Exploring the SSBreakome: genome‐wide mapping of DNA single‐strand breaks by next‐generation sequencing

Abstract

Mapping the genome-wide distribution of DNA lesions is key to understanding damage signalling and DNA repair in the context of genome and chromatin structure. Analytical tools based on high-throughput next-generation sequencing have revolutionized our progress with such investigations, and numerous methods are now available for various base lesions and modifications as well as for DNA double-strand breaks. Considering that single-strand breaks are by far the most common type of lesion and arise not only from exposure to exogenous DNA-damaging agents, but also as obligatory intermediates of DNA replication, recombination and repair, it is surprising that our insight into their genome-wide patterns, that is the 'SSBreakome', has remained rather obscure until recently, due to a lack of suitable mapping technology. Here we briefly review classical methods for analysing single-strand breaks and discuss and compare in detail a series of recently developed high-resolution approaches for the genome-wide mapping of these lesions, their advantages and limitations and how they have already provided valuable insight into the impact of this type of damage on the genome.

Genome-wide analysis of 8-oxo-7,8-dihydro-2'-deoxyguanosine at single-nucleotide resolution unveils reduced occurrence of oxidative damage at G-quadruplex sites

“…Therefore, it is difficult to assess and compare the specificity of low-resolution methods. Although other single nucleotide resolution sequencing methods for AP sites ( 44 ) and single strand breaks ( 45 ) could also be used for OGs if combined with OGG1 or FPG (and APE1), to the best of our knowledge, only click-code-seq had detected OGs at single-nucleotide resolution in yeast ( 25 ). Notably, click-code-seq used a G-derivate nucleotide analog to fill the gap generated by FPG and APE1, thus the detected damage sites were nearly exclusively Gs ( 25 ).…”

SSBlazer: a genome-wide nucleotide-resolution model for predicting single-strand break sites

“…The successful construction of SSBlazer has enabled a plethora of applications related to SSBs. SSB frequency is considered an implicit feature of genomic integrity [ 32 ], which could be linked to differences in the evolutionary process across diverse species. Cross-species evaluation in human and mouse datasets indicated that SSBs across diverse species might share similar genomic patterns.…”

Common occurrence of hotspots of single strand DNA breaks at transcriptional start sites

“…Unrepaired or improperly repaired DNA damage can lead to serious consequences to the cell and whole ogranism, as shown by the vast body of evidence that connects DNA damage to aging, cancer, neurological and many other diseases [ 2 – 4 ]. The cornerstone importance of DNA damage for basic biology and human disease has created significant amount of research interest into analysis of various types of DNA damage at the genome level [ 5 – 8 ] in order to understand the intricate details of how different lesions impact cell physiology. Recently, our group has published the development and application of SSiNGLe and SSiNGLe-AP methods for high-resolution genome-wide profiling of two most abundant types of DNA damage, single-strand DNA breaks (SSBs) and abasic (AP) sites respectively [ 9 , 10 ].…”