A5076498573- Genetic Associations and Epidemiology
- Genomics and Chromatin Dynamics
- Fungal and yeast genetics research
- Epigenetics and DNA Methylation
- Genomic variations and chromosomal abnormalities
- Bioinformatics and Genomic Networks
- Genomics and Rare Diseases
- RNA Research and Splicing
- Genetics and Neurodevelopmental Disorders
- Cancer-related gene regulation
- Genomics and Phylogenetic Studies
- Single-cell and spatial transcriptomics
- Adsorption and biosorption for pollutant removal
- RNA modifications and cancer
- Heavy metals in environment
- RNA and protein synthesis mechanisms
- Chromium effects and bioremediation
- Health, Environment, Cognitive Aging
- Gene expression and cancer classification
- CRISPR and Genetic Engineering
- Genetic Mapping and Diversity in Plants and Animals
- DNA Repair Mechanisms
- Ubiquitin and proteasome pathways
- Autism Spectrum Disorder Research
- Cancer Cells and Metastasis
Huazhong Agricultural University
2021-2025
Changchun Institute of Technology
2025
Central South University
2015-2024
China Medical University
2021-2024
The Ohio State University
2024
Huazhong University of Science and Technology
2021-2024
Second Xiangya Hospital of Central South University
2021-2024
Renji Hospital
2024
Shanghai Jiao Tong University
2021-2024
Shenyang Agricultural University
2024
Most genetic risk for psychiatric disease lies in regulatory regions, implicating pathogenic dysregulation of gene expression and splicing. However, comprehensive assessments transcriptomic organization diseased brains are limited. In this work, we integrated genotypes RNA sequencing brain samples from 1695 individuals with autism spectrum disorder (ASD), schizophrenia, bipolar disorder, as well controls. More than 25% the transcriptome exhibits differential splicing or expression,...
Despite progress in defining genetic risk for psychiatric disorders, their molecular mechanisms remain elusive. Addressing this, the PsychENCODE Consortium has generated a comprehensive online resource adult brain across 1866 individuals. The contains ~79,000 brain-active enhancers, sets of Hi-C linkages, and topologically associating domains; single-cell expression profiles many cell types; quantitative-trait loci (QTLs); further QTLs associated with chromatin, splicing, cell-type...
Genes implicated in neuropsychiatric disorders are active human fetal brain, yet difficult to study a longitudinal fashion. We demonstrate that organoids from pluripotent cells model cerebral cortical development on the molecular level before 16 weeks postconception. A multiomics analysis revealed differentially genes and enhancers, with greatest changes occurring at transition stem progenitors. Networks of converging gene enhancer modules were assembled into six four global patterns...
A multiprotein complex isolated from murine cells is identified as a counterpart of the yeast Mediator transcriptional regulation on basis following: homologs two subunits Mediator, Srb7 and Med7, copurify with complex; peptide sequencing reveals, in addition, Rgr1 Med6; mouse binds to RNA polymerase II C-terminal domain (CTD) stimulates phosphorylation CTD by TFIIH. Peptide also identifies component relative Ring-3 protein, mitogen-activated nuclear protein kinase, raising possibility an...
Single particles of the mediator transcriptional regulation (Mediator) and RNA polymerase II holoenzyme were revealed by electron microscopy image processing. Mediator alone appeared compact, but at high pH or in presence it displayed an extended conformation. Holoenzyme contained a fully state, partially enveloping globular polymerase, with points apparent contact vicinity carboxyl-terminal domain DNA-binding channel. A similarity appearance conformational behavior yeast murine complexes...
Sin4 and Rgr1 proteins, previously shown by genetic studies to play both positive negative roles in the transcriptional regulation of many genes, are identified here as components mediator RNA polymerase II holoenzyme complexes. Results with deletion truncation strains indicate association these proteins a subcomplex comprising Sin4, Rgr1, Gal11, 50-kDa polypeptide. Taken together previous evidence, our findings point role repression well activation.
Structures of yeast Mediator complex, a related complex from mouse cells and thyroid hormone receptor-associated protein human have been determined by three-dimensional reconstruction electron micrographs single particles. All three complexes show division in two parts, “head” domain combined “middle-tail” domain. The head domains the appear most similar interact closely with RNA polymerase II. middle-tail greatest structural divergence and, case tail domain, may not at all. Consistent this...
