Abstract
UV radiation may lead to melanoma and nonmelanoma skin cancers by causing helix-distorting DNA damage such as cyclobutane pyrimidine dimers (CPDs). These DNA lesions, if located in important genes and not repaired promptly, are mutagenic and may eventually result in carcinogenesis. Examining CPD formation and repair processes across the genome can shed light on the mutagenesis mechanisms associated with UV damage in relevant cancers. We recently developed CPD-Seq, a high-throughput and single-nucleotide resolution sequencing technique that can specifically capture UV-induced CPD lesions across the genome. This novel technique has been increasingly used in studies of UV damage and can be adapted to sequence other clinically relevant DNA lesions. Although the library preparation protocol has been established, a systematic protocol to analyze CPD-Seq data has not been described yet. To streamline the various general or specific analysis steps, we developed a protocol named CPDSeqer to assist researchers with CPD-Seq data processing. CPDSeqer can accommodate both a single- and multiple-sample experimental design, and it allows both genome-wide analyses and regional scrutiny (such as of suspected UV damage hotspots). The runtime of CPDSeqer scales with raw data size and takes roughly 4 h per sample with the possibility of acceleration by parallel computing. Various guiding graphics are generated to help diagnose the performance of the experiment and inform regional enrichment of CPD formation. UV damage comparison analyses are set forth in three analysis scenarios, and the resulting HTML pages report damage directional trends and statistical significance. CPDSeqer can be accessed at https://github.com/shengqh/cpdseqer.
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Data availability
All datasets (GSE1034875, GSE799773 and GSE1192496) used in the demonstration for this protocol are available through the NCBI Short Read Archive (https://www.ncbi.nlm.nih.gov/sra). All figures used in this article are original. All preprocessed resource files listed in Supplementary Data 1 are available at https://cqsweb.app.vumc.org/Data/cpdseqer/.
Code availability
This protocol, including all scripts (Shell, Python and R), is hosted at https://github.com/shengqh/cpdseqer. A comprehensive test case involving all 17 steps entails an empirical CPD-Seq dataset and corresponding stepwise testing code scripts, which are available at https://cqsweb.app.vumc.org/Data/cpdseqer/.
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Acknowledgements
This study was supported by a Cancer Center Support Grant (P30CA118100) and R01ES030993-01A1 from the National Cancer Institute, funding from the National Institutes of Health (R21ES029302), a pilot grant from the UNM Center for Metals in Biology and Medicine (P20GM130422), the Bioinformatics Shared Resources and the Biostatistics Shared Resources at The Comprehensive Cancer Center. None of the funding bodies were involved in the study design; data collection, analysis or interpretation; or writing of the manuscript.
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Contributions
Q.S., H.Y. and L.J. developed code for the protocol. M.D. and J.H. performed protocol testing. H.K. provided statistical support. J.J.W. and P.M. provided knowledge support for CPD-Seq. Y.G., P.M., H.Y. and S.N. wrote the manuscript. Y.G. and P.M. supervised the project.
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Peer review information Nature Protocols thanks Ashby J. Morrison, Anna R. Poetsch and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.
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Related links
Key references using this protocol
Mao, P. et al. Nat. Commun. 9, 2626 (2018): https://doi.org/10.1038/s41467-018-05064-0
Mao, P. et al. Genome Res. 30, 12–21 (2020): https://doi.org/10.1101/gr.253146.119
Duan, M. et al. Proc. Natl Acad. Sci. USA 117, 18608–18616 (2020): https://doi.org/10.1073/pnas.2003868117
Supplementary information
Supplementary Data 1
Inventory of pre-compiled resources files for CPDSeqer. Includes file name, download link, brief description and applicable steps of BED files and naked DNA normalization files.
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Sheng, Q., Yu, H., Duan, M. et al. A streamlined solution for processing, elucidating and quality control of cyclobutane pyrimidine dimer sequencing data. Nat Protoc 16, 2190–2212 (2021). https://doi.org/10.1038/s41596-021-00496-3
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DOI: https://doi.org/10.1038/s41596-021-00496-3
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