the CpG islands in the repressor region of the TH promoter were examined in human neural stem cells (NSCs) and dopaminergic neuron-like cells. Using a bisulfite sequencing method, we found that the cytosine residues of CpG islands within the NRSE-R site were specifically methylated in NSCs, but not in SH-SY5Y neuroblastoma cells. In NSCs, CpG methylation correlated with reduced TH gene expression, and inhibition of DNA methylation with 5-azacytidine restored TH expression. Furthermore, methyl-CpG binding domain proteins (MBDs) bound to the highly methylated X-1 and X-2 regions of the TH gene in NSCs. Taken together, these results suggest that region-specific methylation and MBDs play important roles in TH gene regulation in NSCs. (C) 2011 Elsevier Inc. All rights reserved.

http://dx.doi.org//10.1016/j.bbrc.2011.09.141

66. Yang W. et al. Genetic Deletion of Rheb1 in the Brain Reduces Food Intake and Causes Hypoglycemia with Altered Peripheral Metabolism // Int. J. Mol. Sci. 2014. Vol. 15, № 1. P. 1499–1510.

Excessive food/energy intake is linked to obesity and metabolic disorders, such as diabetes. The hypothalamus in the brain plays a critical role in the control of food intake and peripheral metabolism. The signaling pathways in hypothalamic neurons that regulate food intake and peripheral metabolism need to be better understood for developing pharmacological interventions to manage eating behavior and obesity. Mammalian target of rapamycin (mTOR), a serine/threonine kinase, is a master regulator of cellular metabolism in different cell types. Pharmacological manipulations of mTOR complex 1 (mTORC1) activity in hypothalamic neurons alter food intake and body weight. Our previous study identified Rheb1 (Ras homolog enriched in brain 1) as an essential activator of mTORC1 activity in the brain. Here we examine whether central Rheb1 regulates food intake and peripheral metabolism through mTORC1 signaling. We find that genetic deletion of Rheb1 in the brain causes a reduction in mTORC1 activity and impairs normal food intake. As a result, Rheb1 knockout mice exhibit hypoglycemia and increased lipid mobilization in adipose tissue and ketogenesis in the liver. Our work highlights the importance of central Rheb1 signaling in euglycemia and energy homeostasis in animals.

http://dx.doi.org//10.3390/ijms15011499

67. U04533
You L. et al. Genome-wide screen identifies PVT1 as a regulator of Gemcitabine sensitivity in human pancreatic cancer cells // Biochem. Biophys. Res. Commun. 2011. Vol. 407, № 1. P. 1–6.

Gemcitabine has been a first-line chemotherapy agent for advanced pancreatic cancer, which is associated with one of the lowest 5 years survival rates among human cancers. Due to our lack of understanding of the genetic determinants of Gemcitabine sensitivity in pancreatic cancer, the therapeutic effectiveness of Gemcitabine chemotherapy is typically unpredictable. Using a genome-wide and piggyBac transposon-based genetic screening platform, we identified the PVT1 gene as a regulator of Gemcitabine sensitivity and showed that functional inactivation of the PVT1 gene led to enhanced Gemcitabine sensitivity in human pancreatic cancer ASPC-1 cells. The integration of the piggyBac transposon-based vector system into intron 3 of PVT1 was within a common site of oncogenic retroviral insertions and chromosomal translocations. PVT1 is a non-protein encoding gene; the genomic arrangement of PVT1 and its co-amplification with MYC have been implicated in the tumorigenesis of a variety of cancers. The molecular mechanism of PVT1 transcripts in gene regulation remains a puzzle. We demonstrated that overexpression of a full length PVT1 cDNA in the antisense orientation reconstituted enhanced sensitivity to Gemcitabine in naive ASPC-1 cells, whereas overexpression of a full length PVT1 cDNA in the sense orientation resulted in decreased sensitivity to Gemcitabine. Our results identified PVT-1 as a regulator of Gemcitabine sensitivity in pancreatic cancer cells and validated the genome-wide genetic screening approach for the identification of genetic determinants as well as potential biomarkers for the rational design of Gemcitabine chemotherapies for pancreatic cancer. (C) 2011 Published by Elsevier Inc.

http://dx.doi.org//10.1016/j.bbrc.2011.02.027

68. U04533
Zhang A. et al. Genetic analysis of SIRT1 gene promoter in sporadic Parkinson’s disease // Biochem. Biophys. Res. Commun. 2012. Vol. 422, № 4. P. 693–696.

