Nick-seq for single-nucleotide resolution genomic maps of DNA modifications and damage
Name
gkaa473.pdf
Description
Published version
Size
1.56 MB
Format
Unknown
Checksum (MD5)
26b96a1313b8c45932533cd933c840af
Author(s)
Cao, Bo
Wu, Xiaolin
Zhou, Jieliang
Wu, Hang
Liu, Lili
Zhang, Qinghua
DeMott, Michael S
Gu, Chen
Wang, Lianrong
You, Delin
Date Issued
July 2020
Journal
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Version
Final published version
Abstract
© 2020 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research. DNA damage and epigenetic marks are well established to have profound influences on genome stability and cell phenotype, yet there are few technologies to obtain high-resolution genomic maps of the many types of chemical modifications of DNA. Here we present Nick-seq for quantitative, sensitive, and accurate mapping of DNA modifications at single-nucleotide resolution across genomes. Pre-existing breaks are first blocked and DNA modifications are then converted enzymatically or chemically to strand-breaks for both 3′-extension by nick-translation to produce nuclease-resistant oligonucleotides and 3′-terminal transferase tailing. Following library preparation and next generation sequencing, the complementary datasets are mined with a custom workflow to increase sensitivity, specificity and accuracy of the map. The utility of Nick-seq is demonstrated with genomic maps of site-specific endonuclease strand-breaks in purified DNA from Eschericia coli, phosphorothioate epigenetics in Salmonella enterica Cerro 87, and oxidation-induced abasic sites in DNA from E. coli treated with a sublethal dose of hydrogen peroxide. Nick-seq applicability is demonstrated with strategies for >25 types of DNA modification and damage.
MIT Department
Massachusetts Institute of Technology. Department of Biological Engineering
Singapore-MIT Alliance in Research and Technology (SMART)
Massachusetts Institute of Technology. Center for Environmental Health Sciences
Terms of Use
Creative Commons Attribution NonCommercial License 4.0
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DOI of Published Version
https://doi.org/10.1093/NAR/GKAA473
