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Analysis of chromatin accessibility in decidualizing human endometrial stromal cells

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Vrljicak, Pavle, Lucas, Emma S., Lansdowne, Lauren, Lucciola, Raffaella, Muter, Joanne, Dyer, Nigel P., Brosens, Jan J. and Ott, Sascha (2018) Analysis of chromatin accessibility in decidualizing human endometrial stromal cells. FASEB Journal, 32 (5). 2467-2477 . doi:10.1096/fj.201701098R ISSN 0892-6638.

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Official URL: http://doi.org/10.1096/fj.201701098R

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Abstract

Spontaneous decidualization of the endometrium in response to progesterone signaling is confined to menstruating species, including humans and other higher primates. During this process, endometrial stromal cells (EnSCs) differentiate into specialized decidual cells that control embryo implantation. We subjected undifferentiated and decidualizing human EnSCs to an assay for transposase accessible chromatin with sequencing (ATAC-seq) to map the underlying chromatin changes. A total of 185,084 open DNA loci were mapped accurately in EnSCs. Altered chromatin accessibility upon decidualization was strongly associated with differential gene expression. Analysis of 1533 opening and closing chromatin regions revealed over-representation of DNA binding motifs for known decidual transcription factors (TFs) and identified putative new regulators. ATAC-seq footprint analysis provided evidence of TF binding at specific motifs. One of the largest footprints involved the most enriched motif-basic leucine zipper-as part of a triple motif that also comprised the estrogen receptor and Pax domain binding sites. Without exception, triple motifs were located within Alu elements, which suggests a role for this primate-specific transposable element (TE) in the evolution of decidual genes. Although other TEs were generally under-represented in open chromatin of undifferentiated EnSCs, several classes contributed to the regulatory DNA landscape that underpins decidual gene expression.

Item Type: Journal Article
Subjects: R Medicine > RG Gynecology and obstetrics
Divisions: Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School > Biomedical Sciences
Faculty of Science, Engineering and Medicine > Science > Computer Science
Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- )
Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School
SWORD Depositor: Library Publications Router
Library of Congress Subject Headings (LCSH): Human embryo -- Transplantation -- Physiological aspects, Endometrium, Progesterone, Genetic regulation, Chromatin
Journal or Publication Title: FASEB Journal
Publisher: Federation of American Societies for Experimental Biology
ISSN: 0892-6638
Official Date: 1 May 2018
Dates:
DateEvent
1 May 2018Published
19 December 2017Available
4 December 2017Accepted
Volume: 32
Number: 5
Page Range: 2467-2477
DOI: 10.1096/fj.201701098R
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Open Access (Creative Commons)
Date of first compliant deposit: 3 January 2018
Date of first compliant Open Access: 29 October 2018
RIOXX Funder/Project Grant:
Project/Grant IDRIOXX Funder NameFunder ID
UNSPECIFIEDUniversity Hospitals Coventry and Warwickshire NHS Trusthttp://viaf.org/viaf/152707181
UNSPECIFIEDWarwick Medical Schoolhttp://dx.doi.org/10.13039/501100004443

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