Mapping Ribonucleotides Incorporated into DNA by Hydrolytic End-Sequencing

Methods Mol Biol. 2018:1672:329-345. doi: 10.1007/978-1-4939-7306-4_23.

Abstract

Ribonucleotides embedded within DNA render the DNA sensitive to the formation of single-stranded breaks under alkali conditions. Here, we describe a next-generation sequencing method called hydrolytic end sequencing (HydEn-seq) to map ribonucleotides inserted into the genome of Saccharomyce cerevisiae strains deficient in ribonucleotide excision repair. We use this method to map several genomic features in wild-type and replicase variant yeast strains.

Keywords: Bioinformatics; DNA polymerase; DNA repair; DNA replication; Genomics; HydEn-seq; Next-generation sequencing; RNase H2; Ribonucleotide excision repair.

Publication types

  • Research Support, N.I.H., Intramural

MeSH terms

  • Computational Biology / methods
  • DNA Repair
  • DNA Replication*
  • DNA* / isolation & purification
  • DNA* / metabolism
  • DNA, Fungal / isolation & purification
  • Gene Library
  • Genomics / methods
  • High-Throughput Nucleotide Sequencing*
  • Hydrolysis
  • Ribonuclease H / metabolism
  • Ribonucleotides*
  • Yeasts

Substances

  • DNA, Fungal
  • Ribonucleotides
  • DNA
  • Ribonuclease H