CRISPR Reveals a Distal Super-Enhancer Required for Sox2 Expression in Mouse Embryonic Stem Cells
Open accessAbstract
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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The SCR is a strong enhancer that accounts for most of the transcriptional activity of endogenous Sox2.
“The SCR is a strong enhancer that accounts for most of the transcriptional activity of endogenous Sox229,30.”
From Nonlinear control of transcription through enhancer–promoter interactions (2022) · cites this paper as [30]
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- Authors
- Li, Y., Rivera, C. M., Ishii, H., Jin, F., Selvaraj, S., Lee, A. Y., Dixon, J. R., & Ren, B.
- Affiliations
- Ludwig Cancer Research (US)
- University of California San Diego (US)
- Corresponding author
- Ren, Bing
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2014-12-08
- Volume
- 9
- Issue
- 12
- Pages
- e114485
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC4259346
- OpenAlex
- W2050090238
- Cited by
- 212
- References
- 6
- Citations by year
- 2026: 13 · 2025: 11 · 2024: 18 · 2023: 22 · 2022: 19 · 2021: 16 · 2020: 18 · 2019: 14 · 2018: 23 · 2017: 22 · 2016: 16 · 2015: 19
- FWCI
- 7.80
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS ONE (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- Funders
- Ludwig Institute for Cancer Research (U54 HG006997)
- National Institutes of Health
- University of California, San Diego (T32 GM008666, GM008666)
- National Human Genome Research Institute (U54HG006997)
- National Institute of General Medical Sciences (GM008666, T32GM008666, T32GM007198)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Pluripotent Stem Cells Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Keywords
- super-enhancers, SOX2, mouse embryonic stem cells, pluripotency, Oct4, Nanog, Mediator complex, DNA looping, cis-regulatory elements, gene deserts, enhancer deletion, transcriptional regulation
- MeSH terms
- Animals, Cell Line, Chromosome Mapping, Enhancer Elements, Genetic, Gene Expression Regulation, Transcription, Genetic, Gene Deletion, Computational Biology, Epigenesis, Genetic, Mice, Embryonic Stem Cells, SOXB1 Transcription Factors, Clustered Regularly Interspaced Short Palindromic Repeats
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