Abstract:
BACKGROUND:Transversions (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. RESULTS:Here, 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. CONCLUSIONS:Tv'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.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Guo C,McDowell IC,Nodzenski M,Scholtens DM,Allen AS,Lowe WL,Reddy TEdoi
10.1186/s12864-017-3785-4subject
Has Abstractpub_date
2017-05-19 00:00:00pages
394issue
1issn
1471-2164pii
10.1186/s12864-017-3785-4journal_volume
18pub_type
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