The role of topoisomerase II beta in the formation of transcriptional hubs in prostate cancer cells

Heather C Wick1,*, Michael Haffner2,3,*, David Esopi2, William Nelson2,3, Srinivasan Yegnasubramanian2,3,&, Sarah Wheelan1,2,&, 1: Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA, 2: Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA, 3: Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
*: Contributed equally; &: Co-mentors


Cellular transcriptional programs requiring changes in expression of multiple genes may be more efficient when the target genes are brought into physical proximity by chromatin conformational changes. We hypothesize that topoisomerases, which induce transient single and double stranded breaks in DNA to relieve topological constraints, are required to facilitate the formation of such transcriptional hubs upon stimulation of transcriptional programs. Prior work from the lab has shown that one of these topoisomerases, topoisomerase II beta (TOP2B), binds and exerts catalytic activity at the genes TMPRSS2, an androgen receptor (AR) target gene, and ERG, an Ets transcription factor oncogene, recurrently fused in prostate cancer. Illegitimate repair of TOP2B-mediated double stranded DNA breaks incurred during the induction of androgen receptor signaling may contribute to gene fusions and other genomic rearrangements commonly seen in prostate cancer. Understanding the effects of AR and TOP2B binding on gene expression and chromosomal conformation in prostate cancer cells may give us insight about the formation and progression of prostate cancer.
The role of TOP2B in the coordination of transcriptional hubs was studied in LNCaP prostate cancer cells stimulated with and without the AR agonist dihydrotestosterone (DHT). The phenomena of interest are the multifaceted and coordinated cellular changes induced by DHT, requiring investigation of multiple processes: gene expression was measured with RNA-seq; AR and TOP2B binding were measured with ChIP-seq; and spatial genome interactions were measured with Hi-C. Integration of this data together with publically available ChIP-seq data of RNA Polymerase II binding and occupancy of histone marks was used to create a more complete picture of the effect of TOP2B and AR on the formation of these androgen-induced transcriptional hubs.