Parkinson's disease (PD) is one of the most common neurodegenerative diseases. To date, genetic causes and underlying molecular mechanisms for sporadic PD remain largely unknown. Sirtuis are highly conserved NAD-dependent class III deacetylases. SIRT1, the closest to yeast Sir2, has deacetylase activity and ADP-ribosyltransferase activity. SIRT1 gene has been connected to many cellular processes and implicated in human diseases, such as obesity, type 2 diabetes, cancer and neurodegenerative diseases. Studies in animal model have also associated SIRT1 with aggregation of alpha-synuclein, a critical protein in the PD pathogenesis. We hypothesized that the genetic variants within the regulatory regions of SIRT1 gene that repress its gene expression, rather than mutations in its coding region that abolish SIRT1 function, may contribute to PD as a risk factor. In this study, we genetically analyzed the promoter region of SIRT1 gene in sporadic PD patients and ethic-matched healthy controls. Three novel heterozygous sequence variants, g.69644133C > G, g.69644213G > A and g.69644351G > A, were identified in PD patients, but in none of controls, which may alter the transcriptional activities of SIRT1 gene promoter, resulting in reduced SIRT1 levels. One novel heterozygous variant, g.69644219G > A, linked with single-nucleotide polymorphism - g.69644217A > C (rs932658), was only found in one control, which may have no functional activity. Therefore, our results suggested that genetic variants within the SIRT1 gene promoter may repress SIRT1 gene expression, contributing to PD as a risk factor. (C) 2012 Elsevier Inc. All rights reserved.

http://dx.doi.org/10.1016/j.bbrc.2012.05.059

69. Zhao J. et al. A Burden of Rare Variants Associated with Extremes of Gene Expression in Human Peripheral Blood // Am. J. Hum. Genet. 2016. Vol. 98, № 2. P. 299–309.

In order to evaluate whether rare regulatory variants in the vicinity of promoters are likely to impact gene expression, we conducted a novel burden test for enrichment of rare variants at the extremes of expression. After sequencing 2-kb promoter regions of 472 genes in 410 healthy adults, we performed a quadratic regression of rare variant count on bins of peripheral blood transcript abundance from microarrays, summing over ranks of all genes. After adjusting for common eQTLs and the major axes of gene expression covariance, a highly significant excess of variants with minor allele frequency less than 0.05 at both high and low extremes across individuals was observed. Further enrichment was seen in sites annotated as potentially regulatory by RegulomeDB, but a deficit of effects was associated with known metabolic disease genes. The main result replicates in an independent sample of 75 individuals with RNA-seq and whole-genome sequence information. Three of four predicted large-effect sites were validated by CRISPR/Cas9 knockdown in K562 cells, but simulations indicate that effect sizes need not be unusually large to produce the observed burden. Unusually divergent low-frequency promoter haplotypes were observed at 31 loci, at least 9 of which appear to be derived from Neandertal admixture, but these were not associated with divergent gene expression in blood. The overall burden test results are consistent with rare and private regulatory variants driving high or low transcription at specific loci, potentially contributing to disease.

http://dx.doi.org//10.1016/j.ajhg.2015.12.023

70. U04533
Zu Y. et al. Genetic variation in a miR-335 binding site in BIRC5 alters susceptibility to lung cancer in Chinese Han populations // Biochem. Biophys. Res. Commun. 2013. Vol. 430, № 2. P. 529–534.

