Proteome-Wide Analysis of Disease-Associated SNPs That Show Allele-Specific Transcription Factor Binding

Abstract

A causative role for single nucleotide polymorphisms (SNPs) in many genetic disorders has become evident through numerous genome-wide association studies. However, identification of these common causal variants and the molecular mechanisms underlying these associations remains a major challenge. Differential transcription factor binding at a SNP resulting in altered gene expression is one possible mechanism. Here we apply PWAS (“proteome-wide analysis of SNPs”), a methodology based on quantitative mass spectrometry that enables rapid screening of SNPs for differential transcription factor binding, to 12 SNPs that are highly associated with type 1 diabetes at the IL2RA locus, encoding the interleukin-2 receptor CD25. We report differential, allele-specific binding of the transcription factors RUNX1, LEF1, CREB, and TFAP4 to IL2RA SNPs rs12722508*A, rs12722522*C, rs41295061*A, and rs2104286*A and demonstrate the functional influence of RUNX1 at rs12722508 by reporter gene assay. Thus, PWAS may be able to contribute to our understanding of the molecular consequences of human genetic variability underpinning susceptibility to multi-factorial disease.

Decoding neuroproteomics: integrating the genome, translatome and functional anatomy

“…A recent survey of the mouse CNS revealed 1,300 ASE transcripts that favour the maternal allele during brain development, while in the adult the bias shifts toward the paternal allele 85 . Mass-spectrometry has also been used to identify and assess levels of allele-specific transcription factor binding (ASB) and define allelic regions of the genome that are disease-associated 86 . Such analyses are appealing due to potential cascade effects caused by ASE/ASB; differential expression or activity of an allelic transcription- or splicing-factor, for example, may have a substantial impact on downstream cellular processes.…”

Dissecting the Causal Genetic Mechanisms of Coronary Heart Disease

“…Complementary approaches to capture this depth of signaling at sites of genetic variation include DNA-affinity pulldown-mass-spectrometry. 86 These studies have applied allele-specific biotinylated oligo-precipitation to capture TF protein binding complexes to regulatory SNPs, which can be identified from eluate fractions using standard LC-MS mass spectrometry. If applied to cross-linked chromatin samples at distinct cellular states and time points, this approach has the potential to provide a more comprehensive view of functional TF complexes at GWAS loci.…”

Contribution OF Non-HLA Genes to Juvenile Idiopathic Arthritis Susceptibility

“…Недавно Butter и соавт. [17] сообщили о дифференциальном аллелеспецифическом связывании транскрипционного фактора TFAP4 с аллелем A маркера rs2104286. Данный факт является экспериментальным свидетельством возможных cis-регуляторных эффектов данного варианта на дифференциальную экспрессию гена IL2RA.…”