Nucleosome repositioning during differentiation of a human myeloid leukemia cell line

dc.contributor.author Teif, Vladimir B.
dc.contributor.author Mallm, Jan-Philipp
dc.contributor.author Sharma, Tanvi
dc.contributor.author Mark Welch, David B.
dc.contributor.author Rippe, Karsten
dc.contributor.author Eils, Roland
dc.contributor.author Langowski, Jörg
dc.contributor.author Olins, Ada L.
dc.contributor.author Olins, Donald E.
dc.date.accessioned 2017-05-18T15:56:26Z
dc.date.available 2017-05-18T15:56:26Z
dc.date.issued 2017-02-23
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.abstract Cell 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.sponsorship The 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.identifier.citation Nucleus 8 (2017): 188-204 en_US
dc.identifier.doi 10.1080/19491034.2017.1295201
dc.identifier.uri https://hdl.handle.net/1912/8989
dc.language.iso en en_US
dc.publisher Taylor & Francis en_US
dc.relation.uri https://doi.org/10.1080/19491034.2017.1295201
dc.rights Attribution-NonCommercial-NoDerivatives 4.0 International *
dc.rights.uri http://creativecommons.org/licenses/by-nc-nd/4.0/ *
dc.subject CTCF: Epichromatin en_US
dc.subject Histone modifications en_US
dc.subject Nucleosome positioning en_US
dc.subject Nucleosome repeat length en_US
dc.subject Transcription factor binding en_US
dc.title Nucleosome repositioning during differentiation of a human myeloid leukemia cell line en_US
dc.type Article en_US
dspace.entity.type Publication
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