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dc.contributor.authorTeif, Vladimir B.  Concept link
dc.contributor.authorMallm, Jan-Philipp  Concept link
dc.contributor.authorSharma, Tanvi  Concept link
dc.contributor.authorMark Welch, David B.  Concept link
dc.contributor.authorRippe, Karsten  Concept link
dc.contributor.authorEils, Roland  Concept link
dc.contributor.authorLangowski, Jörg  Concept link
dc.contributor.authorOlins, Ada L.  Concept link
dc.contributor.authorOlins, Donald E.  Concept link
dc.identifier.citationNucleus 8 (2017): 188-204en_US
dc.description© The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nucleus 8 (2017): 188-204, doi:10.1080/19491034.2017.1295201.en_US
dc.description.abstractCell differentiation is associated with changes in chromatin organization and gene expression. In this study, we examine chromatin structure following differentiation of the human myeloid leukemia cell line (HL-60/S4) into granulocytes with retinoic acid (RA) or into macrophage with phorbol ester (TPA). We performed ChIP-seq of histone H3 and its modifications, analyzing changes in nucleosome occupancy, nucleosome repeat length, eu-/heterochromatin redistribution and properties of epichromatin (surface chromatin adjacent to the nuclear envelope). Nucleosome positions changed genome-wide, exhibiting a specific class of alterations involving nucleosome loss in extended (»1kb) regions, pronounced in enhancers and promoters. Genes that lost nucleosomes at their promoters showed a tendency to be upregulated. On the other hand, nucleosome gain did not show simple effects on transcript levels. The average genome-wide nucleosome repeat length (NRL) did not change significantly with differentiation. However, we detected an approximate 10 bp NRL decrease around the haematopoietic transcription factor (TF) PU.1 and the architectural protein CTCF, suggesting an effect on NRL proximal to TF binding sites. Nucleosome occupancy changed in regions associated with active promoters in differentiated cells, compared with untreated HL-60/S4 cells. Epichromatin regions revealed an increased GC content and high nucleosome density compared with surrounding chromatin. Epichromatin showed depletion of major histone modifications and revealed enrichment with PML body-associated genes. In general, chromatin changes during HL-60/S4 differentiation appeared to be more localized to regulatory regions, compared with genome-wide changes among diverse cell types studied elsewhere.en_US
dc.description.sponsorshipThe Guest Scientist Program at the DKFZ supported ALO and DEO while working in Heidelberg. VBT is supported by the Wellcome Trust grant 200733/Z/16/Z.en_US
dc.publisherTaylor & Francisen_US
dc.rightsAttribution-NonCommercial-NoDerivatives 4.0 International*
dc.subjectCTCF: Epichromatinen_US
dc.subjectHistone modificationsen_US
dc.subjectNucleosome positioningen_US
dc.subjectNucleosome repeat lengthen_US
dc.subjectTranscription factor bindingen_US
dc.titleNucleosome repositioning during differentiation of a human myeloid leukemia cell lineen_US

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Attribution-NonCommercial-NoDerivatives 4.0 International
Except where otherwise noted, this item's license is described as Attribution-NonCommercial-NoDerivatives 4.0 International