Structural effects of linkage disequilibrium on the transcriptome.

Area of Science:

• Genomics
• Molecular Biology
• RNA Structure

Background:

• Single nucleotide polymorphisms (SNPs) frequently occur in noncoding genomic regions and are linked to human diseases via genome-wide association studies (GWAS).
• Disease-associated SNPs in the 5' untranslated region (UTR) of the Ferritin Light Chain (FTL) gene are predicted to modify mRNA structural ensembles.

Purpose of the Study:

• To investigate the impact of disease-associated SNPs on mRNA structure using high-accuracy chemical mapping.
• To validate computational predictions of SNP-induced structural changes and the efficacy of rescue mutations.
• To explore the concept of 'RiboSNitch' elements and RNA structure-stabilizing haplotypes (SSHs) in the human genome.

Main Methods:

• High-accuracy single nucleotide resolution chemical mapping of mRNA structures.
• Computational prediction of mRNA structural ensembles.
• Analysis of SNP-associated structural changes and rescue mutations in the FTL gene 5' UTR.
• Genome-wide identification of SNP pairs forming RNA structure-stabilizing haplotypes (SSHs) in UTRs.

Main Results:

• Experimental data confirmed that disease-associated SNPs in the FTL 5' UTR significantly alter the mRNA structural ensemble, matching computational predictions.
• Six identified rescue mutations were computationally predicted and experimentally confirmed to restore the mRNA to its wild-type structure.
• The FTL 5' UTR was confirmed as a 'RiboSNitch', where SNPs induce structural changes that likely regulate translation, analogous to bacterial Riboswitches.
• 484 SNP pairs forming SSHs were identified in human UTRs, with eight of ten SSH-containing transcripts showing stabilized RNA-protein binding sites.
• The prevalence of SSHs suggests evolutionary conservation of haplotypes to prevent deleterious RiboSNitch formation.

Conclusions:

• Disease-associated SNPs can create functional RNA elements ('RiboSNitches') by altering mRNA structures, impacting gene regulation.
• RNA structure-stabilizing haplotypes (SSHs) are prevalent in the human genome and can stabilize RNA-protein interactions.
• Evolutionary conservation of specific haplotypes may be driven by the need to avoid the formation of disease-associated RiboSNitches.