Modulation of Transcription Factor Chromatin Association and Gene Transcription Program in Embryonic Stem Cell and Triple Negative Breast Cancer by Poly (ADP-Ribose) Polymerase 1

Poly(ADP-ribose) polymerase-1 (PARP-1), also referred to as ADP-ribosyltransferase Diphtheria toxin-like 1 (ARTD1), is an abundant nuclear protein that plays key roles in a variety of nuclear processes, including the regulation of transcription. PARP-1 possesses an intrinsic enzymatic activity that catalyzes the transfer of ADP-ribose (ADPR) units from nicotinamide adenine dinucleotide (NAD+) onto target gene regulatory proteins, thereby modulating their activities. Although great strides have been made in the past decade in deciphering the seemingly opposing and varied roles of PARP-1 in gene regulation, many puzzles remain in this field. Using a combination of cell biology, molecular biology, genomics and biochemistry methods, I investigated the functions of PARP-1 in regulating gene transcription program in mouse embryonic stem cells and human triple negative breast cancer cells. I found that in mouse embryonic stem cells, PARP-1 functions as a pre-pioneering factor, stabilizing transcription factor Sox2 interaction with nucleosomes. This function is required for maintaining gene transcription program in embryonic stem cells. Depletion of PARP-1 causes disrupted embryonic stem cell gene expression profile, including decreased expression of Nanog, as well as increased expression of differentiation genes. Furthermore, using human triple negative breast cancer cells, I showed that this gene transcriptional regulation mechanism through PARP-1-Sox2 interplay is conserved in different physiological models. Interestingly, inhibiting PARylation activity causes gain of Sox2 binding to a set of genomic locations in TNBC cells, indicating that PARylation activity plays an antagonizing role in PARP-1-regulated Sox2 chromatin interaction. In summary, our results illustrate how PARP-1 can act at the level of the nucleosome to produce global effects on transcription factor binding and biologically important gene expression outcomes.