Enhanced DNA repair of bleomycin-induced 3′-phosphoglycolate termini at the transcription start sites of actively transcribed genes in human cells

Abstract

The anti-tumour agent, bleomycin, cleaves DNA to give 3′-phosphoglycolate and 5′-phosphate termini. The removal of 3′-phosphoglycolate to give 3′-OH ends is a very important step in the DNA repair of these lesions. In this study, next-generation DNA sequencing was utilised to investigate the repair of these 3′-phosphoglycolate termini at the transcription start sites (TSSs) of genes in HeLa cells. The 143,600 identified human TSSs in HeLa cells comprised 82,596 non-transcribed genes and 61,004 transcribed genes; and the transcribed genes were divided into quintiles of 12,201 genes comprising the top 20%, 20–40%, 40–60%, 60–80%, 80–100% of expressed genes. Repair of bleomycin-induced 3′-phosphoglycolate termini was enhanced at actively transcribed genes. The top 20% and 20–40% quintiles had a very similar level of enhanced repair, the 40–60% quintile was intermediate, while the 60–80% and 80–100% quintiles were close to the low level of enhancement found in non-transcribed genes. There were also interesting differences regarding bleomycin repair on the sense and antisense strands of DNA at TSSs. The sense strand had highly enhanced repair between 0 and 250bp relative to the TSS, while for the antisense strand highly enhanced repair was between 150 and 450bp. Repair of DNA damage is a major mechanism of resistance to anti-tumour drugs and this study provides an insight into this process in human tumour cells.