Chromatin topology defines estradiol-primed progesterone receptor and PAX2 binding in endometrial cancer cells
- Biology and Experimental Medicine Institute, Argentina
- Institute of Nuclear Technologies for Health, Argentina
- Centre for Genomic Regulation, Spain
- Córdoba University, Argentina
Abstract
Estrogen (E2) and Progesterone (Pg), via their specific receptors (ERalpha and PR), are major determinants in the development and progression of endometrial carcinomas, However, their precise mechanism of action and the role of other transcription factors involved are not entirely clear. Using Ishikawa endometrial cancer cells, we report that E2 treatment exposes a set of progestin-dependent PR binding sites which include both E2 and progestin target genes. ChIP-seq results from hormone-treated cells revealed a non-random distribution of PAX2 binding in the vicinity of these estrogen-promoted PR sites. Altered expression of hormone regulated genes in PAX2 knockdown cells suggests a role for PAX2 in fine-tuning ERalpha and PR interplay in transcriptional regulation. Analysis of long-range interactions by Hi-C coupled with ATAC-seq data showed that these regions, that we call 'progestin control regions' (PgCRs), exhibited an open chromatin state even before hormone exposure and were non-randomly associated with regulated genes. Nearly 20% of genes potentially influenced by PgCRs were found to be altered during progression of endometrial cancer. Our findings suggest that endometrial response to progestins in differentiated endometrial tumor cells results in part from binding of PR together with PAX2 to accessible chromatin regions. What maintains these regions open remains to be studied.
Data availability
All raw and processed sequencing data generated in this study have been submitted to the NCBI Gene Expression Omnibus under accession number GSE139398 (reviewer access: ergbqgaebbmjrmt).Source data file has been provided for Figure 6.T47D ChIPseq data is available under GEO accession number GSE41466 (Ballare et al, 2013) and Hi-C data in GEO accession GSE53463 (Le-Dily et al, 2014). RNAseq datasets from proliferative (GSM3890623, GSM3890624, GSM3890625 and GSM3890626) and mid-secretory (GSM3890627, GSM3890628, GSM3890629, GSM3890630 and GSM3890631) human endometrium were obtained from GEO accession GSE132711 (SuperSeries GSE132713) (Chi et al, 2020). ChIPseq coverage data of proliferative and secretory normal endometrium were downloaded from GEO accession GSE132712 (SuperSeries GSE132713) (Chi et al, 2020). Human endometrial cancer RNAseq samples (n=575) were downloaded from The Cancer Genome Atlas (TCGA), project TCGA-UCEC. Additional normal and endometrial cancer samples (n=109) were accessed through CPTAC program in the National Cancer Institute using cptac platform installed with python (Dou et al, 2020).
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Endometrial transcriptome and PGR cistrome in cycling fertile womenNCBI Gene Expression Omnibus, GSE132713.
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Hormone induced repression of genes requires BRG1-mediated H1.2 deposition at target promotersNCBI Gene Expression Omnibus, GSE83785.
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Nucleosome driven transcription factor binding and gene regulationNCBI Gene Expression Omnibus, GSE41466.
Article and author information
Author details
Alejandro La Greca
Patricia Saragüeta
Funding
Consejo Nacional de Investigaciones Científicas y Técnicas (PIP 2015-682)
- Patricia Saragüeta
Fondo para la Investigación Científica y Tecnológica (PICT 2015-3426)
- Patricia Saragüeta
H2020 European Research Council (FP7/2007-2013 grant agreement 609989)
- Miguel Beato
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Inez Rogatsky, Hospital for Special Surgery, United States
Version history
- Preprint posted: August 20, 2019 (view preprint)
- Received: December 22, 2020
- Accepted: January 11, 2022
- Accepted Manuscript published: January 12, 2022 (version 1)
- Version of Record published: March 1, 2022 (version 2)
Copyright
© 2022, La Greca et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Chromatin topology defines estradiol-primed progesterone receptor and PAX2 binding in endometrial cancer cells
eLife 11:e66034.
https://doi.org/10.7554/eLife.66034
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