A Genome-Wide Screen for Genetic Variants That Modify the Recruitment of REST to Its Target Genes

Abstract

Increasing numbers of human diseases are being linked to genetic variants, but our understanding of the mechanistic links leading from DNA sequence to disease phenotype is limited. The majority of disease-causing nucleotide variants fall within the non-protein-coding portion of the genome, making it likely that they act by altering gene regulatory sequences. We hypothesised that SNPs within the binding sites of the transcriptional repressor REST alter the degree of repression of target genes. Given that changes in the effective concentration of REST contribute to several pathologies—various cancers, Huntington's disease, cardiac hypertrophy, vascular smooth muscle proliferation—these SNPs should alter disease-susceptibility in carriers. We devised a strategy to identify SNPs that affect the recruitment of REST to target genes through the alteration of its DNA recognition element, the RE1. A multi-step screen combining genetic, genomic, and experimental filters yielded 56 polymorphic RE1 sequences with robust and statistically significant differences of affinity between alleles. These SNPs have a considerable effect on the the functional recruitment of REST to DNA in a range of in vitro, reporter gene, and in vivo analyses. Furthermore, we observe allele-specific biases in deeply sequenced chromatin immunoprecipitation data, consistent with predicted differenes in RE1 affinity. Amongst the targets of polymorphic RE1 elements are important disease genes including NPPA, PTPRT, and CDH4. Thus, considerable genetic variation exists in the DNA motifs that connect gene regulatory networks. Recently available ChIP–seq data allow the annotation of human genetic polymorphisms with regulatory information to generate prior hypotheses about their disease-causing mechanism.

A CRISPR Path to Engineering New Genetic Mouse Models for Cardiovascular Research

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News about the Role of the Transcription Factor REST in Neurons: From Physiology to Pathology

“…Although present in all, low REST is not homogeneous but somewhat variable in distinct types of mature neurons. Such differences contribute, directly and indirectly, to the observed variabilities of phenotype and function, observed during their life in groups and single neurons [6]. The level in neurons is not fully stable but increases transiently in some physiological states, for example, during intense stimulation [3].…”

Identification and Initial Functional Characterization of a Human Vascular Cell–Enriched Long Noncoding RNA

“…First, genome-wide RNA expression studies show widespread transcription across the mouse and human genomes with roughly equal amounts of polyadenylated and nonpolyadenylated RNA 2–7 . Second, the combined efforts of the ENC yclopedia O f D NA E lements (ENCODE) Consortium and many other labs have revealed the existence of millions of codes that punctuate the human genome, most notably codes for transcription factor binding 8–12 . These findings, coupled with the notion that much of the human genome is functional with 50%–90% comprising transcribed sequences 13, 14 , debunk the concept of “junk DNA” and point to a genome replete with information essential for human life.…”