Evidence map›Paper›PMID 32213323›Full record

ArticleMolecular cell2020

Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding.

Tsung-Han S Hsieh, Claudia Cattoglio, Elena Slobodyanyuk, Anders S Hansen, Oliver J Rando, Robert Tjian, Xavier Darzacq

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

Article in Molecular cell, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 411 papers.

0numbers the graph read from it
0cells of the map it votes in
411citing papers in PubMed
31.2field-weighted citation impact, top 1% 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

411 citing papers in PubMed, 659 citations in OpenAlex.

  1. Revealing High-Resolution Open Chromatin-Associated Interactions by NicE-C.Methods in molecular biology (Clifton, N.J.) · 2027
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  6. Regulation of immune signal integration and memory by inflammation-induced chromosome conformation.Proceedings of the National Academy of Sciences of the United States of America · 2026
    Article
  7. Article
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  9. Transcription and Three-Dimensional Genome Organization: Cause, Consequence, or Coordination?BioEssays : news and reviews in molecular, cellular and developmental biology · 2026
    Review
  10. Article
  11. Article
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  13. Article
  14. Review
  15. CAD-C: An engineered nuclease enables repair-freebioRxiv : the preprint server for biology · 2026
    Article
  16. Article
  17. Review
  18. Genome-wide absolute quantification of chromatin looping.Nature structural & molecular biology · 2026
    Article
  19. Article
  20. Article

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

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

7 authors at 3 institutions in 1 country.

Tsung-Han S HsiehDepartment of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, CA 94720, USA; CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA 94720, USA; Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
Claudia CattoglioDepartment of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, CA 94720, USA; CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
Elena SlobodyanyukDepartment of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, CA 94720, USA; CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
Anders S HansenDepartment of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, CA 94720, USA; CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
Oliver J RandoDepartment of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
Robert TjianDepartment of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, CA 94720, USA; CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA. Electronic address: jmlim@berkeley.edu.
Xavier DarzacqDepartment of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, CA 94720, USA; CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA 94720, USA; Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA. Electronic address: darzacq@berkeley.edu.
Howard Hughes Medical Institute · USUniversity of California, Berkeley · USUniversity of Massachusetts Chan Medical School · US

Funding

Center for 3D Structure and Physics of the GenomeU54DK107980 · NIDDK · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI DEKKER, JOB, MIRNY, LEONID A · 2015 to 2019
$14.9M
Tools For Imaging the Functional Genome in Living Cells and TissuesU01EB021236 · NIBIB · ALBERT EINSTEIN COLLEGE OF MEDICINE, INC · PI DARZACQ, XAVIER, SINGER, ROBERT H · 2015 to 2017
$2.5M
Molecular mechanisms regulating chromatin looping in time and spaceR00GM130896 · NIGMS · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI HANSEN, ANDERS SEJR · 2020 to 2022
$747k
Genome Sequencer FLXS10RR029668 · NCRR · UNIVERSITY OF CALIFORNIA BERKELEY · PI NGAI, JOHN J. · 2010 to 2010
$623k
Illumina Sequencer to Facilitate Functional Genomics at BerkeleyS10RR027303 · NCRR · UNIVERSITY OF CALIFORNIA BERKELEY · PI TAYLOR, JOHN W. · 2010 to 2010
$500k
Molecular mechanisms regulating chromatin looping in time and spaceK99GM130896 · NIGMS · UNIVERSITY OF CALIFORNIA BERKELEY · PI HANSEN, ANDERS SEJR · 2019 to 2019
$94k
Howard Hughes Medical Institute 003061NCRR NIH HHS S10 RR027303NCRR NIH HHS S10 RR029668NIBIB NIH HHS U01 EB021236NIDDK NIH HHS U54 DK107980NIGMS NIH HHS K99 GM130896NIGMS NIH HHS R00 GM130896
6 · The paper itself

Abstract

Whereas folding of genomes at the large scale of epigenomic compartments and topologically associating domains (TADs) is now relatively well understood, how chromatin is folded at finer scales remains largely unexplored in mammals. Here, we overcome some limitations of conventional 3C-based methods by using high-resolution Micro-C to probe links between 3D genome organization and transcriptional regulation in mouse stem cells. Combinatorial binding of transcription factors, cofactors, and chromatin modifiers spatially segregates TAD regions into various finer-scale structures with distinct regulatory features including stripes, dots, and domains linking promoters-to-promoters (P-P) or enhancers-to-promoters (E-P) and bundle contacts between Polycomb regions. E-P stripes extending from the edge of domains predominantly link co-expressed loci, often in the absence of CTCF and cohesin occupancy. Acute inhibition of transcription disrupts these gene-related folding features without altering higher-order chromatin structures. Our study uncovers previously obscured finer-scale genome organization, establishing functional links between chromatin folding and gene regulation.

Indexed as

Transcription, GeneticAnimalsCCCTC-Binding FactorChromatinChromatin Assembly and DisassemblyDNA Polymerase IIEmbryonic Stem CellsEnhancer Elements, GeneticGene Expression RegulationGenome ComponentsMicePromoter Regions, GeneticTranscription FactorsCCCTC-Binding FactorChromatinCtcf protein, mouseDNA Polymerase IITranscription Factors30 nm chromatin fiber3D genomeCTCFenhancer-promoter (E-P) interactionsloop extrusionMicro-CPol IITADtranscription

Identifiers

PMID32213323
PMCPMC7703524
OpenAlexW3013167866

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.