Transversions have larger regulatory effects than transitions

Abstract

BackgroundTransversions (Tv’s) are more likely to alter the amino acid sequence of proteins than transitions (Ts’s), and local deviations in the Ts:Tv ratio are indicative of evolutionary selection on genes. Whether the two different types of mutations have different effects in non-protein-coding sequences remains unknown. Genetic variants primarily impact gene expression by disrupting the binding of transcription factors (TFs) and other DNA-binding proteins. Because Tv’s cause larger changes in the shape of a DNA backbone, we hypothesized that Tv’s would have larger impacts on TF binding and gene expression.ResultsHere, we provide multiple lines of evidence demonstrating that Tv’s have larger impacts on regulatory DNA including analyses of TF binding motifs and allele-specific TF binding. In these analyses, we observed a depletion of Tv’s within TF binding motifs and TF binding sites. Using massively parallel population-scale reporter assays, we also provided empirical evidence that Tv’s have larger effects than Ts’s on the activity of human gene regulatory elements.ConclusionsTv’s are more likely to disrupt TF binding, resulting in larger changes in gene expression. Although the observed differences are small, these findings represent a novel, fundamental property of regulatory variation. Understanding the features of functional non-coding variation could be valuable for revealing the genetic underpinnings of complex traits and diseases in future studies.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3785-4) contains supplementary material, which is available to authorized users.

Dissecting the regulatory activity and sequence content of loci with exceptional numbers of transcription factor associations

“…Elements with 5-bp mutations exhibited slightly less activity than reference sequence elements on average ( Figure S13). We found the effects on activity of most mutations were highly correlated between strands ( Figure S14) and transversions tended to have more impact than transitions, as previously reported ( Figure S15) (Guo et al 2017). Furthermore, we successfully validated 14 high-impact mutations (including a gain-of-activity mutation) and 14 adjacent lowimpact control mutations with individual luciferase reporter experiments using two different plasmids that place the test element either upstream or downstream of the reporter (Figure S16-S17, Table S9).…”

Saturation mutagenesis of disease-associated regulatory elements

“…Despite our greater power for assaying transitions, transversions had larger absolute effect sizes (Wilcoxon Rank Sum test with continuity correction, p-value < 10 −16 , location shift 0.14). This observation supports a model were regulatory elements evolved some level of robustness to the more frequent transitional changes (as for coding sequences 39 ), and is consistent with previous research showing that transversions have a larger impact on TF motifs and allele-specific TF binding 40 .…”

Pan-cancer analysis of somatic mutations and epigenetic alterations in insulated neighbourhood boundaries

“…In general, the ratio of transitions versus transversions depends on the type of DNA element. In particular, the ratio in binding sites and regulatory regions is not well characterized, although we note recent results in germline mutations [41] that indicate that transversions have a slightly larger effect on DNA shape and transcription factor binding than transitions. Assuming that similar results can be generalised to somatic alterations, this finding suggests that transversions on CTCF motifs might have a stronger effect than transitions, which could hint towards a positive selection of transversions rather than transitions in insulated neighborhood boundaries in tumour cells, as these alterations are more likely to disrupt boundaries than transitions.…”