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Nonlinear relationship between chromatin accessibility and estradiol-regulated gene expression

Oncogene volume 40, pages 1332–1346 (2021)Cite this article

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Abstract

Chromatin accessibility is central to basal and inducible gene expression. Through ATAC-seq experiments in estrogen receptor-positive (ER+) breast cancer cell line MCF-7 and integration with multi-omics data, we found estradiol (E2) induced chromatin accessibility changes in a small number of breast cancer-relevant E2-regulated genes. As expected, open chromatin regions associated with E2-inducible gene expression showed enrichment of estrogen response element (ERE) and those associated with E2-repressible gene expression were enriched for ERE, PBX1, and PBX3. While a significant number of open chromatin regions showed pioneer factor FOXA1 occupancy in the absence of E2, E2-treatment further enhanced FOXA1 occupancy suggesting that ER–E2 enhances chromatin occupancy of FOXA1 to a subset of E2-regulated genes. Surprisingly, promoters of 80% and enhancers of 60% of E2-inducible genes displayed closed chromatin configuration both in the absence and presence of E2. Integration of ATAC-seq data with ERα ChIP-seq data revealed that ~40% ERα binding sites in the genome are found in chromatin regions that are not accessible as per ATAC-seq. Such ERα binding regions were enriched for binding sites of multiple nuclear receptors including ER, ESRRB, ERRγ, COUP-TFII (NR2F2), RARα, EAR2 as well as traditional pioneer factors FOXA1 and GATA3. Similar data were also obtained when ERα ChIP-seq data were integrated with MNase-seq and DNase-seq data sets. In summation, our results reveal complex mechanisms of ER–E2 interaction with nucleosomes. Notably, “closed chromatin” configuration as defined by ATAC-seq or by other techniques is not necessarily associated with lack of gene expression and technical limitations may preclude ATAC-seq to demonstrate accessibility of chromatin regions that are bound by ERα.

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Fig. 1: E2-regulated changes in chromatin accessibility in MCF-7 cells.
Fig. 2: Association between chromatin accessibility and E2-regulated gene expression.
Fig. 3: E2 alters chromatin accessibility of widely studied E2-regulated genes.
Fig. 4: Motif enrichment analyses of regulatory regions defined as accessible or closed as per ATAC-seq.
Fig. 5: Integration of ATAC-seq data with ERα ChIP-seq data.
Fig. 6: Validation of RNA-seq data of select E2-inducible and E2-repressed genes and chromatin modifications in corresponding genes.
Fig. 7: Integration of multiple “omics” data to establish relationship between chromatin accessibility (ATAC-seq), RNA polymerase II activity (GRO-seq), and DNA–RNA hybrid formation (DRIP-seq) with E2-regulated gene expression (RNA-seq).

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Data availability

All high-throughput data are available in GSE144580.

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Acknowledgements

Susan G Komen for the Cure (SAC110025 to HN) supported this work. We also thank the members of the Medical Genomics core for sequencing and help with data analyses.

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  1. These authors contributed equally: Duojiao Chen, Taylor M. Parker

Authors and Affiliations

  1. Departments of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA

    Duojiao Chen, Xiaona Chu, Yunlong Liu & Yue Wang

  2. Departments of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA

    Taylor M. Parker, Poornima Bhat-Nakshatri & Harikrishna Nakshatri

  3. Departments of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA

    Harikrishna Nakshatri

  4. Roudebush VA Medical Center, Indianapolis, IN, 46202, USA

    Harikrishna Nakshatri

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Contributions

DC: bioinformatics data analyses and paper writing. TP: biologic assays including cell culture, qRT-PCR, and ChIP-PCR. PN: qRT-PCRs and paper writing/editing. XC: ATAC-seq and paper editing. YL: bioinformatics, data interpretation, and paper editing. YW: ATAC-seq, data interpretation, and paper editing. HN: study supervision, data interpretation, and paper writing.

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Correspondence to Yue Wang or Harikrishna Nakshatri.

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Chen, D., Parker, T.M., Bhat-Nakshatri, P. et al. Nonlinear relationship between chromatin accessibility and estradiol-regulated gene expression. Oncogene 40, 1332–1346 (2021). https://doi.org/10.1038/s41388-020-01607-2

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