Genome-wide Nucleotide-Resolution Mapping of DNA Replication Patterns, Single-Strand Breaks, and Lesions by GLOE-Seq

Summary

DNA single-strand breaks (SSBs) are among the most common lesions in the genome, arising spontaneously and as intermediates of many DNA transactions. Nevertheless, in contrast to double-strand breaks (DSBs), their distribution in the genome has hardly been addressed in a meaningful way. We now present a technique based on genome-wide ligation of 3′-OH ends followed by sequencing (GLOE-Seq) and an associated computational pipeline designed for capturing SSBs but versatile enough to be applied to any lesion convertible into a free 3′-OH terminus. We demonstrate its applicability to mapping of Okazaki fragments without prior size selection and provide insight into the relative contributions of DNA ligase 1 and ligase 3 to Okazaki fragment maturation in human cells. In addition, our analysis reveals biases and asymmetries in the distribution of spontaneous SSBs in yeast and human chromatin, distinct from the patterns of DSBs.

Graphical Abstract

Highlights

• •

  GLOE-Seq detects 3′-OH ends with nucleotide resolution in purified genomic DNA

• •

  GLOE-Seq maps single-strand breaks, lesions, and replication and repair intermediates

• •

  GLOE-Seq reveals insight into the use of ligases 1 and 3 in human cells

• •

  GLOE-Seq detects asymmetries in spontaneous nicks in yeast and human chromatin

Abstract

We present a method for genome-wide, nucleotide-resolution mapping of DNA single-strand breaks in purified genomic DNA based on capture of 3′-OH ends followed by sequencing (GLOE-Seq). We validate the method and demonstrate its applicability to mapping of human and yeast Okazaki fragments, spontaneous single-strand breaks, and various other DNA lesions.