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


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2014-12

AUTHORS

Jason A. West, April Cook, Burak H. Alver, Matthias Stadtfeld, Aimee M. Deaton, Konrad Hochedlinger, Peter J. Park, Michael Y. Tolstorukov, Robert E. Kingston

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. More... »

PAGES

4719

References to SciGraph publications

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/ncomms5719

DOI

http://dx.doi.org/10.1038/ncomms5719

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1036433655

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/25158628


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