ArticlePloS one2014
CRISPR reveals a distal super-enhancer required for Sox2 expression in mouse embryonic stem cells.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 129 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
129 citing papers in PubMed, 216 citations in OpenAlex.
- Single-cell 3D genome imaging shows super-enhancer hubs are rare, nonspecific, and neither necessary nor sufficient for transcriptional bursting.Cell genomics · 2026Article
- TheiScience · 2026Article
- LAWS-HiC: A Locally Adaptive Weighting and Screening (LAWS) Approach to Improve Detection of Long-Range Chromatin Interactions from Hi-C Data.Methods and protocols · 2026Article
- Mechanisms and functional implications of long-range enhancer-dependent gene regulation.Nature genetics · 2026Review
- Temporal dynamics of intragenic enhancer RNAs regulate Lin28a expression in response to external stimuli in embryonic stem cells.Nucleic acids research · 2026Article
- Promoter strength and position govern promoter competition through transcript-dependent insulation.Nature genetics · 2026Article
- Synthetic Regulatory Genomics.Annual review of genomics and human genetics · 2026Review
- Cohesin-mediated loop extrusion and enhancer-associated factors additively contribute toGenes & development · 2026Article
- Understanding super enhancers in genome architecture and their roles in livestock breeding.BMC genomics · 2026Review
- Article
- 3D-super-enhancers are condensate-associated cis-regulatory communities.Nucleic acids research · 2026Article
- Synergy between regulatory elements can render cohesin dispensable for distal enhancer function.Science (New York, N.Y.) · 2026Article
- A developmentally regulated long-range enhancer-promoter contact mediates human neural development.bioRxiv : the preprint server for biology · 2026Article
- NIPBL-mediated 3D genome folding translates enhancer priming into gene activation and safeguards lineage fidelity during embryonic transitions.bioRxiv : the preprint server for biology · 2025Article
- Iterative improvement of deep learning models using synthetic regulatory genomics.Genome research · 2025Article
- Functional maps of a genomic locus reveal confinement of an enhancer by its target gene.Science (New York, N.Y.) · 2025Article
- Deciphering the role of cis-regulatory elements and TFAP2C in the activation of zygotic Sox2 expression in mouse preimplantation embryos.Development (Cambridge, England) · 2025Article
- Klf5-adjacent super-enhancer functions as a 3D genome structure-dependent transcriptional driver to safeguard ESC identity.Nature communications · 2025Article
- CASCADES, a novel SOX2 super-enhancer-associated long noncoding RNA, regulates cancer stem cell specification and differentiation in glioblastoma.Molecular oncology · 2025Article
- geomeTriD: a Bioconductor package for interactive and integrative visualization of 3D structural model with multi-omics data.Bioinformatics advances · 2025Article
69 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
Abstract
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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.