Transcriptional control of gene expression requires a carefully orchestrated set of physical and functional interactions among DNA-binding activators, transcriptional coregulators, the RNA polymerase II transcriptional machinery, and the chromatin template. In this proposal, we explore the role of poly(ADP- ribose) polymerase-1 (PARP-1), a nucleosome-binding protein, in the chromatin-dependent control of both basal and estrogen-regulated transcription. PARP-1 has an intrinsic enzymatic activity that catalyzes the polymerization of ADP-ribose chains on target proteins from donor nicotinamide adenine dinucleotide (NAD+) molecules. Recent studies have revealed an important role for PARP-1 as a modulator of estrogen receptor-dependent transcription. Yet, among the many gene regulatory factors with enzymatic activities, PARP-1 is one of the least well characterized. In particular, the mechanisms directing PARP-1 to specific target promoters in the genome, the effects of PARP-1 on the composition and structure of promoter chromatin, and the role of nuclear NAD+ metabolism in regulating PARP-1 activity are not well understood. The long-term objective of these studies is to achieve a better understanding of the chromatin- dependent molecular mechanisms underlying the control of basal and signal-regulated transcription by PARP-1 and its associated factors. Our broad hypothesis is that the gene regulatory activity of PARP-1 is determined by (1) the local chromatin environment (e.g., chromatin composition, histone modifications), (2) physical and functional interactions among PARP-1, signal-regulated DNA-binding activators (e.g., estrogen receptor 1;ER1), and other coregulators, and (3) the availability of NAD+ in the nucleus. In this proposal, we outline a series of experiments using an integrated approach with a complementary set of biochemical, biophysical, and cell-based assays that will test the broad hypothesis noted above and address three specific aims which will determine: (1) the molecular mechanisms underlying the modulation of basal gene expression by PARP-1 and its associated factors in cells, (2) the molecular mechanisms underlying the regulation of estrogen-dependent gene expression by PARP-1 and its associated factors in cells, and (3) the biochemical mechanisms underlying the chromatin- dependent regulation of gene expression by PARP-1 and its associated factors in vitro. Collectively, the studies outlined in these aims will provide new insights into the molecular mechanisms of PARP-1's gene regulatory activity in the context of chromatin, including those relevant to ER1-dependent transcription. In addition, these studies will provide new insights into the role of nuclear NAD+ signaling in hormone-regulated transcription, an exciting new area that is only now beginning to be understood. Given the roles of PARP-1 and ER1 in human disease, our studies could also lead to new ways to exploit these factors as therapeutic targets.

Public Health Relevance

Statement Poly(ADP-ribose) polymerase-1 (PARP-1) and estrogen receptor alpha (ER1) are two nuclear factors that play key roles in human diseases, such as breast cancers. Understanding the molecular actions of PARP- 1 and ER1, as well as the functional interplay between these two proteins, may suggest new ways to target these factors for the treatment of breast cancers and other hormone-regulated diseases.

Agency
National Institute of Health (NIH)
Institute
National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)
Type
Research Project (R01)
Project #
5R01DK069710-06
Application #
7828094
Study Section
Special Emphasis Panel (ZRG1-EMNR-G (05))
Program Officer
Margolis, Ronald N
Project Start
2004-09-30
Project End
2010-09-10
Budget Start
2010-06-01
Budget End
2010-09-10
Support Year
6
Fiscal Year
2010
Total Cost
$59,528
Indirect Cost
Name
Cornell University
Department
Biochemistry
Type
Schools of Earth Sciences/Natur
DUNS #
872612445
City
Ithaca
State
NY
Country
United States
Zip Code
14850
Liu, Ziying; Kraus, W Lee (2017) Catalytic-Independent Functions of PARP-1 Determine Sox2 Pioneer Activity at Intractable Genomic Loci. Mol Cell 65:589-603.e9
Lin, Ken Y; Kraus, W Lee (2017) PARP Inhibitors for Cancer Therapy. Cell 169:183
Gupte, Rebecca; Liu, Ziying; Kraus, W Lee (2017) PARPs and ADP-ribosylation: recent advances linking molecular functions to biological outcomes. Genes Dev 31:101-126
Luo, Xin; Ryu, Keun Woo; Kim, Dae-Seok et al. (2017) PARP-1 Controls the Adipogenic Transcriptional Program by PARylating C/EBP? and Modulating Its Transcriptional Activity. Mol Cell 65:260-271
Gibson, Bryan A; Zhang, Yajie; Jiang, Hong et al. (2016) Chemical genetic discovery of PARP targets reveals a role for PARP-1 in transcription elongation. Science 353:45-50
Ryu, Keun Woo; Kim, Dae-Seok; Kraus, W Lee (2015) New facets in the regulation of gene expression by ADP-ribosylation and poly(ADP-ribose) polymerases. Chem Rev 115:2453-81
Chae, Minho; Danko, Charles G; Kraus, W Lee (2015) groHMM: a computational tool for identifying unannotated and cell type-specific transcription units from global run-on sequencing data. BMC Bioinformatics 16:222
Winans, Bethany; Nagari, Anusha; Chae, Minho et al. (2015) Linking the aryl hydrocarbon receptor with altered DNA methylation patterns and developmentally induced aberrant antiviral CD8+ T cell responses. J Immunol 194:4446-57
Kraus, W Lee (2015) PARPs and ADP-Ribosylation: 50 Years … and Counting. Mol Cell 58:902-10
Liu, Xiuli; Kraus, W Lee; Bai, Xiaoying (2015) Ready, pause, go: regulation of RNA polymerase II pausing and release by cellular signaling pathways. Trends Biochem Sci 40:516-25

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