Nucleosomal occupancy changes locally over key regulatory regions during cell differentiation and reprogramming

Jason A. West, April Cook, Burak H. Alver, Matthias Stadtfeld, Aimee M. Deaton, Konrad Hochedlinger, Peter J. Park (), Michael Y. Tolstorukov () and Robert E. Kingston ()
Additional contact information
Jason A. West: Massachusetts General Hospital
April Cook: Massachusetts General Hospital
Burak H. Alver: Center for Biomedical Informatics, Harvard Medical School
Matthias Stadtfeld: The Helen L. and Martin S. Kimmel Center for Biology and Medicine, The Skirball Institute of Biomolecular Medicine, New York University School of Medicine
Aimee M. Deaton: Massachusetts General Hospital
Konrad Hochedlinger: Howard Hughes Medical Institute and the Center for Regenerative Medicine, Massachusetts General Hospital
Peter J. Park: Center for Biomedical Informatics, Harvard Medical School
Michael Y. Tolstorukov: Massachusetts General Hospital
Robert E. Kingston: Massachusetts General Hospital

Nature Communications, 2014, vol. 5, issue 1, 1-12

Abstract: Abstract Chromatin structure determines DNA accessibility. We compare nucleosome occupancy in mouse and human embryonic stem cells (ESCs), induced-pluripotent stem cells (iPSCs) and differentiated cell types using MNase-seq. To address variability inherent in this technique, we developed a bioinformatic approach to identify regions of difference (RoD) in nucleosome occupancy between pluripotent and somatic cells. Surprisingly, most chromatin remains unchanged; a majority of rearrangements appear to affect a single nucleosome. RoDs are enriched at genes and regulatory elements, including enhancers associated with pluripotency and differentiation. RoDs co-localize with binding sites of key developmental regulators, including the reprogramming factors Klf4, Oct4/Sox2 and c-Myc. Nucleosomal landscapes in ESC enhancers are extensively altered, exhibiting lower nucleosome occupancy in pluripotent cells than in somatic cells. Most changes are reset during reprogramming. We conclude that changes in nucleosome occupancy are a hallmark of cell differentiation and reprogramming and likely identify regulatory regions essential for these processes.

Date: 2014
References: Add references at CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/ncomms5719 Abstract (text/html)

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:natcom:v:5:y:2014:i:1:d:10.1038_ncomms5719

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

DOI: 10.1038/ncomms5719

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

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