Mapping genomic hotspots of DNA damage by a single-strand-DNA-compatible and strand-specific ChIP-seq method

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...

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Bibliographic Details
Published in:Genome research 2013-04, Vol.23 (4), p.705-715
Main Authors: Zhou, Zhi-Xiong, Zhang, Mei-Jun, Peng, Xu, Takayama, Yuko, Xu, Xing-Ya, Huang, Ling-Zhi, Du, Li-Lin
Format: Article
Language:English
Subjects:
Chromatin Immunoprecipitation - methods
Chromosome Mapping
DNA Breaks, Double-Stranded
DNA Damage
DNA Helicases - genetics
DNA Replication
DNA, Single-Stranded
Genomics
High-Throughput Nucleotide Sequencing - methods
Histone Deacetylases - genetics
Histones - genetics
Histones - metabolism
Method
Protein Binding
Rad52 DNA Repair and Recombination Protein - metabolism
Schizosaccharomyces - genetics
Schizosaccharomyces - metabolism
Schizosaccharomyces pombe
Schizosaccharomyces pombe Proteins - genetics
Schizosaccharomyces pombe Proteins - metabolism
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Summary: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.
ISSN:1088-9051
1549-5469
DOI:10.1101/gr.146357.112