Landscape of cohesin-mediated chromatin loops in the human genome

Fabian Grubert, Rohith Srivas, Damek V Spacek, Maya Kasowski, Mariana Ruiz-Velasco, Nasa Sinnott-Armstrong, Peyton Greenside, Anil Narasimha, Qing Liu, Benjamin Geller, Akshay Sanghi, Michael Kulik, Silin Sa, Marlene Rabinovitch, Anshul Kundaje, Stephen Dalton, Judith B. Zaugg and Michael Snyder ()
Additional contact information
Fabian Grubert: Stanford University School of Medicine
Rohith Srivas: Stanford University School of Medicine
Damek V Spacek: Stanford University School of Medicine
Maya Kasowski: Stanford University School of Medicine
Mariana Ruiz-Velasco: European Molecular Biology Laboratory
Nasa Sinnott-Armstrong: Stanford University School of Medicine
Peyton Greenside: Stanford University School of Medicine
Anil Narasimha: Stanford University School of Medicine
Qing Liu: Stanford University School of Medicine
Benjamin Geller: Stanford University School of Medicine
Akshay Sanghi: Stanford University School of Medicine
Michael Kulik: University of Georgia
Silin Sa: Stanford University School of Medicine
Marlene Rabinovitch: Stanford University School of Medicine
Anshul Kundaje: Stanford University School of Medicine
Stephen Dalton: University of Georgia
Judith B. Zaugg: European Molecular Biology Laboratory
Michael Snyder: Stanford University School of Medicine

Nature, 2020, vol. 583, issue 7818, 737-743

Abstract: Abstract Physical interactions between distal regulatory elements have a key role in regulating gene expression, but the extent to which these interactions vary between cell types and contribute to cell-type-specific gene expression remains unclear. Here, to address these questions as part of phase III of the Encyclopedia of DNA Elements (ENCODE), we mapped cohesin-mediated chromatin loops, using chromatin interaction analysis by paired-end tag sequencing (ChIA-PET), and analysed gene expression in 24 diverse human cell types, including core ENCODE cell lines. Twenty-eight per cent of all chromatin loops vary across cell types; these variations modestly correlate with changes in gene expression and are effective at grouping cell types according to their tissue of origin. The connectivity of genes corresponds to different functional classes, with housekeeping genes having few contacts, and dosage-sensitive genes being more connected to enhancer elements. This atlas of chromatin loops complements the diverse maps of regulatory architecture that comprise the ENCODE Encyclopedia, and will help to support emerging analyses of genome structure and function.

Date: 2020
References: Add references at CitEc
Citations: View citations in EconPapers (5)

Downloads: (external link)
https://www.nature.com/articles/s41586-020-2151-x Abstract (text/html)
Access to the full text of the articles in this series is restricted.

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:nature:v:583:y:2020:i:7818:d:10.1038_s41586-020-2151-x

Ordering information: This journal article can be ordered from
https://www.nature.com/

DOI: 10.1038/s41586-020-2151-x

Access Statistics for this article

Nature is currently edited by Magdalena Skipper

More articles in Nature from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().