Polymorphisms in 3' untranslated region (UTR) of cancer-related genes might affect their regulation by microRNAs (miRNAs) and thereby contribute to carcinogenesis. In this study, we screened single nucleotide polymorphisms (SNPs) in 3' UTR of cancer-related genes and investigated their effects on risk of lung cancer. First, we genotyped seven SNPs in a Chinese Han population with 600 lung cancer patients and 600 matched healthy controls and found that compared with the TT genotype of rs2239680 in 3' UTR of baculoviral IAP repeat containing 5 (BIRC5), C allele was associated with a significantly increased risk of lung cancer and advanced pathologic stage, with the odds ratio for participants carrying the CT or CC genotype being 1.50 [95% confidence interval (CI) 1.20-1.89, P < 0.01] and 2.29 (95% CI 1.64-3.18, P < 0.01), respectively. These results were further replicated and confirmed in another independent population with 1000 lung cancer cases and 1000 matched healthy controls. In support of the postulation that the 3' UTR SNP may directly affect miRNA-binding site, reporter gene assays indicated BIRC5 was a direct target of miR-335, and the rs2239680 T > C change resulted in altered regulation of BIRC5 expression. Moreover, BIRC5 was over expressed in lung cancer tissues compared with the normal lung tissues, and the protein levels of BIRC5 correlated with SNP genotypes in normal lung tissues. Our findings defined a 3' UTR SNP in human BIRC5 oncogene that may increase individual susceptibility to lung cancer probably by attenuating the interaction between miR-335 and BIRC5. (C) 2012 Elsevier Inc. All rights reserved.

http://dx.doi.org//10.1016/j.bbrc.2012.12.001

71. 010021
Амахин Д.В. Особенности суммации Гамк- и глутамат- опосредованных ионных токов изолированных нейронов коры головного мозга крысы // Российский физиологический журнал им. И. М. Сеченова 2012 Т. 98, № 12. С. 1490-1506.

В изолированных нейронах префронтальной коры головного мозга крыс методом пэтч-кламп в конфигурации «целая клетка» проведено исследование особенностей суммации ионных токов, вызванных аппликациями глутамата и ГАМК. Для регистрации ионных токов использовалось два различных пипеточных раствора: на основе хлорида и фторида цезия. При регистрации с применением раствора на основе хлорида цезия пиковая амплитуда тока, вызванного совместной аппликацией ГАМК и глутамата (по 200 мкМ), совпадала с пиковой амплитудой тока, вызванного аппликацией только ГАМК, и была достоверно меньше арифметической суммы амплитуд ответов на аппликации нейромедиаторов по отдельности. При использовании пипеточного раствора на основе фторида цезия ответ на совместную аппликацию смеси глутамата и ГАМК практически совпадал с арифметической суммой индивидуальных ответов. При действии этих нейромедиаторов в насыщающих концентрациях (5 мМ) регистрируемый ответ на совместную аппликацию был достоверно меньше, чем ответ на аппликацию только ГАМК. Полученные результаты позволяют предположить наличие механизма взаимодействия между ГАМК А- и ионотропными глутаматными рецепторами (АМРА и каинатными). По-видимому, при совместной аппликации глутамата и ГАМК активация ГАМК А-рецепторов в большей мере влияет на глутаматные рецепторы, чем активация глутаматных на ГАМК А-рецепторы.

https://elibrary.ru/item.asp?id=18528229

72. 08698139
Борзых А.А., Гайнуллина Д.К., Кузьмин И.В., Шарова А.П., Тарасова О.С., Виноградова О.Л. СРАВНИТЕЛЬНЫЙ АНАЛИЗ ЭКСПРЕССИИ ГЕНОВ В ЛОКОМОТОРНЫХ МЫШЦАХ И ДИАФРАГМЕ КРЫСЫ // Российский физиологический журнал им. И.М. Сеченова. 2012. Т. 98. № 12. С. 1587-1594.

Методом количественной ПЦР исследовали профиль экспрессии генов в диафрагме по сравнению с тремя принципиально различными по характеристикам мышцами задней конечности (камбаловидной мышцей, красной и белой частями икроножной мышцы). Показано, что уровни экспрессии мРНК PGC-1? и миогенина в диафрагме находятся в соответствии с ее миозиновым фенотипом и активностью цитратсинтазы. Вместе с тем диафрагма характеризуется необычно высоким содержанием мРНК MyoD, а также высоким содержанием мРНК IGF-1 и низким содержанием мРНК миостатина. Последние два наблюдения позволяют предположить высокую интенсивность белкового синтеза в мышечных волокнах диафрагмы, несмотря на то что они мельче, чем в локомоторных мышцах.

http://elibrary.ru/item.asp?id=18528283

73. 000617
Климов Л.О., Федосеева Л.А., Рязанова М.А., Дымшиц Г.М., Маркель А.Л. ЭКСПРЕССИЯ ГЕНОВ РЕНИН-АНГИОТЕНЗИНОВОЙ СИСТЕМЫ В СТРУКТУРАХ МОЗГА КРЫС ЛИНИИ НИСАГ СО СТРЕССЧУВСТВИТЕЛЬНОЙ АРТЕРИАЛЬНОЙ ГИПЕРТЕНЗИЕЙ // Дымшиц Г.М., Маркель А.Л. Бюллетень экспериментальной биологии и медицины. 2012. Т. 154. № 9. С. 342-345.

