Evidence map›Paper›PMID 39868261›Full record

ArticlebioRxiv : the preprint server for biology2025

Native nucleosome-positioning elements for the investigation of nucleosome repositioning.

Ruo-Wen Chen, Shane D Stoeber, Ilana M Nodelman, Hengye Chen, Lloyd Yang, Gregory D Bowman, Lu Bai, Michael G Poirier

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
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

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

8 authors.

Ruo-Wen ChenOhio State Biochemistry Graduate Program, The Ohio State University, Columbus, OH 43210, USA.
Shane D StoeberDepartment of Biochemistry and Molecular Biology, Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA.
Ilana M NodelmanTC Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA.
Hengye ChenDepartment of Biochemistry and Molecular Biology, Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA.
Lloyd YangDepartment of Physics, The Ohio State University, Columbus, OH 43210, USA.
Gregory D BowmanTC Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA.ORCID 0000-0001-8025-4315
Lu BaiDepartment of Biochemistry and Molecular Biology, Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA.
Michael G PoirierOhio State Biochemistry Graduate Program, The Ohio State University, Columbus, OH 43210, USA.ORCID 0000-0002-1563-5792

Funding

Structural and Functional Characterization of the Chd1 Chromatin RemodelerR01GM084192 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI BOWMAN, GREGORY DEAN · 2008 to 2024
$6.3M
Mechanism of Chromatin Accessibility, 3D Chromosome Organization, and Their Functions in Gene RegulationR35GM139654 · NIGMS · PENNSYLVANIA STATE UNIVERSITY, THE · PI Lu Bai · 2021 to 2026
$3.8M
Mechanisms of chromatin regulation of transcriptionR35GM139564 · NIGMS · OHIO STATE UNIVERSITY · PI POIRIER, MICHAEL GUY · 2021 to 2025
$3.6M
NIGMS NIH HHS R01 GM084192NIGMS NIH HHS R35 GM139564NIGMS NIH HHS R35 GM139654
6 · The paper itself

Abstract

Nucleosome repositioning is essential for establishing nucleosome-depleted regions (NDRs) to initiate transcription. This process has been extensively studied using structural, biochemical, and single-molecule approaches, which require homogenously positioned nucleosomes. This is often achieved using the Widom 601 sequence, a highly efficient nucleosome positioning element (NPE) selected for its unusually strong binding to the H3-H4 histone tetramer. Due to the artificial nature of 601, native NPEs are needed to explore the role of DNA sequence in nucleosome repositioning. Here, we characterize the position distributions and nucleosome formation free energy for a set of yeast native nucleosomes (YNNs) from

Indexed as

ATP-dependent chromatin remodelingchromatin biologynucleosome dynamicsnucleosome positioningtranscription factors

Identifiers

PMID39868261
PMCPMC11760725

What OpenQuestion holds

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LicenceCC BY-NC-ND
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Registered trials

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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.