Date of Award

January 2023

Document Type


Degree Name

Doctor of Philosophy (PhD)


Biomedical Sciences

First Advisor

Alexei Tulin


Poly(ADP-ribose) polymerase 1 (PARP-1), a multifunctional nuclear enzyme, plays a crucial role in transcriptional regulation through its three functional domains: the N-terminal DNA-binding domain (DBD), the automodification domain (AD), and the C-terminal domain, which includes the WGR and the catalytic domains. Despite its importance, the mechanisms directing PARP-1 to chromatin remain unclear and PARP-1’s role in development is still poorly understood. In chapter II, we interrogated the role of PARP-1 domains in PARP-1 to chromatin. We used ChIP-seq of YFP-tagged deletional isoforms of PARP-1 and a construct that lacks only the first zinc finger domain (ΔZnI). Interestingly, our findings suggest that the presence of other PARP-1 domains is enough to target PARP-1 to active genes in the absence of the first zinc finger domain and PARP-1 domains cooperatively target PARP-1 to PARP-1-dependent genes. In chapter III, we interrogated the role of PARP-1 in transcriptional regulation during development. Mutants deficient in PARP-1 undergo developmental arrest during the larval-to-pupal transition, revealing its essential role in development. We found that PARP-1 represses highly active metabolic genes, such as genes involved in glycolysis, while it activates low-expression developmental genes, including a subset of bivalent genes marked by H3K4me3 and H3K27me3 and a unimodal H3K4me1 enrichment at their promoters. Importantly, in PARP-1 mutants, the normal metabolic gene repression during the larval-to-pupal transition and simultaneous activation of developmental genes are misregulated. Thus, we showed that PARP-1 is involved in balancing gene expression programs in Drosophila during development. Additionally, metabolic imbalances, such as reduced glucose and ATP levels, were observed in PARP-1 mutants, highlighting the critical role of PARP-1 in metabolic regulation. In chapter IV, we interrogated the role of specific histone modifications in targeting PARP-1 to chromatin. We showed that PARP-1 binds active histone marks, particularly H4K20me1, H3K4me1, H3K36me1, H3K9me1, and PARP-1 binding is inhibited by repressive marks, H3K9me2/3. We observed a positive correlation between PR-Set7, the sole H4K20 mono-methylase, and PARP-1 dependent gene expression programs, hinting at co-regulation during development. Upon heat stress, PARP-1 relocates from the Hsp70 promoter to its gene body, promoting gene activation. Furthermore, PARP-1 and PR-Set7 are necessary for the activation of Hsp70 and a subset of heat shock genes, with dynamic enrichment of H4K20me1 observed at their gene bodies during heat stress. Thus, H4K20me1 may be required for PARP-1 binding during PARP-1-dependent gene expression during development and heat shock. In conclusion, we propose that PARP-1, through its specific domain structures and interactions with histone marks, plays a significant role in the coordinated regulation of metabolic and developmental gene expression programs during development and the activation of heat shock genes during stress conditions. These findings deepen our understanding of PARP-1's role in gene regulation, with potential implications for further research in other cellular processes and disease.

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