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.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM102362-02
Application #
8598916
Study Section
Macromolecular Structure and Function B Study Section (MSFB)
Program Officer
Preusch, Peter C
Project Start
2013-01-01
Project End
2017-12-31
Budget Start
2014-01-01
Budget End
2014-12-31
Support Year
2
Fiscal Year
2014
Total Cost
$559,550
Indirect Cost
$198,550
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
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

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