title: Mapping genomic hotspots of DNA damage by a single-strand-DNA-compatible and strand-specific ChIP-seq method.
abstract: Spontaneous DNA damage may occur nonrandomly in the genome, especially when genome maintenance mechanisms are undermined. We developed single-strand DNA (ssDNA)-associated protein immunoprecipitation followed by sequencing (SPI-seq) to map genomic hotspots of DNA damage. We demonstrated this method with Rad52, a homologous recombination repair protein, which binds to ssDNA formed at DNA lesions. SPI-seq faithfully detected, in fission yeast, Rad52 enrichment at artificially induced double-strand breaks (DSBs) as well as endogenously programmed DSBs for mating-type switching. Applying Rad52 SPI-seq to fission yeast mutants defective in DNA helicase Pfh1 or histone H3K56 deacetylase Hst4, led to global views of DNA lesion hotspots emerging in these mutants. We also found serendipitously that histone dosage aberration can activate retrotransposon Tf2 and cause the accumulation of a Tf2 cDNA species bound by Rad52. SPI-seq should be widely applicable for mapping sites of DNA damage and uncovering the causes of genome instability.
authors.affiliation: Graduate Program, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China.
authors.forename: Zhi-Xiong
authors.initials: ZX
authors.lastname: Zhou
authors.forename: Mei-Jun
authors.initials: MJ
authors.lastname: Zhang
authors.forename: Xu
authors.initials: X
authors.lastname: Peng
authors.forename: Yuko
authors.initials: Y
authors.lastname: Takayama
authors.forename: Xing-Ya
authors.initials: XY
authors.lastname: Xu
authors.forename: Ling-Zhi
authors.initials: LZ
authors.lastname: Huang
authors.forename: Li-Lin
authors.initials: LL
authors.lastname: Du
mesh_terms: D047369:Chromatin Immunoprecipitation / Q000379:methods; D002874:Chromosome Mapping; D053903:DNA Breaks, Double-Stranded; D004249:DNA Damage; D004265:DNA Helicases / Q000235:genetics; D004261:DNA Replication; D004277:DNA, Single-Stranded; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006655:Histone Deacetylases / Q000235:genetics; D006657:Histones / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding; D051721:Rad52 DNA Repair and Recombination Protein / Q000378:metabolism; D012568:Schizosaccharomyces / Q000235:genetics / Q000378:metabolism; D029702:Schizosaccharomyces pombe Proteins / Q000235:genetics / Q000378:metabolism
chemical_list: D004277:DNA, Single-Stranded; D006657:Histones; D051721:Rad52 DNA Repair and Recombination Protein; D029702:Schizosaccharomyces pombe Proteins; C083145:Tf2-6 protein, S pombe; C530050:Hst4 protein, S pombe; D006655:Histone Deacetylases; D004265:DNA Helicases; C468287:Pfh1 protein, S pombe