Exploring the Human Genome for Functional Non-Coding Sequences and Variation: Implications for Understanding Peripheral Nerve Biology.

Abstract

The vast array of cells and tissues in the human body contain nearly identical genetic information, yet each tissue expresses only a subset of genes present in the genome. The precise spatiotemporal expression patterns of these genes are regulated by transcription factors, which bind to short sequences of DNA called transcription factor binding sites (TFBSs). While it is well-established that mutations within protein-coding sequences cause human disease, sequence variation within TFBSs (regulatory SNPs; rSNPs) can result in allele-specific differences in DNA binding affinity, which can also cause or modify disease phenotypes. Our objective was to identify rSNPs that impact regulatory function at loci important for peripheral nerve function. Such rSNPs represent excellent candidate modifier loci that may explain phenotypic variability in patients with peripheral neuropathies. A challenge in studying the effects of rSNPs on gene function is absent or incomplete catalogs of TFBSs. To address this, we developed a computational and functional pipeline to identify and characterize putative TFBSs. We utilized genome-wide sequence conservation to prioritize candidate regulatory regions that harbor a SNP. We assessed a pilot set of 159 regions on chromosomes 21, 22, and X for regulatory activity in cells relevant for the peripheral nerve. We identified 28 active regions, of which 13 showed allele-specific differences in regulatory activity. We next incorporated known transcription factor binding site information into our pipeline. The transcription factor SOX10 is essential for Schwann cell function and has a well-characterized consensus site. We assessed the allele-specific activity of 22 prioritized regions that contain a conserved SOX10 consensus site overlapping a SNP. We deeply characterized one