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Cited by 83Genomics and Chromatin DynamicsPluripotent Stem Cells ResearchEpigenetics and DNA Methylation

STARR-seq identifies active, chromatin-masked, and dormant enhancers in pluripotent mouse embryonic stem cells

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Peng, Tianran, Zhai, Yanan, Atlasi, Yaser, ter Huurne, Menno, Marks, Hendrik, Stunnenberg, Hendrik G., Megchelenbrink, Wout·2020·Genome Biology
DOI 10.1186/s13059-020-02156-3PMC PMC7488044
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Abstract

Background: Enhancers are distal regulators of gene expression that shape cell identity and control cell fate transitions. In mouse embryonic stem cells (mESCs), the pluripotency network is maintained by the function of a complex network of enhancers, that are drastically altered upon differentiation. Genome-wide chromatin accessibility and histone modification assays are commonly used as a proxy for identifying putative enhancers and for describing their activity levels and dynamics. Results: Here, we applied STARR-seq, a genome-wide plasmid-based assay, as a read-out for the enhancer landscape in “ground-state” (2i+LIF; 2iL) and “metastable” (serum+LIF; SL) mESCs. This analysis reveals that active STARR-seq loci show modest overlap with enhancer locations derived from peak calling of ChIP-seq libraries for common enhancer marks. We unveil ZIC3-bound loci with significant STARR-seq activity in SL-ESCs. Knock-out of Zic3 removes STARR-seq activity only in SL-ESCs and increases their propensity to differentiate towards the endodermal fate. STARR-seq also reveals enhancers that are not accessible, masked by a repressive chromatin signature. We describe a class of dormant, p53 bound enhancers that gain H3K27ac under specific conditions, such as after treatment with Nocodazol, or transiently during reprogramming from fibroblasts to pluripotency. Conclusions: In conclusion, loci identified as active by STARR-seq often overlap with those identified by chromatin accessibility and active epigenetic marking, yet a significant fraction is epigenetically repressed or display condition-specific enhancer activity.

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  • SRR2 can drive modest activity in episomal reporter assays and is responsible for the ~10% residual expression of Sox2 that persists after removing the SCR.

    “It can drive modest activity in episomal reporter assays (35, 45) and is responsible for the ~10% residual expression of Sox2 that persists after removing the SCR (Fig. 4F and fig. S26C).”

    From Synergy between regulatory elements can render cohesin dispensable for distal enhancer function (2026) · cites this paper as [45]

    The Methods describe plasmid-based reporter assays, but the passages retrieved for “SRR2” and “Sox2 control region” do not identify SRR2 or report its activity. The cited paper therefore does not verify the modest episomal activity attributed to it. The ~10% residual Sox2 expression is cited to the citing paper’s own figures, not to this source. (LLM, conf=0.72)

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Cited by

Sorted by citations

Authors
Peng, T., Zhai, Y., Atlasi, Y., ter Huurne, M., Marks, H., Stunnenberg, H. G., & Megchelenbrink, W.
Affiliations
Radboud University Nijmegen (NL)
Corresponding author
  • Stunnenberg, Hendrik G.
  • Megchelenbrink, Wout
ORCID
Venue
Genome Biology
Publisher
Springer Science and Business Media LLC
Published
2020-09-10
Volume
21
Issue
1
Pages
243-243
ISSN
  • 1465-6906 (ISSN-L)
  • 1474-760X
DOI
10.1186/s13059-020-02156-3
PMC
PMC7488044
OpenAlex
W3084198752
Cited by
83
References
11
Citations by year
2026: 10 · 2025: 17 · 2024: 13 · 2023: 14 · 2022: 11 · 2021: 16 · 2020: 2
FWCI
4.06
Type
journal article
Language
en
Open access
Licence
Locations
  • Genome biology (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Research Portal (Queen's University Belfast) (submittedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Archivio Istituzionale della Ricerca - Università degli Studi della Campania "Luigi Vanvitelli" (submittedVersion)
  • Radboud Repository (Radboud University) (submittedVersion)
  • Radboud Repository (Radboud University) (submittedVersion, other-oa)
Funders
  • European Research Council (ERC-2013-ADG-339431)
  • Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO-VIDI 864.12.007)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Pluripotent Stem Cells Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
Keywords
enhancers, mouse embryonic stem cells, STARR-seq, enhancer activity, ZIC3, p53, H3K27ac, chromatin accessibility, pluripotency, endoderm differentiation, nocodazole
MeSH terms
Whole Genome Sequencing, Animals, Cell Differentiation, Enhancer Elements, Genetic, Transcription Factors, Homeodomain Proteins, DNA Methylation, Endogenous Retroviruses, Pluripotent Stem Cells, Mice, Embryonic Stem Cells

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