In:
Nucleic Acids Research, Oxford University Press (OUP), Vol. 48, No. 12 ( 2020-07-09), p. 6715-6725
Kurzfassung:
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 & gt;25 types of DNA modification and damage.
Materialart:
Online-Ressource
ISSN:
0305-1048
,
1362-4962
Sprache:
Englisch
Verlag:
Oxford University Press (OUP)
Publikationsdatum:
2020
ZDB Id:
1472175-2
SSG:
12
