Allelic expression mapping across cell lineages reveal repressor disruption among disease SNPs
Transcriptomics Dataset
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| Accession | GSE53837 |
| Title | Allelic expression mapping across cell lineages reveal repressor disruption among disease SNPs |
| Description | Most variants associated to diseases are located in non-coding regions of the genome, and are thought to be regulatory in nature. Cis-regulatory SNPs (cis-rSNPs) impacting transcription can be identified through the mapping of differences in allelic expression (AE). We mapped common cis-rSNPs of protein coding and non-coding genes in 3 distinct cell-types. We show 70%% sharing across tissues and similar genetically controlled transcription for protein-coding genes and lincRNAs. Candidate cis-rSNPs altering the expression of 42 non-coding RNA overlap SNPs underlying GWAS associations for 39 diseases. We uncover a new class of cis-rSNPs leading to disruption of footprint-derived de novo motifs, predominantly bind by repressive factors and implicated in disease susceptibility through overlaps with GWAS SNPs. Finally, we provide proof-of-principle for a new approach for genome-wide functional validation of transcription factor SNP interactions. We perturbed NFB action in lymphoblasts and identified 489 cis-regulated transcripts with altered AE after NFkB perturbation. Altogether, we performed a comprehensive analysis of cis-variation in four cell-populations, and provide new tools for the identification of functional variants associated to complex diseases. |
| Landing Page | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53837 |
| Repository | Gene Expression Omnibus |
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