Evidence map›Paper›PMID 23141536›Full record

ArticleCell2012

Nucleosomal elements that control the topography of the barrier to transcription.

Lacramioara Bintu, Toyotaka Ishibashi, Manchuta Dangkulwanich, Yueh-Yi Wu, Lucyna Lubkowska, Mikhail Kashlev, Carlos Bustamante

Open access · bronzeAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 106 papers.

0numbers the graph read from it
0cells of the map it votes in
106citing papers in PubMed
7.2field-weighted citation impact, top 2% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

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.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

106 citing papers in PubMed, 193 citations in OpenAlex.

  1. Article
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  8. Article
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  10. Article
  11. Article
  12. A nucleosome switch primes Hepatitis B Virus infection.bioRxiv : the preprint server for biology · 2024
    Article
  13. Review
  14. Review
  15. Frontiers in epigenetics and epigenomics · 2024
    Article
  16. Article
  17. Review
  18. Article
  19. Review
  20. Article

46 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

7 authors at 3 institutions in 1 country.

Lacramioara BintuJason L. Choy Laboratory of Single-Molecule Biophysics and Department of Physics, University of California, Berkeley, Berkeley, CA 94720, USA.
Toyotaka IshibashiQB3 Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
Manchuta DangkulwanichDepartment of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA.
Yueh-Yi WuDepartment of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
Lucyna LubkowskaNCI Center for Cancer Research, Frederick, MD 21702, USA.
Mikhail KashlevNCI Center for Cancer Research, Frederick, MD 21702, USA.
Carlos BustamanteJason L. Choy Laboratory of Single-Molecule Biophysics and Department of Physics, University of California, Berkeley, Berkeley, CA 94720, USA; QB3 Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA. Electronic address: carlos@alice.berkeley.edu.
University of California, Berkeley · USCenter for Cancer Research · USHoward Hughes Medical Institute · US

Funding

Mechanisms of transcription pausing and fidelity in prokaryotes and eukaryotesZIABC010795 · NCI · DIVISION OF BASIC SCIENCES - NCI · PI KASHLEV, MIKHAIL · 2009 to 2025
$18.1M
THE PHYSICAL CHEMISTRY OF NUCLEIC ACIDSR01GM032543 · NIGMS · UNIVERSITY OF OREGON · PI CARLOS Jose BUSTAMANTE · 1985 to 2026
$6.4M
Howard Hughes Medical InstituteNIGMS NIH HHS R01 GM032543NIGMS NIH HHS R01-GM032543-31
6 · The paper itself

Abstract

The nucleosome represents a mechanical barrier to transcription that operates as a general regulator of gene expression. We investigate how each nucleosomal component-the histone tails, the specific histone-DNA contacts, and the DNA sequence-contributes to the strength of the barrier. Removal of the tails favors progression of RNA polymerase II into the entry region of the nucleosome by locally increasing the wrapping-unwrapping rates of the DNA around histones. In contrast, point mutations that affect histone-DNA contacts at the dyad abolish the barrier to transcription in the central region by decreasing the local wrapping rate. Moreover, we show that the nucleosome amplifies sequence-dependent transcriptional pausing, an effect mediated through the structure of the nascent RNA. Each of these nucleosomal elements controls transcription elongation by affecting distinctly the density and duration of polymerase pauses, thus providing multiple and alternative mechanisms for control of gene expression by chromatin remodeling and transcription factors.

Indexed as

Gene Expression RegulationNucleosomesTranscription, GeneticDNAHistonesRNA Polymerase IIYeastsDNAHistonesNucleosomesRNA Polymerase II

Identifiers

PMID23141536
PMCPMC3508686
OpenAlexW2006855885

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

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.