Opposing chromatin remodelers control transcription initiation frequency and start site selection
Open accessPublished version of a preprint
Abstract
Precise nucleosome organization at eukaryotic promoters is thought to be generated by multiple chromatin remodeler (CR) enzymes and to affect transcription initiation. Using an integrated analysis of chromatin remodeler binding and nucleosome occupancy following rapid remodeler depletion, we investigated the interplay between these enzymes and their impact on transcription in yeast. We show that many promoters are affected by multiple CRs that operate in concert or in opposition to position the key transcription start site (TSS)-associated +1 nucleosome. We also show that nucleosome movement after CR inactivation usually results from the activity of another CR and that in the absence of any remodeling activity, +1 nucleosomes largely maintain their positions. Finally, we present functional assays suggesting that +1 nucleosome positioning often reflects a trade-off between maximizing RNA polymerase recruitment and minimizing transcription initiation at incorrect sites. Our results provide a detailed picture of fundamental mechanisms linking promoter nucleosome architecture to transcription initiation.
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.
Integrity signals
Registry
Cites
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.
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?
SWI/SNF localises to nucleosome-depleted regions (NDRs) in promoters and regulates the position of the transcription start site (TSS)-associated (or '+1') nucleosome critical for transcription initiation.
“SWI/SNF localises to nucleosome-depleted regions (NDRs) in promoters and regulates the position of the transcription start site (TSS)-associated (or ‘+1’) nucleosome critical for transcription initiation20.”
From SWI/SNF and the histone chaperone Rtt106 drive expression of the Pleiotropic Drug Resistance network genes (2022) · cites this paper as [20]
Histone chaperones and ATP-dependent chromatin-remodelling complexes are important for gene regulation because they regulate nucleosome dynamics at promoters, restricting or increasing promoter accessibility for recruitment of transcription factors and RNA polymerase II (Pol II).
“Histone chaperones and ATP-dependent chromatin-remodelling complexes are accordingly important for gene regulation given they regulate nucleosome dynamics at promoters, restricting or increasing promoter accessibility for recruitment of transcription factors and RNA polymerase II (Pol II)19–23.”
From SWI/SNF and the histone chaperone Rtt106 drive expression of the Pleiotropic Drug Resistance network genes (2022) · cites this paper as [20]
SWI/SNF modulates nucleosome position to regulate the expression of a subset of genes including stress-responsive genes.
“SWI/SNF modulates nucleosome position to regulate the expression of a subset of genes including stress-responsive genes20,37–40.”
From SWI/SNF and the histone chaperone Rtt106 drive expression of the Pleiotropic Drug Resistance network genes (2022) · cites this paper as [20]
In the absence of Snf2, the +1 nucleosome is shifted towards the TATA-box at the PDR5 promoter.
“We utilised the published datasets of nucleosome occupancy20 and TSS49 and observed that in the absence of Snf2 the +1 nucleosome is shifted towards the TATA-box at the PDR5 promoter (Fig. 6a, red rectangle).”
From SWI/SNF and the histone chaperone Rtt106 drive expression of the Pleiotropic Drug Resistance network genes (2022) · cites this paper as [20]
SWI/SNF regulates the expression of PDR5 by shifting the TSS-associated +1 nucleosome.
“Our results and a published report20 suggest that SWI/SNF regulates the expression of PDR5 by shifting the TSS-associated +1 nucleosome, which is critical for transcription initiation.”
From SWI/SNF and the histone chaperone Rtt106 drive expression of the Pleiotropic Drug Resistance network genes (2022) · cites this paper as [20]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
The citation lists haven’t been fetched yet
References 79 · Cited by 126
- Authors
- Kubik, S., Bruzzone, M. J., Challal, D., Dreos, R., Mattarocci, S., Bucher, P., Libri, D., & Shore, D.
- Affiliations
- Institute of Genetics and Genomics in Geneva (CH)
- Centre National de la Recherche Scientifique (FR)
- École Polytechnique Fédérale de Lausanne (CH)
- Corresponding author
- Shore, David
- ORCID
- Venue
- Nature Structural & Molecular Biology
- Published
- 2019-08
- Volume
- 26
- Issue
- 8
- Pages
- 744-754
- ISSN
- 1545-9985 (ISSN-L)
- 1545-9993
- OpenAlex
- W2966463765
- Cited by
- 126
- References
- 79
- Citations by year
- 2026: 8 · 2025: 13 · 2024: 22 · 2023: 25 · 2022: 15 · 2021: 30 · 2020: 8 · 2019: 5
- FWCI
- 4.77
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- Locations
- Nature Structural & Molecular Biology (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, other-oa)
- PubMed (publishedVersion)
- Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion, cc-by-nc-nd)
- Funders
- National Science Foundation
- Agence Nationale de la Recherche (ANR-11-LABX-0071, ANR-16-CE12-0022, ANR-11-IDEX-0005)
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (170153)
- Université de Genève
- Canton de Genève
- Institute of Genetics and Genomics of Geneva
- 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
- chromatin remodelers, transcription initiation, transcription start site selection, nucleosome positioning, promoter architecture, Saccharomyces cerevisiae, RNA polymerase recruitment, nucleosome occupancy, chromatin remodeling
- MeSH terms
- DNA, Fungal, Micrococcal Nuclease, Nucleosomes, Saccharomyces cerevisiae, DNA, Intergenic, Transcription Initiation Site, Saccharomyces cerevisiae Proteins, Chromatin Assembly and Disassembly, Macromolecular Substances, Transcription Initiation, Genetic
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
