Cited by 186Genomics and Chromatin DynamicsChromatin Remodeling and CancerEpigenetics and DNA Methylation

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Regulation of nucleosome landscape and transcription factor targeting at tissue-specific enhancers by BRG1

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Hu, Gangqing, Schones, Dustin E., Cui, Kairong, Ybarra, River, Northrup, Daniel, Tang, Qingsong, Gattinoni, Luca, Restifo, Nicholas P., Huang, Suming, Zhao, Keji·2011·Genome Research

DOI 10.1101/gr.121145.111PMC PMC3202282

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Abstract

Enhancers of transcription activate transcription via binding of sequence-specific transcription factors to their target sites in chromatin. In this report, we identify GATA1-bound distal sites genome-wide and find a global reorganization of the nucleosomes at these potential enhancers during differentiation of hematopoietic stem cells (HSCs) to erythrocytes. We show that the catalytic subunit BRG1 of BAF complexes localizes to these distal sites during differentiation and generates a longer nucleosome linker region surrounding the GATA1 sites by shifting the flanking nucleosomes away. Intriguingly, we find that the nucleosome shifting specifically facilitates binding of TAL1 but not GATA1 and is linked to subsequent transcriptional regulation of target genes.

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An RNA binding module of SWI/SNF is required for activation of cell-type specific enhancers and super-enhancers in early developmentPreprint
Saha, D., Animireddy, S., Lee, J., Lin, Y.-C., Feola, K. C., Jain, A. K., Lu, Y., Liu, B., & Bartholomew, B. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.09.06.506785 · Cited by 1
“increasing accessibility at the enhancers (Bossen et al., 2015; Hu et al., 2011; Ni et al., 2008).”
BackgroundInfluential
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Ryder: Epigenome normalization using a two-tier model and internal reference regions.
Cao, Y.-Q., Ge, G.-Z., & Zhao, K.-J. (2026) · Bioinformatics · doi:10.1093/bioinformatics/btag753
“…we found that inhibition of BRG1 using a chemical inhibitor, BRM014, resulted in increased nucleosome occupancy at enhancer centers and decreased occupancy in flanking regions, consistent with our previous finding that BRG1 acts to maintain a nucleosome-free region at enhancers ( 31, 34 ).”
Self-citation
The Zelda Interactome Reveals Diverse Co-factors Essential for Pioneer Factor-Mediated Zygotic Genome ActivationPreprint
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TDG orchestrates ATF4-dependent gene transcription during retinoic acid-induced cell fate acquisition
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ASCL1 interacts with the mSWI/SNF at distal regulatory elements to regulate neural differentiationPreprint
Păun, O., Tan, Y. X., Patel, H., Strohbuecker, S., Ghanate, A. D., Gigli, C. C., Sopeña, M. L., Gerontogianni, L., Goldstone, R. J., Ang, S., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.10.09.510609 · Cited by 2
“, 2020), and/or interaction with other transcription factors and proteins with chromatin remodeling capacity (Hu et al., 2011; King and Klose, 2017; Takaku et al., 2016; Theodorou et al., 2013; Wang et al., 2014).”
BackgroundInfluential
BRG1 promotes transcriptional patterns that are permissive to proliferation in cancer cells
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PBAP chromatin remodeler mediates enhancer-driven transcription in DrosophilaPreprint
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Background
Characterizing higher order structures of chromatin in human cells
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“Plusieurs travaux ont montré que le positionnement des nucléosomes variait en fonction de différentes conditions tissulaires physiologiques ou pathologiques (Schones et al, 2008; Hu et al, 2011; Valouev et al, 2011; Gaffney et al, 2012).”
Background
NEXT-GENERATION SEQUENCING APPROACH FOR TRANSCRIPTOME AND EPIGENOME DEFINITION OF HUMAN HEMATOPOIETIC STEM/PROGENITOR CELLS AND THEIR EARLY ERYTHROID AND MYELOID COMMITTED PROGENY
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Non Parametric Unsupervised Clustering of ChIP Enrichment Regions Provides Isolation Vectors for Differential Functional Analysis
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“From the hematopoietic lineage HSCs [50, 54, 55], Erythroid [56, 57, 58], Megakaryocyte [59], and T-ALL cell lines and primary cells [39, 56] were contributed.”
Background
Characterization of Higher-order Chromatin Structure in Bone Differentiation and Breast Cancer: A Dissertation
Barutcu, A. R. (2016) · eScholarship@UMassChan · doi:10.13028/m2t01z
“[247; 248] and B-cells [245] and colocalizes with pluripotency factors [249], suggesting”
Background

Authors: Hu, G., Schones, D. E., Cui, K., Ybarra, R., Northrup, D., Tang, Q., Gattinoni, L., Restifo, N. P., Huang, S., & Zhao, K.
Affiliations: National Institutes of Health (US)
University of Florida Health (US)
ORCID: Hu, Gangqing
Schones, Dustin E.
Northrup, Daniel
Tang, Qingsong
Gattinoni, Luca
Restifo, Nicholas P.
Huang, Suming
Zhao, Keji
Venue: Genome Research
Publisher: Cold Spring Harbor Laboratory
Published: 2011-07-27
Volume: 21
Issue: 10
Pages: 1650-1658
ISSN: 1088-9051 (ISSN-L)
DOI: 10.1101/gr.121145.111
PMC: PMC3202282
OpenAlex: W2119037385
Cited by: 186
References: 0
Citations by year: 2026: 5 · 2025: 5 · 2024: 6 · 2023: 4 · 2022: 10 · 2021: 19 · 2020: 12 · 2019: 14 · 2018: 15 · 2017: 11 · 2016: 18 · 2015: 11 · 2014: 25 · 2013: 15 · 2012: 16
Type: posted content
Language: en
Open access: bronze
doi.org
Locations: Genome Research (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
HighWire Press Open Archive (submittedVersion)
Funders: National Institutes of Health
National Heart, Lung, and Blood Institute (R01HL091929, K22HL101950, R01HL090589)
NHLBI Division of Intramural Research
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
Keywords: SMARCA4, BAF chromatin remodeling complex, nucleosome positioning, enhancers, GATA-1, TAL1, hematopoietic stem cell differentiation, erythropoiesis, transcription factor binding, chromatin regulation
MeSH terms: T-Cell Acute Lymphocytic Leukemia Protein 1, CCCTC-Binding Factor, Binding Sites, Cell Differentiation, Cells, Cultured, DNA Helicases, Enhancer Elements, Genetic, Gene Expression Regulation, Hematopoiesis, Hematopoietic Stem Cells, Humans, Nuclear Proteins, Nucleosomes, Organ Specificity, Proto-Oncogene Proteins, Repressor Proteins, Transcription Factors, Transcription, Genetic, Chromatin Assembly and Disassembly, Chromatin Immunoprecipitation, GATA1 Transcription Factor, Basic Helix-Loop-Helix Proteins, Primary Cell Culture

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Regulation of nucleosome landscape and transcription factor targeting at tissue-specific enhancers by BRG1

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