ArticleRNA (New York, N.Y.)2012
Structural effects of linkage disequilibrium on the transcriptome.
Article in RNA (New York, N.Y.), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
What it found
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
28 citing papers in PubMed, 47 citations in OpenAlex.
- AStruct: detection of allele-specific RNA secondary structure in structuromic probing data.BMC bioinformatics · 2024Article
- Disease-associated human genetic variation through the lens of precursor and mature RNA structure.Human genetics · 2022Review
- Experimental demonstration and pan-structurome prediction of climate-associated riboSNitches in Arabidopsis.Genome biology · 2022Article
- A genetic variant alters the secondary structure of the lncRNA H19 and is associated with dilated cardiomyopathy.RNA biology · 2021Article
- Article
- Identification and analysis of RNA structural disruptions induced by single nucleotide variants using Riprap and RiboSNitchDB.NAR genomics and bioinformatics · 2020Article
- Detection of Allosteric Effects of lncRNA Secondary Structures Altered by SNPs in Human Diseases.Frontiers in cell and developmental biology · 2020Article
- Article
- Integrative Analysis of Somatic Mutations in Non-coding Regions Altering RNA Secondary Structures in Cancer Genomes.Scientific reports · 2019Article
- dStruct: identifying differentially reactive regions from RNA structurome profiling data.Genome biology · 2019Article
- Genetic variants in mRNA untranslated regions.Wiley interdisciplinary reviews. RNA · 2018Review
- Allele-specific SHAPE-MaP assessment of the effects of somatic variation and protein binding on mRNA structure.RNA (New York, N.Y.) · 2018Article
- Comparative Visualization of the RNA Suboptimal Conformational Ensemble In Vivo.Biophysical journal · 2017Article
- Effects of Pathogenic Variations in the Human Rhodopsin Gene (hRHO) on the Predicted Accessibility for a Lead Candidate Ribozyme.Investigative ophthalmology & visual science · 2017Article
- Classification of RNA structure change by 'gazing' at experimental data.Bioinformatics (Oxford, England) · 2017Article
- The roles of RNA processing in translating genotype to phenotype.Nature reviews. Molecular cell biology · 2017Review
- Multiple conformations are a conserved and regulatory feature of the RB1 5' UTR.RNA (New York, N.Y.) · 2015Article
- Detecting riboSNitches with RNA folding algorithms: a genome-wide benchmark.Nucleic acids research · 2015Article
- Article
- Small RNAs derived from lncRNA RNase MRP have gene-silencing activity relevant to human cartilage-hair hypoplasia.Human molecular genetics · 2014Article
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
Abstract
A majority of SNPs (single nucleotide polymorphisms) map to noncoding and intergenic regions of the genome. Noncoding SNPs are often identified in genome-wide association studies (GWAS) as strongly associated with human disease. Two such disease-associated SNPs in the 5' UTR of the human FTL (Ferritin Light Chain) gene are predicted to alter the ensemble of structures adopted by the mRNA. High-accuracy single nucleotide resolution chemical mapping reveals that these SNPs result in substantial changes in the structural ensemble in agreement with the computational prediction. Furthermore six rescue mutations are correctly predicted to restore the mRNA to its wild-type ensemble. Our data confirm that the FTL 5' UTR is a "RiboSNitch," an RNA that changes structure if a particular disease-associated SNP is present. The structural change observed is analogous to that of a bacterial Riboswitch in that it likely regulates translation. These data further suggest that specific pairs of SNPs in high linkage disequilibrium (LD) will form RNA structure-stabilizing haplotypes (SSHs). We identified 484 SNP pairs that form SSHs in UTRs of the human genome, and in eight of the 10 SSH-containing transcripts, SNP pairs stabilize RNA protein binding sites. The ubiquitous nature of SSHs in the transcriptome suggests that certain haplotypes are conserved to avoid RiboSNitch formation.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.