Evidence map›Paper›PMID 38585764›Full record

ArticlebioRxiv : the preprint server for biology2024

Multifaceted roles of cohesin in regulating transcriptional loops.

Minji Kim, Ping Wang, Patricia A Clow, I Eli Chien, Xiaotao Wang, Jianhao Peng, Haoxi Chai, Xiyuan Liu, Byoungkoo Lee, Chew Yee Ngan and 7 more

Open access · greenAbstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2024. 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, 5 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

17 authors at 9 institutions in 2 countries.

Minji KimThe Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.ORCID 0000-0002-7282-8224
Ping WangThe Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.
Patricia A ClowThe Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.
I Eli ChienDepartment of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61820, USA.ORCID 0000-0002-7606-7768
Xiaotao WangObstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China.
Jianhao PengDepartment of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61820, USA.
Haoxi ChaiThe Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.
Xiyuan LiuThe Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.
Byoungkoo LeeThe Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.
Chew Yee NganThe Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.
Feng YueDepartment of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Evanston, IL, 60201, USA.
Olgica MilenkovicDepartment of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61820, USA.
Jeffrey H ChuangThe Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.ORCID 0000-0002-3298-2358
Chia-Lin WeiThe Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.
Rafael CasellasHematopoietic Biology and Malignancy, MD Anderson Cancer Center, Houston, TX, 77054, USA.
Albert W ChengSchool of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, 85281, USA.
Yijun RuanLife Sciences Institute, Zhejiang University, Hangzhou, Zhejiang Province, 310058, P.R. China.ORCID 0000-0001-5881-569X
Jackson Laboratory · USNorthwestern University · USUniversity of Illinois Urbana-Champaign · USFudan University · CNGeorgia Institute of Technology · USThe University of Texas MD Anderson Cancer Center · USUniversity of Michigan · USUniversity of Washington · USWenzhou Medical University · CN

Funding

Comprehensive Mapping of Long-Range Chromatin Interactions in Humanand Mouse GenomesUM1HG009409 · NHGRI · JACKSON LABORATORY · PI LEE, CHARLES · 2017 to 2021
$9.8M
Modular Platform for Combinatorial Epigenome ManipulationR01HG009900 · NHGRI · JACKSON LABORATORY · PI ADAMS, MARK D · 2018 to 2022
$3.7M
Nucleome Positioning System for Spatiotemporal Genome Organization and RegulationU54DK107967 · NIDDK · JACKSON LABORATORY · PI WEI, CHIA-LIN · 2015 to 2019
$3.6M
Single Cell and Single Molecule Technologies for Multiplex Chromatin Interaction AnalysisR01HG011253 · NHGRI · UNIVERSITY OF WASHINGTON · PI WEI, CHIA-LIN · 2020 to 2023
$3.3M
Development of Single Molecule Chromatin Interaction Assays (smChIA) in Single NucleiR01GM127531 · NIGMS · JACKSON LABORATORY · PI WEI, CHIA-LIN · 2019 to 2022
$2.3M
Roles of allele-specific chromatin interactions in transcription regulation during developmentK99HG011542 · NHGRI · JACKSON LABORATORY · PI KIM, MINJI · 2021 to 2022
$259k
NHGRI NIH HHS K99 HG011542NHGRI NIH HHS R01 HG009900NHGRI NIH HHS R01 HG011253NHGRI NIH HHS UM1 HG009409NIDDK NIH HHS U54 DK107967NIGMS NIH HHS R01 GM127531
6 · The paper itself

Abstract

Cohesin is required for chromatin loop formation. However, its precise role in regulating gene transcription remains largely unknown. We investigated the relationship between cohesin and RNA Polymerase II (RNAPII) using single-molecule mapping and live-cell imaging methods in human cells. Cohesin-mediated transcriptional loops were highly correlated with those of RNAPII and followed the direction of gene transcription. Depleting RAD21, a subunit of cohesin, resulted in the loss of long-range (>100 kb) loops between distal (super-)enhancers and promoters of cell-type-specific genes. By contrast, the short-range (<50 kb) loops were insensitive to RAD21 depletion and connected genes that are mostly housekeeping. This result explains why only a small fraction of genes are affected by the loss of long-range chromatin interactions due to cohesin depletion. Remarkably, RAD21 depletion appeared to up-regulate genes located in early initiation zones (EIZ) of DNA replication, and the EIZ signals were amplified drastically without RAD21. Our results revealed new mechanistic insights of cohesin's multifaceted roles in establishing transcriptional loops, preserving long-range chromatin interactions for cell-specific genes, and maintaining timely order of DNA replication.

Indexed as

3D genome mappingauxin-inducible degron (AID)chromatin loop formationCohesinlive-cell imagingmultiplex chromatin interactionRNAPIIsuper-enhancerstranscription regulation

Identifiers

PMID38585764
PMCPMC10996690
OpenAlexW4393215628

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.