Evidence map›Paper›PMID 34381042›Full record

ArticleNature communications2021

Chd1 protects genome integrity at promoters to sustain hypertranscription in embryonic stem cells.

Aydan Bulut-Karslioglu, Hu Jin, Yun-Kyo Kim, Brandon Cho, Marcela Guzman-Ayala, Andrew J K Williamson, Miroslav Hejna, Maximilian Stötzel, Anthony D Whetton, Jun S Song and 1 more

Open access · goldAbstract read
In one paragraph

Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.

0numbers the graph read from it
0cells of the map it votes in
14citing papers in PubMed
1.1field-weighted citation impact, top 24% 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

14 citing papers in PubMed, 24 citations in OpenAlex.

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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 at 6 institutions in 4 countries.

Aydan Bulut-KarsliogluEli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences and Diabetes Center, University of California, San Francisco, San Francisco, CA, USA. Aydan.karslioglu@molgen.mpg.de.ORCID 0000-0002-0413-9718
Hu JinCarl R. Woese Institute for Genomic Biology, Urbana, IL, USA.ORCID 0000-0002-8657-5686
Yun-Kyo KimLunenfeld-Tanenbaum Research Institute and Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
Brandon ChoLunenfeld-Tanenbaum Research Institute and Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
Marcela Guzman-AyalaEli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences and Diabetes Center, University of California, San Francisco, San Francisco, CA, USA.
Andrew J K WilliamsonStoller Biomarker Discovery Centre, The University of Manchester, Manchester, UK.
Miroslav HejnaCarl R. Woese Institute for Genomic Biology, Urbana, IL, USA.
Maximilian StötzelMax Planck Institute for Molecular Genetics, Berlin, Germany.
Anthony D WhettonStoller Biomarker Discovery Centre, The University of Manchester, Manchester, UK.
Jun S SongCarl R. Woese Institute for Genomic Biology, Urbana, IL, USA.
Miguel Ramalho-SantosEli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences and Diabetes Center, University of California, San Francisco, San Francisco, CA, USA. mrsantos@lunenfeld.ca.ORCID 0000-0003-0177-5556
University of California, San Francisco · USUniversity of Illinois Urbana-Champaign · USUniversity of Manchester · GBUniversity of Toronto · CAHarvard University · USMax Planck Institute for Molecular Genetics · DE

Funding

Translational InformaticsP30CA082103 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Kate Taylor Shumate · 1999 to 2026
$209.7M
Predicting Transcriptional and Epigenetic Networks in Cancer from Sequencing DataR01CA163336 · NCI · UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN · PI Jun S Song · 2012 to 2026
$4.4M
Regulation of developmental potency by the transposon LINE1R01GM123556 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI MCMANUS, MICHAEL T · 2017 to 2020
$1.6M
Role of Chd1 in the transcriptional output and development of pluripotent cellsR01GM113014 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI RAMALHO-SANTOS, MIGUEL · 2015 to 2018
$1.2M
Cancer Research UK C5759/A25254CIHR 420231Department of HealthNCI NIH HHS P30 CA082103NCI NIH HHS R01 CA163336NIGMS NIH HHS R01 GM113014NIGMS NIH HHS R01 GM123556
6 · The paper itself

Abstract

Stem and progenitor cells undergo a global elevation of nascent transcription, or hypertranscription, during key developmental transitions involving rapid cell proliferation. The chromatin remodeler Chd1 mediates hypertranscription in pluripotent cells but its mechanism of action remains poorly understood. Here we report a novel role for Chd1 in protecting genome integrity at promoter regions by preventing DNA double-stranded break (DSB) accumulation in ES cells. Chd1 interacts with several DNA repair factors including Atm, Parp1, Kap1 and Topoisomerase 2β and its absence leads to an accumulation of DSBs at Chd1-bound Pol II-transcribed genes and rDNA. Genes prone to DNA breaks in Chd1 KO ES cells are longer genes with GC-rich promoters, a more labile nucleosomal structure and roles in chromatin regulation, transcription and signaling. These results reveal a vulnerability of hypertranscribing stem cells to accumulation of endogenous DNA breaks, with important implications for developmental and cancer biology.

Indexed as

Promoter Regions, GeneticTranscription, GeneticAnimalsChromatinDNA-Binding ProteinsDNA Breaks, Double-StrandedDNA RepairDNA, RibosomalDNA Topoisomerases, Type IIMiceMouse Embryonic Stem CellsPoly-ADP-Ribose Binding ProteinsSignal TransductionTranscription Initiation SiteChd1 protein, mouseChromatinDNA-Binding ProteinsDNA, RibosomalDNA Topoisomerases, Type IIPoly-ADP-Ribose Binding ProteinsTop2b protein, mouse

Identifiers

PMID34381042
PMCPMC8357957
OpenAlexW3192620725

What OpenQuestion holds

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LicenceCC BY
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.