CREMOFAC—a database of chromatin remodeling factors

Agrawal, Shipra; Kumar, Chandan; Rao, M. R. S.

doi:10.1093/bioinformatics/btl509

Cited by 21 publications

(17 citation statements)

References 8 publications

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“…The rationale behind this analysis was to search for those remodeling factors that are overexpressed in haploid round spermatids, as these were likely to be involved in chromatin remodeling later in spermiogenesis. The list of chromatin remodeling factors was obtained from CREMOFAC, a database that was developed in our laboratory (28). Tetraploid and haploid germ cell populations were isolated by the method of centrifugal elutriation, and 10-day-old rat testes served as a source of gametic diploid cells (23,29).…”

Section: Resultsmentioning

confidence: 99%

Insights into Role of Bromodomain, Testis-specific (Brdt) in Acetylated Histone H4-dependent Chromatin Remodeling in Mammalian Spermiogenesis

Dhar¹,

Thota

2012

Journal of Biological Chemistry

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Background: Brdt is a double bromodomain containing, testis-specific protein known to recognize acetylated H4. Results: Smarce1, identified as a novel Brdt interacting partner, shows enhanced interaction upon hyperacetylation of histone H4. Conclusion: Brdt, a chromatin remodeling factor, associates with Smarce1 in haploid spermatids. Significance: This study sheds light on the molecular events underlying global chromatin remodeling during mammalian spermiogenesis.

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Section: Resultsmentioning

confidence: 99%

Insights into Role of Bromodomain, Testis-specific (Brdt) in Acetylated Histone H4-dependent Chromatin Remodeling in Mammalian Spermiogenesis

Dhar¹,

Thota

2012

Journal of Biological Chemistry

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“…We identified several functional/disease gene sets in ASD for gene set enrichment analysis (GSEA): (1) two lists of RBFOX1 (RNA-binding protein, fox-1 homolog 1)-regulating RNA targets: RBFOX1-1 [44]; RBFOX1-2 [45]; (2) two lists of fragile X mental retardation protein (FMRP) mRNA targets: FMRP-1 [46]; FMRP-2 [47]; (3) evolutionarily constrained genes (ECGs) [48]; (4) synapse-related gene lists: postsynapse-related genes from proteomic profiling of human neocortical biopsies (Hpsd), protein complexes of the postsynaptic density (PSD; PSD-95, ARC, mGluR5, NMDAR), and genes related to presynaptic proteins, presynaptic active zone, and synaptic vesicles [49, 50]; (5) chromatin remodeling factors (CRFs) [51]; (6) histone modification enzymes (HMEs) [52]; (7) differentially expressed genes from cortical samples of autism (DEs) [44]. All genes including candidates and known gene sets were mapped to current human gene symbols (HGNC) to assure the consistency of nomenclature.…”

Section: Methodsmentioning

confidence: 99%

Leveraging blood serotonin as an endophenotype to identify de novo and rare variants involved in autism

et al. 2017

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BackgroundAutism spectrum disorder (ASD) is one of the most highly heritable neuropsychiatric disorders, but underlying molecular mechanisms are still unresolved due to extreme locus heterogeneity. Leveraging meaningful endophenotypes or biomarkers may be an effective strategy to reduce heterogeneity to identify novel ASD genes. Numerous lines of evidence suggest a link between hyperserotonemia, i.e., elevated serotonin (5-hydroxytryptamine or 5-HT) in whole blood, and ASD. However, the genetic determinants of blood 5-HT level and their relationship to ASD are largely unknown.MethodsIn this study, pursuing the hypothesis that de novo variants (DNVs) and rare risk alleles acting in a recessive mode may play an important role in predisposition of hyperserotonemia in people with ASD, we carried out whole exome sequencing (WES) in 116 ASD parent-proband trios with most (107) probands having 5-HT measurements.ResultsCombined with published ASD DNVs, we identified USP15 as having recurrent de novo loss of function mutations and discovered evidence supporting two other known genes with recurrent DNVs (FOXP1 and KDM5B). Genes harboring functional DNVs significantly overlap with functional/disease gene sets known to be involved in ASD etiology, including FMRP targets and synaptic formation and transcriptional regulation genes. We grouped the probands into High-5HT and Normal-5HT groups based on normalized serotonin levels, and used network-based gene set enrichment analysis (NGSEA) to identify novel hyperserotonemia-related ASD genes based on LoF and missense DNVs. We found enrichment in the High-5HT group for a gene network module (DAWN-1) previously implicated in ASD, and this points to the TGF-β pathway and cell junction processes. Through analysis of rare recessively acting variants (RAVs), we also found that rare compound heterozygotes (CHs) in the High-5HT group were enriched for loci in an ASD-associated gene set. Finally, we carried out rare variant group-wise transmission disequilibrium tests (gTDT) and observed significant association of rare variants in genes encoding a subset of the serotonin pathway with ASD.ConclusionsOur study identified USP15 as a novel gene implicated in ASD based on recurrent DNVs. It also demonstrates the potential value of 5-HT as an effective endophenotype for gene discovery in ASD, and the effectiveness of this strategy needs to be further explored in studies of larger sample sizes.Electronic supplementary materialThe online version of this article (doi:10.1186/s13229-017-0130-3) contains supplementary material, which is available to authorized users.

