Abstract 1006: Non-linear relationship between estradiol-regulated changes in chromatin architecture and gene expression
Authors: Parker Taylor M. , Chen Duojiao , Bhat-Nakshatri Poornima , Chu Xiaona , Liu Yunlong , Wang Yue , Nakshatri Harikrishna 
Published: August 2019

Gene expression in estrogen receptor (ER)-positive breast cancer cells is predominantly driven by ER-estradiol (E2) signaling. However, the effects of ER-E2 signaling on the overall chromatin architecture and accessibility to transcription regulators are not well understood. Chromatin architecture is a key determinant to gene expression patterns and therefore a comprehensive notation is essential for the interpretation of the ER cistrome. To investigate the effects of E2 signaling on chromatin architecture, we employed Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq), a high-throughput method to map chromatin accessibility via a hyperactive transposase that inserts sequencing tags into open regions. ATAC-seq was performed on MCF-7 cells, an ERα+ breast cancer cell line, treated with E2 or vehicle control for 1 or 3 hours. Results from the ATAC-seq were compared to RNA-seq data of 3-hours E2-treated MCF-7 cells to determine which regions of E2-regulated open or closed chromatin coincide with increased or decreased respective gene expression. Interestingly, we observed greater chromatin accessibility changes in genes repressed by E2 compared to genes induced by E2. Integration of ATAC-seq and RNA-seq data revealed distinct categories of E2-induced chromatin remodeling and downstream gene expression including increased chromatin accessibility, but repression of the corresponding gene, as well as decreased chromatin accessibility, but induction of the corresponding gene. Validation of the chromatin configurations predicted by ATAC-seq of select corresponding genes is currently being performed by ChIP-qPCR against specific histone modifications, such as H3K27Ac, a marker of open chromatin. To mechanistically dissect the distinct modes of E2 chromatin remodelling, we performed motif enrichment analysis of chromatin regions affected by E2. This analysis showed expected enrichment of estrogen response element (ERE), and pioneer factor FOXA1 and GATA3 response elements in E2-inducible genes with enhanced chromatin accessibility after E2-treatment. Regions in which the corresponding mRNA showed decreased transcript levels but displayed open chromatin in their promoter or enhancer region were enriched for the PBX3 motif and the ERE motif, respectively. Our results reveal previously unrecognized modes of E2-mediated restructuring of chromatin architecture and its correlation with transcription dynamics. This study provides grounds for future work to study fundamental relationships between chromatin accessibility and gene regulation in breast cancer under E2 and anti-estrogen treated conditions as well as in metastatic breast cancers with ERα mutations.

Citation Format: Taylor M. Parker, Duojiao Chen, Poornima Bhat-Nakshatri, Xiaona Chu, Yunlong Liu, Yue Wang, Harikrishna Nakshatri. Non-linear relationship between estradiol-regulated changes in chromatin architecture and gene expression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1006.