A growing number of genomic tools and databases were developed to facilitate the interpretation variants, particularly in coding regions. However, these are separately available different online websites or databases, making it challenging for general clinicians, geneticists biologists obtain first-hand information regarding some particular variants genes interest. Starting with regions splice sties, we artificially generated all possible single nucleotide (n = 110 154 363) cataloged...
POU3F2 regulates expression of key genes in postmortem brain tissue from patients with schizophrenia or bipolar disorder.
Cellular heterogeneity in the human brain obscures identification of robust cellular regulatory networks, which is necessary to understand function non-coding elements and impact genetic variation. Here we integrate genome-wide chromosome conformation data from purified neurons glia with transcriptomic enhancer profiles, characterize gene landscape two major cell classes brain. We then leverage cell-type-specific landscapes gain insight into etiology several disorders. find that Alzheimer's...
We have cloned and sequenced the SIN4 gene determined that is identical to TSF3, identified as a negative regulator of GAL1 transcription (S. Chen, R.W. West, Jr., S.L. Johnson, H. Gans, J. Ma, submitted for publication). Yeast strains bearing sin4 delta null mutation been constructed are temperature sensitive growth display defects in both positive regulation transcription. Transcription CTS1 reduced mutants, suggesting Sin4 functions transcriptional regulator. Additionally, Sin4-LexA...
Transcription factors (TFs) are important regulators of gene expression. To better understand TF-encoding genes in maize (Zea mays L.), a genome-wide TF prediction was performed using the updated B73 reference genome. A total 2298 were identified, which can be classified into 56 families. The largest family, known as MYB superfamily, comprises 322 and MYB-related genes. expression patterns 2 014 (87.64%) examined RNA-seq data, resulted identification subset TFs that specifically expressed...
Microbial consortia have opened new avenues for heavy-metal remediation. However, the limited understanding of overall effect interspecific interactions on remediation efficacy hinders its application. Here, effects multispecies growth and biofilm formation Cd immobilization were explored from direct multiple through random combinations two or three rhizosphere bacteria. In monocultures, stress resulted in an average decrease planktonic biomass 26%, but cooperation, was attenuated dual (21%)...
Abstract Psychiatric disorders are highly heritable yet polygenic, potentially involving hundreds of risk genes. Genome-wide association studies have identified genomic susceptibility loci with to psychiatric disorders; however, the contribution these underlying psychopathology and etiology remains elusive. Here we generated deep human brain proteomics data by quantifying 11,608 proteins across 268 subjects using 11-plex tandem mass tag coupled two-dimensional liquid chromatography-tandem...
Many psychiatric disorders exhibit sex differences, but the underlying mechanisms remain poorly understood. We analyzed transcriptomics data from 2160 postmortem adult prefrontal cortex brain samples PsychENCODE consortium in a sex-stratified study design. compared of patients with schizophrenia (SCZ), bipolar disorder (BD), and autism spectrum (ASD) control brains individuals without known history disease. found that females SCZ, BD, ASD showed higher burden transcriptomic dysfunction than...
Act3p/Arp4, an essential actin-related protein ofSaccharomyces cerevisiae located within the nucleus, is, according to genetic data, involved in transcriptional regulation. In addition basal core structure of actin family members, which is responsible for ATPase activity, Act3p possesses two insertions, insertions I and II, latter predicted form a loop-like protruding from beyond surface molecule. Because constituent chromatin but itself does not bind DNA, we hypothesized that insertion II...
The SIN4 and RGR1 genes of Saccharomyces cerevisiae were identified by mutations in quite different genetic screens. We have shown that the gene product is required for proper transcriptional regulation many a sin4 mutation can affect either activation or repression specific genes. suggested this dual nature due to its involvement chromatin organization. now report role similar SIN4. both function as negative regulators HO IME1, lead decreased expression other including CTS1. Strains with...
DNA methylation is a widespread epigenetic modification that plays an essential role in gene expression through transcriptional regulation and chromatin remodeling. The emergence of whole genome bisulfite sequencing (WGBS) represents important milestone the detection methylation. Characterization differential methylated regions (DMRs) fundamental as well for further functional analysis. In this study, we present swDMR (http://sourceforge.net/projects/swdmr/) comprehensive analysis DMRs from...