Evidence map›Paper›PMID 41377493›Full record

ArticlebioRxiv : the preprint server for biology2025

Fragile nucleosomes are essential for RNA Polymerase II to transcribe in eukaryotes.

Lingbo Li, Samuel Hunter, Sonia Leach, Yonghua Zhuang, Haolin Liu, Junfeng Gao, Qianqian Zhang, Timothy J Stasevich, Hiroshi Kimura, Robin Dowell and 1 more

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

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

11 authors.

Lingbo LiDepartment of Immunology and Genomic Medicine, National Jewish Health, Denver, USA.
Samuel HunterDepartment of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, USA.
Sonia LeachDepartment of Immunology and Genomic Medicine, National Jewish Health, Denver, USA.
Yonghua ZhuangBiostatistics Shared Resource, University of Colorado Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, USA.
Haolin LiuDepartment of Immunology and Genomic Medicine, National Jewish Health, Denver, USA.
Junfeng GaoDepartment of Immunology and Genomic Medicine, National Jewish Health, Denver, USA.
Qianqian ZhangSchool of Medicine, Zhejiang University, Hangzhou, China.
Timothy J StasevichDepartment of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, USA.ORCID 0000-0002-0151-6274
Hiroshi KimuraCell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8501, Japan.ORCID 0000-0003-0854-083X
Robin DowellDepartment of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, USA.ORCID 0000-0001-7665-9985
Gongyi ZhangDepartment of Immunology and Genomic Medicine, National Jewish Health, Denver, USA.ORCID 0000-0003-3010-3804

Funding

Histone Arginine Demethylation through CleavageR01GM135421 · NIGMS · NATIONAL JEWISH HEALTH · PI ZHANG, GONGYI · 2020 to 2023
$1.7M
NIGMS NIH HHS R01 GM135421
6 · The paper itself

Abstract

Nucleosomes are barriers to RNA Polymerase II (Pol II) transcribing along gene bodies in eukaryotes. We found that a fragile "tailless nucleosome" could be generated to resolve the Pol II pausing caused by the +1 nucleosome in metazoans. We hypothesized that "pan-acetylated nucleosomes" along gene bodies are fragile and are generated to resolve the resistance of nucleosomes to the elongation of Pol II. To confirm this hypothesis, we systematically analyzed pan-acetylation and pan-phosphorylation of the entire human genome in HEK293T cells. Herein, we show that both pan-acetylation and pan-phosphorylation of histones in nucleosomes along gene bodies are coupled with the activities of Pol II. Our results show that there are four major types of fragile nucleosomes required for Pol II to transcribe along gene bodies: nucleosomes without tails, nucleosomes with dominant acetylation, nucleosomes with dominant phosphorylation, and nucleosomes with both acetylation and phosphorylation.

Indexed as

both acetylated and phosphorylated nucleosomeFragile nucleosomePan-acetylated nucleosomePan-phosphorylated nucleosomePol IITail-cleaved nucleosomeTailless nucleosome

Identifiers

PMID41377493
PMCPMC12687975

What OpenQuestion holds

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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.