Cited by 254Genomics and Chromatin DynamicsChromatin Remodeling and CancerNuclear Structure and Function

A Pliable Mediator Acts as a Functional Rather Than an Architectural Bridge between Promoters and Enhancers

Open access
El Khattabi, Laila, Zhao, Haiyan, Kalchschmidt, Jens, Young, Natalie, Jung, Seolkyoung, Van Blerkom, Peter, Kieffer-Kwon, Philippe, Kieffer-Kwon, Kyong-Rim +16 more·2019·Cell

Abstract

While Mediator plays a key role in eukaryotic transcription, little is known about its mechanism of action. This study combines CRISPR-Cas9 genetic screens, degron assays, Hi-C, and cryoelectron microscopy (cryo-EM) to dissect the function and structure of mammalian Mediator (mMED). Deletion analyses in B, T, and embryonic stem cells (ESC) identified a core of essential subunits required for Pol II recruitment genome-wide. Conversely, loss of non-essential subunits mostly affects promoters linked to multiple enhancers. Contrary to current models, however, mMED and Pol II are dispensable to physically tether regulatory DNA, a topological activity requiring architectural proteins. Cryo-EM analysis revealed a conserved core, with non-essential subunits increasing structural complexity of the tail module, a primary transcription factor target. Changes in tail structure markedly increase Pol II and kinase module interactions. We propose that Mediator's structural pliability enables it to integrate and transmit regulatory signals and act as a functional, rather than an architectural bridge, between promoters and enhancers.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1016/j.cell.2019.07.011

Cites

100 of 100 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Promoter Capture Hi-C-based studies did not observe a significant change in enhancer-promoter contacts upon RNAP inhibition, including in cells rapidly depleted of cohesin or CTCF.

    “However, Promoter Capture Hi-C-based studies did not observe a significant change in enhancer–promoter contacts upon RNAP inhibition, including in cells rapidly depleted of cohesin or CTCF [349, 380].”

    From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [380]

    In Results, ‘The role of Mediator in promoter-enhancer interactions’ (page unavailable), promoter capture Hi-C showed little or no change in enhancer–promoter contacts after PolII and Mediator depletion, and no further change when they were depleted alongside cohesin. The paper reports rapid cohesin depletion, but not rapid CTCF depletion; loss of CTCF-dependent loops after cohesin depletion is not the same experiment. (LLM, conf=0.87)

    Experimental — accuracy not yet measured
  • Rapid removal of chromatin-bound Mediator and RNAP does not significantly affect chromosomal architecture, including enhancer-promoter interactions, in spite of triggering widespread transcriptional changes and cell cycle arrest.

    “However, it was shown recently that rapid removal of chromatin-bound Mediator and RNAP does not significantly affect chromosomal architecture, including enhancer–promoter interactions, in spite of triggering widespread transcriptional changes and cell cycle arrest [380].”

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

2 of the 102 references couldn’t be matched to a known paper.

Cited by

Sorted by citations

Authors
El Khattabi, L., Zhao, H., Kalchschmidt, J., Young, N., Jung, S., Van Blerkom, P., Kieffer-Kwon, P., Kieffer-Kwon, K.-R., Park, S., Wang, X., Krebs, J., Tripathi, S., Sakabe, N., Sobreira, D. R., Huang, S.-C., Rao, S. S. P., Pruett, N., Chauss, D., Sadler, E., Lopez, A., Nóbrega, M. A., Aiden, E. L., Asturias, F. J., & Casellas, R.
Affiliations
  • University of Colorado Anschutz (US)
  • National Institute of Arthritis and Musculoskeletal and Skin Diseases (US)
  • University of Chicago (US)
  • Baylor College of Medicine (US)
  • National Institutes of Health (US)
Corresponding author
  • Asturias, Francisco J.
  • Casellas, Rafael
Venue
Cell
Publisher
Elsevier BV
Published
2019-08
Volume
178
Issue
5
Pages
1145-1158.e20
ISSN
0092-8674 (ISSN-L)
OpenAlex
W2967977322
Cited by
244
References
102
Citations by year
2026: 26 · 2025: 22 · 2024: 38 · 2023: 35 · 2022: 44 · 2021: 51 · 2020: 25 · 2019: 3
FWCI
10.17
Type
journal article
Language
en
Open access
Locations
  • Cell (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
Funders
National Institutes of Health
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
Keywords
Mediator complex, RNA polymerase II recruitment, enhancers, transcriptional regulation, Hi-C, cryo-electron microscopy
MeSH terms
Mouse Embryonic Stem Cells, Gene Editing, Cohesins, Animals, Cells, Cultured, Chromosomal Proteins, Non-Histone, Enhancer Elements, Genetic, Humans, Male, Mice, Inbred C57BL, Promoter Regions, Genetic, RNA Polymerase II, Saccharomyces cerevisiae, CD4-Positive T-Lymphocytes, Cell Cycle Proteins, Cryoelectron Microscopy, Protein Structure, Quaternary, Saccharomyces cerevisiae Proteins, Mice, Mediator Complex, CRISPR-Cas Systems

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review