Genomic and Functional Analysis of Estrogen Responsive Cis-regulatory Elements in Breast Cancer Cells

Understanding of estrogen signaling governed gene transcriptional regulation is fundamental to elucidating the biology of hormone-related diseases such as breast cancer and has wide clinical implications. In this thesis, we present a systematic analysis of estrogen-dependent genome-wide interplay between cis-acting chromatin and transcription factors (TFs) in estrogen-responsive breast cancer cell line MCF7. In Chapter 1, we give an overarching introduction of the molecular basis of breast cancer heterogeneity, focusing on the biology of estrogen receptor (ER) mediated estrogen action in ER positive breast cancer. We also give a review on gene transcriptional regulation and the development of recent technology in studying cis-regulatory elements. In Chapter 2, via profiling estrogen-triggered dynamic changes of chromatin accessibility landscape and functional assessment of regulatory activity of massive DNase I hypersensitivity sites (DHSs) in high-throughput manner, we uncover unique chromatin signatures associated with estrogen-responsive DHSs and experimentally identify large amounts of enhancers including estrogen-responsive enhancers. From genomic analysis, we reveal intensive crosstalk and coordinated action of multiple TFs on estrogen-responsive enhancers. In Chapter 3, we focus on a specific ER-responsive TF, KLF4, and functionally characterize the role of KLF4 in estrogen-governed transcriptional regulation. We demonstrate estrogen-dependent interaction between KLF4 and cis-regulatory elements and discover widespread crosstalk between KLF4 and ER at estrogen-responsive DHSs. Finally, we identify KLF4 as a novel estrogen early effector and cooperative TF of ER in regulating genes involved in cell cycle regulation, which is important for maintaining estrogen-dependent cell proliferation of MCF7 cells.