В тканях гипоталамуса и продолговатого мозга крыс гипертензивной линии НИСАГ и нормотензивной линии WAG изучена экспрессия генов, кодирующих ангиотензиноген (Agt), ренин (Ren), ангиотензинпревращающий фермент (ACE) и рецептор ангиотензина 1-го типа (АТ1А). Содержание мРНК гена Agt в гипоталамусе у молодых крыс НИСАГ повышено на 30% относительно контрольной линии WAG. В продолговатом мозге молодых крыс НИСАГ уровень мРНК генов Agt и рецептора АТ1А повышен на 60 и 24% соответственно по сравнению с крысами WAG. У взрослых животных различия с контрольной линией в экспрессии исследуемых генов не обнаружено. Сделано заключение о том, что изменение экспрессии генов ренин-ангиотензиновой системы в мозговых структурах крыс НИСАГ может лежать в основе формирования гипертензивного статуса организма.

http://dx.doi.org//http://elibrary.ru/item.asp?id=17934741

74. 000617
Колобов В.В., Сторожева З.И., Грудень М.А., Шерстнев В.В. РЕГИОНАЛЬНЫЕ ОСОБЕННОСТИ ЭКСПРЕССИИ ГЕНОВ НЕЙРОГЕНЕЗА И АПОПТОЗА В ГОЛОВНОМ МОЗГЕ ЗРЕЛЫХ КРЫС // Бюллетень экспериментальной биологии и медицины. 2012. Т. 153. № 5. С. 707-711.

В префронтальной коре, гиппокампе и мозжечке взрослых крыс определяли экспрессию мРНК генов, вовлеченных в нейрогенез и апоптоз: Apaf1, Ascl1, Bax, Bcl2, Casp3, Casp8, Casp9, Dffb, Myh10, Naip2, Napa, Notch2, Numb, Pura, S100a6 и Tnf. Обнаружено, что в мозжечке относительное содержание мРНК указанных генов, за исключением Apaf1, многократно увеличено по сравнению с их уровнем в гиппокампе и коре мозга, тогда как в гиппокампе по сравнению с префронтальной корой значимо снижена экспрессия Apaf1 и увеличена экспрессия Ascl1, Pura, S100a6 и Tnf. Выявлены региональные различия в направленности, силе и количестве достоверных корреляций между относительными уровнями экспрессии исследованных генов. Документированные особенности генной экспрессии рассматриваются как подтверждение положения о структурно-функциональной сопряженности процессов нейрогенеза и нейроапоптоза на молекулярно-генетическом уровне.

http://elibrary.ru/item.asp?id=19090697

75. 000231
Коржевский Д.Э., Кирик О.В., Алексеева О.С. ЭКСПРЕССИЯ НЕСТИНА В КЛЕТКАХ ЭПЕНДИМЫ БОКОВЫХ ЖЕЛУДОЧКОВ ГОЛОВНОГО МОЗГА КРЫСЫ ПРИ СТАРЕНИИ // Морфология. 2014. Т. 146. № 5. С. 70-72.

Известно, что при развитии головного мозга по мере дифференцировки эпендимоцитов из радиальных глиоцитов происходит прекращение синтеза нестина. Однако показано, что нестин в эпендиме боковых желудочков головного мозга начинает синтезироваться в ответ на ишемическое повреждение. Цель настоящего исследования состояла в проверке гипотезы о возможности восстановления экспрессии нестина в эпендиме при старении. Работа выполнена на крысах-самцах линии Вистар в возрасте 4 (n=4) и 28 мес (n=3). У старых животных установлена экспрессия нестина в эпендиме боковых желудочков головного мозга, причем в области медиальной и верхней стенок бокового желудочка обнаружены участки эпендимы, в которых все клетки имели интенсивную окраску цитоплазмы. Причины обнаруженного факта остаются неясными.

http://elibrary.ru/item.asp?id=22307561

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