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“…To select genes encoding transcription factors we used TFClass database [37]. To classify genes as a transcriptional regulators we used the list of 167 genes encoding proteins with chromatin-modifying activities that was compiled previously [38] from three databases: EntrezGene (http://www.ncbi.nlm.nih.gov/gene), CREMOFAC [39], and CR Cistrome [40]. To annotate genes encoding proteins related to the cilium or BBSome, we used genes extracted from EntrezGene utilizing the GO terms “BBSome” or “cilium” as a query.…”

Section: Methodsmentioning

confidence: 99%

A compendium of human genes regulating feeding behavior and body weight, its functional characterization and identification of GWAS genes involved in brain-specific PPI network

et al. 2016

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BackgroundObesity is heritable. It predisposes to many diseases. The objectives of this study were to create a compendium of genes relevant to feeding behavior (FB) and/or body weight (BW) regulation; to construct and to analyze networks formed by associations between genes/proteins; and to identify the most significant genes, biological processes/pathways, and tissues/organs involved in BW regulation.ResultsThe compendium of genes controlling FB or BW includes 578 human genes. Candidate genes were identified from various sources, including previously published original research and review articles, GWAS meta-analyses, and OMIM (Online Mendelian Inheritance in Man). All genes were ranked according to knowledge about their biological role in body weight regulation and classified according to expression patterns or functional characteristics. Substantial and overrepresented numbers of genes from the compendium encoded cell surface receptors, signaling molecules (hormones, neuropeptides, cytokines), transcription factors, signal transduction proteins, cilium and BBSome components, and lipid binding proteins or were present in the brain-specific list of tissue-enriched genes identified with TSEA tool. We identified 27 pathways from KEGG, REACTOME and BIOCARTA whose genes were overrepresented in the compendium. Networks formed by physical interactions or homological relationships between proteins or interactions between proteins involved in biochemical/signaling pathways were reconstructed and analyzed. Subnetworks and clusters identified by the MCODE tool included genes/proteins associated with cilium morphogenesis, signal transduction proteins (particularly, G protein–coupled receptors, kinases or proteins involved in response to insulin stimulus) and transcription regulation (particularly nuclear receptors). We ranked GWAS genes according to the number of neighbors in three networks and revealed 22 GWAS genes involved in the brain-specific PPI network. On the base of the most reliable PPIs functioning in the brain tissue, new regulatory schemes interpreting relevance to BW regulation are proposed for three GWAS genes (ETV5, LRP1B, and NDUFS3). ConclusionsA compendium comprising 578 human genes controlling FB or BW was designed, and the most significant functional groups of genes, biological processes/pathways, and tissues/organs involved in BW regulation were revealed. We ranked genes from the GWAS meta-analysis set according to the number and quality of associations in the networks and then according to their involvement in the brain-specific PPI network and proposed new regulatory schemes involving three GWAS genes (ETV5, LRP1B, and NDUFS3) in BW regulation. The compendium is expected to be useful for pathology risk estimation and for design of new pharmacological approaches in the treatment of human obesity.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-016-0466-2) contains supplementary material, which is available to authorized users.

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CREMOFAC—a database of chromatin remodeling factors

Abstract: http://www.jncasr.ac.in/cremofac/

Cited by 21 publications

References 8 publications

Insights into Role of Bromodomain, Testis-specific (Brdt) in Acetylated Histone H4-dependent Chromatin Remodeling in Mammalian Spermiogenesis

Insights into Role of Bromodomain, Testis-specific (Brdt) in Acetylated Histone H4-dependent Chromatin Remodeling in Mammalian Spermiogenesis

Leveraging blood serotonin as an endophenotype to identify de novo and rare variants involved in autism

A compendium of human genes regulating feeding behavior and body weight, its functional characterization and identification of GWAS genes involved in brain-specific PPI network

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