A vital challenge that all cells and organisms constantly have to face is numerous harmful DNA lesions in the genome caused by endogenous and environmental agents. It is important that DNA lesions within the highly transcribed genome are dealt with in a specific and efficient manner to prevent stalling of the transcriptional machinery and cell death. A body of evidence indicates RNA polymerase II (Pol II) is a highly selective DNA damage sensor, since it constantly scans the transcribed genome during transcription. Biochemical and genetic studies indicate that the actions of Pol II when encountering DNA damage vary dramatically for different DNA lesions and can be summarized in the following three major categories: Pol II transcription bypass; Pol II backtracking and TFIIS-mediated cleavage; Pol II stalling and initiation of transcription-coupled repair (TCR). However, little is known about the molecular mechanisms by which Pol II senses different DNA damage and signals different downstream processing pathways. We hypothesize that DNA lesions frequently modify bases leading to changes in the interaction patterns between the template DNA, incoming substrate, and Pol II residues. These changes in the interaction patterns, coupled with the chemical nature of DNA lesions, direct Pol II to different processes: bypass, backtracking, and stalling. A clear understanding of the molecular details of the relevant protein-nucleic acid and protein-protein interactions will uncover the mechanisms underlying DNA damage processing pathways. The goal of this research project is to understand how the transcription machinery responds to DNA damage through a multidisciplinary approach that combines structural biology, chemical biology, biophysics, biochemistry, computational biology, and genetics.

Public Health Relevance

A number of severe human diseases including Cockayne Syndrome, Ultraviolet-Sensitive Syndrome, Cerebro-Oculo-Facio-Skeletal Syndrome, Xeroderma Pigmentosum, and Trichothiodystrophy stem from defects in transcription-coupled DNA damage processing pathways. The goal of the proposed research is to elucidate the molecular mechanisms of transcription-coupled DNA damage processing pathways through a multidisciplinary approach, combining structural biology, chemical biology, biochemical, computational biology, and genetic methods. Deciphering the mechanisms of these processes will contribute to our understanding of the cause of premature aging, Cockayne Syndrome, and other related diseases and could be useful for developing potential clinical treatments.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Macromolecular Structure and Function B Study Section (MSFB)
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Preusch, Peter
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University of California San Diego
Schools of Pharmacy
La Jolla
United States
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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
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:
Da, Lin-Tai; Pardo-Avila, Fátima; Xu, Liang et al. (2016) Bridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue. Nat Commun 7:11244
Shin, Ji Hyun; Xu, Liang; Wang, Dong (2016) RNA polymerase II acts as a selective sensor for DNA lesions and endogenous DNA modifications. Transcription 7:57-62
Hwang, Candy S; Xu, Liang; Wang, Wei et al. (2016) Functional interplay between NTP leaving group and base pair recognition during RNA polymerase II nucleotide incorporation revealed by methylene substitution. Nucleic Acids Res 44:3820-8
Xu, Liang; Wang, Wei; Gotte, Deanna et al. (2016) RNA polymerase II senses obstruction in the DNA minor groove via a conserved sensor motif. Proc Natl Acad Sci U S A 113:12426-12431
Walmacq, Celine; Wang, Lanfeng; Chong, Jenny et al. (2015) Mechanism of RNA polymerase II bypass of oxidative cyclopurine DNA lesions. Proc Natl Acad Sci U S A 112:E410-9
Xu, Liang; Wang, Wei; Chong, Jenny et al. (2015) RNA polymerase II transcriptional fidelity control and its functional interplay with DNA modifications. Crit Rev Biochem Mol Biol 50:503-19

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