A Role for Non-B DNA Forming Sequences in Mediating Microlesions Causing Human Inherited Disease

Abstract

Missense/nonsense mutations and micro-deletions/micro-insertions of <21bp together represent ~76% of all mutations causing human inherited disease. Previous studies have shown that their occurrence is influenced by sequences capable of non-B DNA formation (direct, inverted and mirror repeats; G-quartets). We found that a greater than expected proportion (~21%) of both micro-deletions and micro-insertions occur within direct repeats and are explicable by slipped misalignment. A novel mutational mechanism, non-B DNA triplex formation followed by DNA repair, is proposed to explain ~5% of micro-deletions and microinsertions at mirror repeats. Further, G-quadruplex-forming sequences, direct and inverted repeats appear to play a prominent role in mediating missense mutations, whereas only direct and inverted repeats mediate nonsense mutations. We suggest a mutational mechanism involving slipped strand mispairing, slipped structure formation and DNA repair, to explain ~15% of missense and ~12% of nonsense mutations leading to the formation of perfect direct repeats from imperfect repeats, or to the extension of existing direct repeats. Similar proportions of missense and nonsense mutations were explicable by the mechanism of hairpin loop formation and DNA repair leading to the formation of perfect inverted repeats from imperfect repeats. The proposed mechanisms provide new insights into mutagenesis underlying pathogenic micro-lesions.

Non-canonical secondary structures arising from non-B-DNA motifs are determinants of mutagenesis

“…Our findings bring together and reinforce previous observations of indel enrichment at disparate non-B motifs in experimental systems (e.g. IRs 34,35,36,37 ; DRs 38,39 ; and G4s 40,35,41 .We thus conclude that primary sequence features, as represented by non-B DNA motifs, are collectively informative for predicting local mutability across many tissue types, predominantly of substitutions and indels. Is it the physical presence of a non-canonical secondary structure that mechanistically drives the increased likelihood of mutagenesis?…”

“…Partial correlation analysis reveals the association between somatic mutations and non-B motifs remains even after controlling for epigenetic marks and replication timing (Fig. S5), raising the possibility that non-B motifs are independent factors that could contribute to mutability 28,29,23,30 .To explore this in more depth we assessed the predictability of mutation density given the number of non-B motifs (as well as epigenetic features and replication time domains) by constructing models using linear regression and random forest regression (Fig. 2b, Fig.…”

Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error rate

“…With a genome-wide analysis of data generated by a sequencing instrument, we substantially expanded prior knowledge of this phenomenon gained by examination of plasmid constructs, disease-associated genes, and human genetic diversity 4,32,33,35 . Our most prominent observation, the high incidence of mismatches and deletion errors during sequencing of G4 motifs, is in line with these motifs harboring excessive disease-causing point mutations 34 and nucleotide variants (point mutations and indels combined 35 ) based on 1,000 Genomes Project data. Using the level of divergence (or diversity) as a proxy for germline mutation rates, we observed significantly larger SMRT polymerase slowdown and error rates within G4s with very high divergence as compared to G4s with very low divergence (diversity).…”

“…increase in chromosomal rearrangements, including those observed in cancer 30,31 . Moreover, the increased occurrence of point mutations at non-B DNA was demonstrated at individual loci in plasmid constructs (reviewed in 4,32,33 ), at disease-associated genes 34 , and among genetic variants from the 1,000 Genomes Project 35 . Because the effect of non-B DNA on mutagenesis is driven by both the inherent DNA sequence and polymerase fidelity 36 , we hypothesize that these structures can impact the efficiency and accuracy of DNA synthesis.…”

The Human Gene Mutation Database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies

“…They have served to demonstrate not only that human gene mutation is an inherently non-random process, but also that the nature, location and frequency of different types of mutation are shaped in large part by the local DNA sequence environment (Cooper et al 2011). Indeed, HGMD data have been instrumental in demonstrating that electron transfer reactions (Bacolla et al 2013), base-pair flexibility (Bacolla et al 2015) and non-B DNA forming sequences (Kamat et al 2016) all contribute to sequence context-dependent mutagenesis causing inherited disease. HGMD mutation data were used to demonstrate that many in-frame pathogenic variations perturb protein–protein interactions (Das et al 2014).…”