GSE159807 Mapping of DNA damage genome-wide at nucleotide resolution by circle damage sequencing (circle-damage-seq)

Contributors : Seung-Gi Jin ; Dean Pettinga ; Gerd P PfeiferSeries Type : OtherOrganism : Homo sapiens ; Mus musculusTo establish relationships between mutations, for example in cancer genomes, and possible mechanisms linked to DNA damage, it is necessary to know at what sequence positions of the genome the damage occurs. However, it has been challenging to specifically map DNA damage at the nucleotide level of resolution and genome-wide with high sensitivity. Here, we describe a new method, which we named circle damage sequencing (circle-damage-seq), to accomplish this goal. The method is based on circularization of DNA molecules and DNA damage-selective cleavage of the circularized DNA followed by adapter ligation and sequencing. Based on the design of this approach, only DNA damage-containing molecules are sequenced. We conducted proof-of-principle studies to show that mapping of ultraviolet B-induced cyclobutane pyrimidine dimers (CPDs) can easily be achieved and show a specific tetranucleotide sequence context for CPDs (5 ’PyPyPyT/A) with no further sequence enrichment outside of this context. Our approach shows strongly reduced levels of CPDs near transcription start sites and a spike of this damage near the transcription end sites of genes. We then show that 1,N6-etheno-deoxyadenosine DNA adducts created after treatment of cells with the lipid peroxidation product 4-hydroxynonenal can be mapped genome-wide at adenine positions and obtained a preferential sequence c...
Source: GEO: Gene Expression Omnibus - Category: Genetics & Stem Cells Tags: Other Homo sapiens Mus musculus Source Type: research