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Regulation of nucleosome landscape and transcription factor targeting at tissue-specific enhancers by BRG1
Open accessAbstract
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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“The mechanisms of pioneer factor action are still being established [37], but at least some of them (such as FOXA, OCT4 and SOX2/SOX11) have been shown to initiate chromatin opening by direct displacement of histones [38–41], whilst many others recruit chromatin remodelers [42–50].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [48]
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Mapping and quantifying mammalian transcriptomes by RNA-Seq
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Annotation of functional variation in personal genomes using RegulomeDB
Boyle, A. P., Hong, E. L., Hariharan, M., Cheng, Y., Schaub, M. A., Kasowski, M., Karczewski, K. J., Park, J., Hitz, B. C., Weng, S., et al. (2012) · Genome Research · doi:10.1101/gr.137323.112 · Cited by 2,722
“Inaddition, we have included transcriptionfactor ChIP-seq data availablefrom the NCBI Sequence Read Archive (Hollenhorst et al. 2009; Jolma et al. 2010; Verzi et al. 2010; Wei et al. 2010; Hu et al. 2011; Lo et al. 2011; Novershtern et al. 2011; Palii et al. 2011; Yu et al. 2011).”
MethodLatent Enhancers Activated by Stimulation in Differentiated Cells
Ostuni, R., Piccolo, V., Barozzi, I., Polletti, S., Termanini, A., Bonifacio, S., Curina, A., Prosperini, E., Ghisletti, S., & Natoli, G. (2013) · Cell · doi:10.1016/j.cell.2012.12.018 · Cited by 867
“…cis-regulatory landscape entails multiple TF activities, including recruitment of chromatin modifiers, nucleosome remodelers, and histone chaperons (Hu et al., 2011; Ram et al., 2011), eventually resulting in the demarcation of short DNA stretches that contain accessible TF binding sites (TFBS)…”
The SWI/SNF chromatin remodelling complex is required for maintenance of lineage specific enhancers
Alver, B. H., Kim, K. H., Lu, P., Wang, X., Manchester, H. E., Wang, W., Haswell, J. R., Park, P. J., & Roberts, C. W. M. (2017) · Nature Communications · doi:10.1038/ncomms14648 · Cited by 427
DANPOS: Dynamic analysis of nucleosome position and occupancy by sequencingPreprint
Chen, K.-F., Xi, Y., Pan, X.-W., Li, Z.-Y., Kaestner, K., Tyler, J. K., Dent, S., He, X.-W., & Li, W. (2013) · Genome Research · doi:10.1101/gr.142067.112 · Cited by 415
“To demonstrate the broad utility of DANPOS, we analyzed dynamic nucleosomes during differentiation of human hematopoietic stem cells (HSCs) to CD36+ erythrocytes (Hu et al. 2011).”
BackgroundMethodInfluentialHu, G., Cui, K., Northrup, D. L., Liu, C., Wang, C., Tang, Q., Ge, K., Levens, D., Crane‐Robinson, C., & Zhao, K. (2012) · Cell stem cell · doi:10.1016/j.stem.2012.11.003 · Cited by 345
“Consistent with the previous reports (Hu et al., 2011; Tillo et al., 2010), in control ESs, enhancers are associated with increased nucleosome occupancy relative to neighboring regions (Figure 3A, black line), and H2A.”
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Metadata
- 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
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2011-07-27
- Volume
- 21
- Issue
- 10
- Pages
- 1650-1658
- ISSN
- 1088-9051 (ISSN-L)
- 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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