cisplatin-damaged gene locus-replicate 2-L-R1
Cisplatin is a DNA-targeting chemotherapeutic, yet its damaged gene loci are largely unexplored. We utilized a forward chemical genetics strategy to map 7578 cisplatin-damaged genes (CDGs) with >12 fold-enrichment from A549 human lung cancer cells, of which the highly associated signalling pathways include sperm motility, molecular mechanism of cancer, and protein kinase A signalling. The three most frequently cisplatinated penta-nucleotide motifs and genomic region are CTGGG, CCAGG and GCTGG, and promoter, respectively. Among the CDGs are 1330 enzyme, 747 transcription regulator and 486 transporter genes. Importantly, cisplatin targeted 306 protein kinase genes, accounting for 59% of putative protein kinase genes in the human genome, and 92 protein phosphatase genes. This indicates that cisplatin genome-wide disturbs protein phosphorylation. This data set contains the original sequencing data of two biological replicates, matching results to the hg38 genome, and the analysis results of the distribution of the damage areas identified by the two sequencing results.
Steps to reproduce
We used E.coli to express HMGB1-Abox (HMGB1a) protein, which can selectively bind to cisplatin crosslinked double–stranded DNA. Then we constructed the affinity microprobes via the interaction between His6-tag at the N-terminus of the HMGB1a and the nickel modified on the surface of the magnetic beads. By using this affinity microprobes, we can selectively capture platinum-bound DNA fragments from positive sample (DNA fragments obtained from A549 cells treated with cisplatin) and control sample (DNA fragments obtained from A549 cells without treatment) for sequencing. Then, by comparing the total reads of a specific gene in positive/control sample pair, we can identify cisplatin-damaged genes (CDGs).