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CRISPR Reveals a Distal Super-Enhancer Required for Sox2 Expression in Mouse Embryonic Stem Cells

The pluripotency of embryonic stem cells (ESCs) is maintained by a small group of master transcription factors including Oct4, Sox2 and Nanog. These core factors form a regulatory circuit controlling the transcription of a number of pluripotency factors including themselves. Although previous studie...

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Autores principales: Li, Yan, Rivera, Chloe M., Ishii, Haruhiko, Jin, Fulai, Selvaraj, Siddarth, Lee, Ah Young, Dixon, Jesse R., Ren, Bing
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4259346/
https://www.ncbi.nlm.nih.gov/pubmed/25486255
http://dx.doi.org/10.1371/journal.pone.0114485
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author Li, Yan
Rivera, Chloe M.
Ishii, Haruhiko
Jin, Fulai
Selvaraj, Siddarth
Lee, Ah Young
Dixon, Jesse R.
Ren, Bing
author_facet Li, Yan
Rivera, Chloe M.
Ishii, Haruhiko
Jin, Fulai
Selvaraj, Siddarth
Lee, Ah Young
Dixon, Jesse R.
Ren, Bing
author_sort Li, Yan
collection PubMed
description The pluripotency of embryonic stem cells (ESCs) is maintained by a small group of master transcription factors including Oct4, Sox2 and Nanog. These core factors form a regulatory circuit controlling the transcription of a number of pluripotency factors including themselves. Although previous studies have identified transcriptional regulators of this core network, the cis-regulatory DNA sequences required for the transcription of these key pluripotency factors remain to be defined. We analyzed epigenomic data within the 1.5 Mb gene-desert regions around the Sox2 gene and identified a 13kb-long super-enhancer (SE) located 100kb downstream of Sox2 in mouse ESCs. This SE is occupied by Oct4, Sox2, Nanog, and the mediator complex, and physically interacts with the Sox2 locus via DNA looping. Using a simple and highly efficient double-CRISPR genome editing strategy we deleted the entire 13-kb SE and characterized transcriptional defects in the resulting monoallelic and biallelic deletion clones with RNA-seq. We showed that the SE is responsible for over 90% of Sox2 expression, and Sox2 is the only target gene along the chromosome. Our results support the functional significance of a SE in maintaining the pluripotency transcription program in mouse ESCs.
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spelling pubmed-42593462014-12-15 CRISPR Reveals a Distal Super-Enhancer Required for Sox2 Expression in Mouse Embryonic Stem Cells Li, Yan Rivera, Chloe M. Ishii, Haruhiko Jin, Fulai Selvaraj, Siddarth Lee, Ah Young Dixon, Jesse R. Ren, Bing PLoS One Research Article The pluripotency of embryonic stem cells (ESCs) is maintained by a small group of master transcription factors including Oct4, Sox2 and Nanog. These core factors form a regulatory circuit controlling the transcription of a number of pluripotency factors including themselves. Although previous studies have identified transcriptional regulators of this core network, the cis-regulatory DNA sequences required for the transcription of these key pluripotency factors remain to be defined. We analyzed epigenomic data within the 1.5 Mb gene-desert regions around the Sox2 gene and identified a 13kb-long super-enhancer (SE) located 100kb downstream of Sox2 in mouse ESCs. This SE is occupied by Oct4, Sox2, Nanog, and the mediator complex, and physically interacts with the Sox2 locus via DNA looping. Using a simple and highly efficient double-CRISPR genome editing strategy we deleted the entire 13-kb SE and characterized transcriptional defects in the resulting monoallelic and biallelic deletion clones with RNA-seq. We showed that the SE is responsible for over 90% of Sox2 expression, and Sox2 is the only target gene along the chromosome. Our results support the functional significance of a SE in maintaining the pluripotency transcription program in mouse ESCs. Public Library of Science 2014-12-08 /pmc/articles/PMC4259346/ /pubmed/25486255 http://dx.doi.org/10.1371/journal.pone.0114485 Text en © 2014 Li et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Li, Yan
Rivera, Chloe M.
Ishii, Haruhiko
Jin, Fulai
Selvaraj, Siddarth
Lee, Ah Young
Dixon, Jesse R.
Ren, Bing
CRISPR Reveals a Distal Super-Enhancer Required for Sox2 Expression in Mouse Embryonic Stem Cells
title CRISPR Reveals a Distal Super-Enhancer Required for Sox2 Expression in Mouse Embryonic Stem Cells
title_full CRISPR Reveals a Distal Super-Enhancer Required for Sox2 Expression in Mouse Embryonic Stem Cells
title_fullStr CRISPR Reveals a Distal Super-Enhancer Required for Sox2 Expression in Mouse Embryonic Stem Cells
title_full_unstemmed CRISPR Reveals a Distal Super-Enhancer Required for Sox2 Expression in Mouse Embryonic Stem Cells
title_short CRISPR Reveals a Distal Super-Enhancer Required for Sox2 Expression in Mouse Embryonic Stem Cells
title_sort crispr reveals a distal super-enhancer required for sox2 expression in mouse embryonic stem cells
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4259346/
https://www.ncbi.nlm.nih.gov/pubmed/25486255
http://dx.doi.org/10.1371/journal.pone.0114485
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