UMMS Affiliation
Department of Molecular, Cell and Cancer Biology; Department of Biochemistry and Molecular Pharmacology; Program in Molecular Medicine
Publication Date
2015-02-15
Document Type
Article
Subjects
Animals; Chromatin Assembly and Disassembly; DNA Helicases; DNA-Binding Proteins; Embryonic Stem Cells; Gene Expression Regulation, Developmental; Mice; Nuclear Proteins; Nucleosomes; RNA, Untranslated; Transcription Factors
Disciplines
Cell Biology | Genomics | Molecular Biology | Molecular Genetics
Abstract
Approximately 75% of the human genome is transcribed, the majority of which does not encode protein. However, many noncoding RNAs (ncRNAs) are rapidly degraded after transcription, and relatively few have established functions, questioning the significance of this observation. Here we show that esBAF, a SWI/SNF family nucleosome remodeling factor, suppresses transcription of ncRNAs from approximately 57,000 nucleosome-depleted regions (NDRs) throughout the genome of mouse embryonic stem cells (ESCs). We show that esBAF functions to both keep NDRs nucleosome-free and promote elevated nucleosome occupancy adjacent to NDRs. Reduction of adjacent nucleosome occupancy upon esBAF depletion is strongly correlated with ncRNA expression, suggesting that flanking nucleosomes form a barrier to pervasive transcription. Upon forcing nucleosome occupancy near two NDRs using a nucleosome-positioning sequence, we found that esBAF is no longer required to silence transcription. Therefore, esBAF's function to enforce nucleosome occupancy adjacent to NDRs, and not its function to maintain NDRs in a nucleosome-free state, is necessary for silencing transcription over ncDNA. Finally, we show that the ability of a strongly positioned nucleosome to repress ncRNA depends on its translational positioning. These data reveal a novel role for esBAF in suppressing pervasive transcription from open chromatin regions in ESCs.
Keywords
chromatin remodeling, esBAF, ncRNA, nucleosome occupancy, transcription
Rights and Permissions
This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genesdev.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
DOI of Published Version
10.1101/gad.253534.114
Source
Genes Dev. 2015 Feb 15;29(4):362-78. doi: 10.1101/gad.253534.114. Link to article on publisher's site
Journal/Book/Conference Title
Genes and development
Related Resources
PubMed ID
25691467
Repository Citation
Hainer, Sarah J.; Gu, Weifeng; Carone, Benjamin R.; Landry, Benjamin D.; Rando, Oliver J.; Mello, Craig C.; and Fazzio, Thomas G., "Suppression of pervasive noncoding transcription in embryonic stem cells by esBAF" (2015). Molecular, Cell and Cancer Biology Publications. 14.
https://escholarship.umassmed.edu/mccb_pubs/14
Creative Commons License
This work is licensed under a Creative Commons Attribution-Noncommercial 4.0 License
Included in
Cell Biology Commons, Genomics Commons, Molecular Biology Commons, Molecular Genetics Commons