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Beagrie, R.A.* ; Thieme, C.J.* ; Annunziatella, C.* ; Baugher, C.* ; Zhang, Y.* ; Schueler, M.* ; Kukalev, A.* ; Kempfer, R.* ; Chiariello, A.M.* ; Bianco, S.* ; Li, Y.* ; Davis, T.* ; Scialdone, A. ; Welch, L.R.* ; Nicodemi, M.* ; Pombo, A.*

Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C.

Nat. Methods 20, 1037-1047 (2023)
Postprint DOI PMC
Open Access Hybrid
Creative Commons Lizenzvertrag
Technology for measuring 3D genome topology is increasingly important for studying gene regulation, for genome assembly and for mapping of genome rearrangements. Hi-C and other ligation-based methods have become routine but have specific biases. Here, we develop multiplex-GAM, a faster and more affordable version of genome architecture mapping (GAM), a ligation-free technique that maps chromatin contacts genome-wide. We perform a detailed comparison of multiplex-GAM and Hi-C using mouse embryonic stem cells. When examining the strongest contacts detected by either method, we find that only one-third of these are shared. The strongest contacts specifically found in GAM often involve ‘active’ regions, including many transcribed genes and super-enhancers, whereas in Hi-C they more often contain ‘inactive’ regions. Our work shows that active genomic regions are involved in extensive complex contacts that are currently underestimated in ligation-based approaches, and highlights the need for orthogonal advances in genome-wide contact mapping technologies.
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Publikationstyp Artikel: Journalartikel
Dokumenttyp Wissenschaftlicher Artikel
Schlagwörter Rna-polymerase-ii; Organization; Reveals; Principles; Dynamics
Sprache englisch
Veröffentlichungsjahr 2023
HGF-Berichtsjahr 2023
ISSN (print) / ISBN 1548-7091
e-ISSN 1548-7105
Zeitschrift Nature Methods
Quellenangaben Band: 20, Heft: 7, Seiten: 1037-1047 Artikelnummer: , Supplement: ,
Verlag Nature Publishing Group
Verlagsort New York, NY
Begutachtungsstatus Peer reviewed
Institut(e) Institute of Epigenetics and Stem Cells (IES)
Institute of Functional Epigenetics (IFE)
Institute of Computational Biology (ICB)
POF Topic(s) 30204 - Cell Programming and Repair
30203 - Molecular Targets and Therapies
30205 - Bioengineering and Digital Health
Forschungsfeld(er) Stem Cell and Neuroscience
Helmholtz Diabetes Center
Enabling and Novel Technologies
PSP-Element(e) G-506290-001
G-502800-001
G-503800-001
Förderungen NIDDK NIH HHS
Wellcome Trust
DOI 10.1038/s41592-023-01903-1
WOS ID 001010677900002
Scopus ID 85162164196
PubMed ID 37336949
Erfassungsdatum 2023-10-18
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