Apr 3, 2020

Natural genetic variation affecting transcription factor spacing at regulatory regions is generally well tolerated

BioRxiv : the Preprint Server for Biology
Z. ShenChristopher K Glass

Abstract

Regulation of gene expression requires the combinatorial binding of sequence-specific transcription factors (TFs) at promoters and enhancers. Single nucleotide polymorphisms (SNPs) and short insertions and deletions (InDels) can influence gene expression by altering the sequences of TF binding sites. Prior studies also showed that alterations in the spacing between TF binding sites can influence promoter and enhancer activity. However, the relative importance of altered TF spacing has not been systematically analyzed in the context of natural genetic variation. Here, we exploit millions of InDels provided by five diverse strains of mice to globally investigate the effects of altered spacing on TF binding and local histone acetylation in macrophages. We find that spacing alterations resulting from InDels are generally well tolerated in comparison to genetic variants that directly alter TF binding sites. These findings have implications for the interpretation of non-coding genetic variation and comparative analysis of regulatory elements across species.

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Mentioned in this Paper

Metabolic Process, Cellular
Neoplasm of Uncertain or Unknown Behavior of Bladder
Mitochondrial Inheritance
DNA, Mitochondrial
Neoplasms
Gene Deletion
Carcinoma in Situ of Bladder
Kidney
Bladder Tissue
Mitochondria

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