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Nat Methods. 2015 Mar;12(3):251-7, 3 p following 257. doi: 10.1038/nmeth.3259. Epub 2015 Jan 26.

Ribose-seq: global mapping of ribonucleotides embedded in genomic DNA.

Author information

1
School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA.
2
Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora, Colorado, USA.

Abstract

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 for capturing unique products generated by alkaline cleavage of DNA at embedded ribonucleotides. High-throughput sequencing of these fragments in DNA from the yeast Saccharomyces cerevisiae 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.

PMID:
25622106
PMCID:
PMC4686381
DOI:
10.1038/nmeth.3259
[Indexed for MEDLINE]
Free PMC Article

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