Ribose-seq: global mapping of ribonucleotides embedded in genomic DNA. Abundant ribonucleotide incorporation in DNA during replication and repair has profound consequences for genome stability, but the global distribution of ribonucleotide incorporation is unknown. We developed Ribose-seq, a method to capture unique products generated by alkaline cleavage of DNA at embedded ribonucleotides. High-throughput sequencing of these fragments from yeast Saccharomyces cerevisiae DNA revealed widespread ribonucleotide distribution with a strong preference for cytidine and guanosine, and identified hotspots of ribonucleotide incorporation in nuclear and mitochondrial DNA. Ribonucleotides were primarily incorporated on the newly-synthesized leading strand of nuclear DNA and were present upstream of G+C-rich tracts in the mitochondrial genome. Ribose-seq is a powerful tool for the systematic profiling of ribonucleotide incorporation in genomic DNA.
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- Xu, Penghao; Storici, Francesca: RESCOT: restriction enzyme set and combination optimization tools for rNMP capture techniques (2021)