A5049090291- Genomics and Chromatin Dynamics
- Epigenetics and DNA Methylation
- Immune Cell Function and Interaction
- RNA modifications and cancer
- T-cell and B-cell Immunology
- RNA Research and Splicing
- Cancer-related gene regulation
- Chromatin Remodeling and Cancer
- IL-33, ST2, and ILC Pathways
- Protein Degradation and Inhibitors
- Cancer-related molecular mechanisms research
- CRISPR and Genetic Engineering
- interferon and immune responses
- RNA and protein synthesis mechanisms
- Cancer Genomics and Diagnostics
- Pluripotent Stem Cells Research
- Chromosomal and Genetic Variations
- Advanced biosensing and bioanalysis techniques
- Genomics and Phylogenetic Studies
- Immunotherapy and Immune Responses
- Single-cell and spatial transcriptomics
- Cancer therapeutics and mechanisms
- Cancer Mechanisms and Therapy
- Histone Deacetylase Inhibitors Research
- Cytokine Signaling Pathways and Interactions
National Heart Lung and Blood Institute
2016-2025
National Institutes of Health
2015-2024
Zhejiang University of Technology
2024
Qiqihar Medical University
2023
Rockefeller University
2018
Center for Systems Biology
2017
Past Global Changes
2017
Institute of Molecular Biology and Biophysics
2014
Center of Molecular Immunology (Cuba)
2013
Medical College of Wisconsin
2012
Chromatin states are the key to gene regulation and cell identity. immunoprecipitation (ChIP) coupled with high-throughput sequencing (ChIP-Seq) is increasingly being used map epigenetic across genomes of diverse species. modification profiles frequently noisy diffuse, spanning regions ranging from several nucleosomes large domains multiple genes. Much early work on identification ChIP-enriched for ChIP-Seq data has focused identifying localized regions, such as transcription factor binding...
Lymphocyte activation is accompanied by visible changes in chromatin structure. We find that antigen receptor signaling induces the rapid association of BAF complex with chromatin. PIP2, which regulated stimuli, sufficient vitro to target chromatin, but it has no effect on related remodeling complexes containing SNF2L or hISWI. Purification and peptide sequencing subunits revealed β-actin as well a novel actin-related protein, BAF53. BAF53 are required for maximal ATPase activity BRG1 also...
Insulators are DNA elements that prevent inappropriate interactions between the neighboring regions of genome. They can be functionally classified as either enhancer blockers or domain barriers. CTCF (CCCTC-binding factor) is only known major insulator-binding protein in vertebrates and has been shown to bind many enhancer-blocking elements. However, it not clear whether plays a role chromatin barriers active repressive domains. Here, we used ChIP-seq map genome-wide binding sites three cell...
Recent studies have demonstrated that the Ten-eleven translocation (Tet) family proteins can enzymatically convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). While 5mC has been studied extensively, little is known about distribution and function of 5hmC. Here we present a genome-wide profile 5hmC in mouse embryonic stem (ES) cells. A combined analysis global gene expression wild-type Tet1-depleted ES cells suggests enriched at both bodies actively transcribed genes extended...
Abstract ChIP-Seq, which combines chromatin immunoprecipitation (ChIP) with ultra high-throughput massively parallel sequencing, is increasingly being used for mapping protein–DNA interactions in-vivo on a genome scale. Typically, short sequence reads from ChIP-Seq are mapped to reference further analysis. Although genomic regions enriched could be inferred as approximate binding regions, read lengths (∼25-50nt) pose challenges determining the exact sites within these regions. Here, we...
Although the function of DNA methylation in gene promoter regions is well established transcriptional repression, evolutionarily conserved widespread distribution body remains incompletely understood. Here, we show that enriched included alternatively spliced exons (ASEs), and inhibition results aberrant splicing ASEs. The methyl-CpG-binding protein MeCP2 ASEs, particularly those are also highly methylated, disrupts specific targeting to exons. Interestingly, ablation increased histone...
Tregs not only keep immune responses to autoantigens in check, but also restrain those directed toward pathogens and the commensal microbiota. Control of peripheral homeostasis by relies on their capacity accumulate at inflamed sites appropriately adapt local environment. To date, factors involved control these aspects Treg physiology remain poorly understood. Here, we show that canonical Th2 transcription factor GATA3 is selectively expressed residing barrier including gastrointestinal...
To understand the molecular basis that supports dynamic gene expression programs unique to T cells, we investigated genomic landscape of activating histone modifications, including H3 K9/K14 diacetylation (H3K9acK14ac), K4 trimethylation (H3K4me3), and repressive modification K27 (H3K27me3) in primary human cells. We show H3K9acK14ac H3K4me3 are associated with active genes required for cell function development, whereas H3K27me3 is silent involved development other types. Unexpectedly, find...
The identity and developmental potential of a human cell is specified by its epigenome that largely defined patterns chromatin modifications including histone acetylation. Here we report high-resolution genome-wide mapping diacetylation H3 at Lys 9 14 in resting activated T cells technique (GMAT). Our data show high levels the acetylation are detected gene-rich regions. accessibility gene expression genetic domain correlated with hyperacetylation promoters other regulatory elements but not...
Distinctive SWI/SNF-like ATP-dependent chromatin remodeling esBAF complexes are indispensable for the maintenance and pluripotency of mouse embryonic stem (ES) cells [Ho L, et al. (2009) Proc Natl Acad Sci USA 10.1073/pnas.0812889106]. To understand mechanism underlying roles these in ES cells, we performed high-resolution genome-wide mapping core ATPase subunit, Brg, using ChIP-Seq technology. We find that esBAF, as represented by binds to genes encoding components transcriptional...
Expression of T1ST2, the IL-33R, by Th2 cells requires GATA3. Resting express little GATA3, which is increased IL-33 and a STAT5 activator, in turn increasing T1ST2 from its low-level expression on resting cells. that have upregulated produce IL-13, but not IL-4, response to plus activator an antigen-independent, NF-kappaB-dependent, cyclosporin A (CsA)-resistant manner. Similarly, Th17 IL-17A IL-1beta STAT3 Th1 IFNgamma IL-18 STAT4 inducer. Thus, each effector Th cell produces cytokines...