Project Summary/Abstract Although androgen ablation is initially effective for advanced prostate cancer treatment, resistance ultimately develops through various mechanisms, causing patient morbidity. Systems analysis of the prostate cancer epigenome is a genome-scale approach to understanding the under-studied epigenetic events that characterize prostate cancer progression to the resistant state. This proposed work is an integral part of the NCI-funded research program U54 CA217297, which focuses on studying epigenetic mechanisms exploited by hormone- resistant cancer cells to acquire growth and invasion advantages. Dr. Qianben Wang’s laboratory has recently performed an integrative analysis of strand specific paired-end ChIP-exo (ChIP-ePENS) and MNase-seq data and discovered an epigenetic mechanism by which genomic and transcriptional regulation are controlled by precise changes to nucleosome positioning within transcription factor (TF) binding sites. This represents the latest in a series of findings that have come out of the work of the research specialist, Dr. Zhong Chen, as the only key, senior member of the Wang laboratory. Dr. Chen facilitated this breakthrough by developing the ChIP- ePENS assay and working with colleagues to develop a new algorithm to perform integrative analysis of ChIP- ePENS and MNase-seq data. The intersection of these innovative techniques led to the identification of unique footprint boundary patterns (FBPs) of TF binding that determine how nucleosomes are positioned in and around androgen receptor (AR)-bound enhancers. Additional evidence that AR bound by anti-androgen activates enhancers with unique FBPs suggested that this epigenetic mechanism is hijacked by hormone-resistant cancer cells for AR redeployment under a therapeutic condition. The U54 project will determine the role of nucleosome repositioning as well as its regulatory proteins in supporting AR redeployment for hormone-resistant prostate cancer. Dr. Chen will be responsible for: (1) generating the high-throughput ChIP-ePENS, MNase-seq, ATAC- seq and RNA-seq datasets from prostate cancer cells and patient tissues; (2) analyzing sequencing data and participating in the development of computational models to assess nucleosome positioning and spacing; and (3) performing molecular and cellular biology experiments including developing novel CRISPR-dCas9-based editing tools to study nucleosome positioning and prostate cancer progression, and using proteomics to identify transcription factors and chromatin remodelers regulating nucleosome positioning. He will design and utilize a functional omics-oriented CRISPR/dCas9-based system for therapeutic prostate cancer epigenome editing, opening up new areas of research in the Wang lab while facilitating the translation of the U54 epigenetic discoveries into therapeutic tools and clinical benefits. The Research Specialist award would provide a stable and ideal research environment in which to pursue his goals in g...