The long-term goal of this project is to understand how DNA lesions are recognized and repaired in the transcribed genome. Harmful DNA lesions, caused by endogenous and environmental agents, must be promptly repaired in order to avoid deleterious threats to genome integrity. Transcription-coupled DNA repair (TCR) is an important DNA repair pathway because it removes DNA lesions within the transcribed genome in a transcription-coupled manner. However, the molecular mechanism of eukaryotic TCR remains elusive. There is evidence that Cockayne Syndrome B protein (CSB), a master TCR coordinator, is recruited to the DNA lesion- arrested Pol II site and plays a key role in the initiation of eukaryotic TCR. However, there is a fundamental gap in understanding the molecular basis of CSB recruitment to the DNA lesion-arrested Pol II. A long-standing question in the field is how CSB recognizes and interacts with the DNA lesion-arrested Pol II and subsequently initiates TCR. The objective of this proposal is to elucidate the roles of CSB in TCR initiation. The central hypothesis is that CSB recognizes the structural features of specific Pol II domains and the nucleic acid scaffold in arrested Pol II complexes, undergoes significant conformational changes, and is subject to autoregulation by its own regulatory motifs. This hypothesis has been formulated on the basis of preliminary data produced in the applicants' laboratories and will be tested by performing structural and functional characterizations of the interactions between CSB and the arrested Pol II complex. This approach is innovative, because it utilizes a novel hybrid method that combines X-ray crystallography, Cryo-EM, biophysics, biochemistry, and genetics. The proposed research is significant and groundbreaking because novel knowledge and structures obtained from this proposal will have a transformative impact on the field of DNA repair and vertically advance the understanding of how transcription-coupled repair is initiated. Ultimately, such knowledge will provide a framework for developing novel TCR targeting therapeutics against cancer and other human diseases.

Public Health Relevance

The proposed research is highly relevant to public health and NIH's mission because transcription-coupled repair (TCR) is an important pathway for removing harmful DNA lesions in the transcribed genome and a critical drug target pathway for anticancer chemotherapy. Mutations in the CSB protein cause several human diseases including Cockayne Syndrome, Cerebro-Oculo-Facio-Skeletal Syndrome, and Ultraviolet?Sensitive Syndrome. This research will provide novel mechanistic insights into the cause of Cockayne Syndrome and other related diseases and provide a framework for developing novel TCR targeting therapeutics against cancer and other human diseases.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM102362-07
Application #
9637397
Study Section
Macromolecular Structure and Function C Study Section (MSFC)
Program Officer
Willis, Kristine Amalee
Project Start
2013-01-01
Project End
2022-01-31
Budget Start
2019-02-01
Budget End
2020-01-31
Support Year
7
Fiscal Year
2019
Total Cost
Indirect Cost
Name
University of California, San Diego
Department
Pharmacology
Type
Schools of Pharmacy
DUNS #
804355790
City
La Jolla
State
CA
Country
United States
Zip Code
92093
Wang, Wei; Walmacq, Celine; Chong, Jenny et al. (2018) Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II. Proc Natl Acad Sci U S A 115:E2538-E2545
Sanz-Murillo, Marta; Xu, Jun; Belogurov, Georgiy A et al. (2018) Structural basis of RNA polymerase I stalling at UV light-induced DNA damage. Proc Natl Acad Sci U S A 115:8972-8977
Wang, Wei; Xu, Jun; Chong, Jenny et al. (2018) Structural basis of DNA lesion recognition for eukaryotic transcription-coupled nucleotide excision repair. DNA Repair (Amst) :
Local, Andrea; Huang, Hui; Albuquerque, Claudio P et al. (2018) Identification of H3K4me1-associated proteins at mammalian enhancers. Nat Genet 50:73-82
Shin, Ji Hyun; Xu, Liang; Wang, Dong (2017) Mechanism of transcription-coupled DNA modification recognition. Cell Biosci 7:9
Xu, Liang; Wang, Wei; Wu, Jiabin et al. (2017) Mechanism of DNA alkylation-induced transcriptional stalling, lesion bypass, and mutagenesis. Proc Natl Acad Sci U S A 114:E7082-E7091
Xu, Jun; Lahiri, Indrajit; Wang, Wei et al. (2017) Structural basis for the initiation of eukaryotic transcription-coupled DNA repair. Nature 551:653-657
Wang, Wei; Xu, Liang; Hu, Lulu et al. (2017) Epigenetic DNA Modification N6-Methyladenine Causes Site-Specific RNA Polymerase II Transcriptional Pausing. J Am Chem Soc 139:14436-14442
Zhang, Lu; Pardo-Avila, Fátima; Unarta, Ilona Christy et al. (2016) Elucidation of the Dynamics of Transcription Elongation by RNA Polymerase II using Kinetic Network Models. Acc Chem Res 49:687-94
Yamamoto, Kenta; Wang, Jiguang; Sprinzen, Lisa et al. (2016) Kinase-dead ATM protein is highly oncogenic and can be preferentially targeted by Topo-isomerase I inhibitors. Elife 5:

Showing the most recent 10 out of 32 publications