ArticleScientific reports2016
Sequence variation between 462 human individuals fine-tunes functional sites of RNA processing.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 41 citations in OpenAlex.
- Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing.Genome research · 2025Article
- Systematically developing a registry of splice-site creating variants utilizing massive publicly available transcriptome sequence data.Nature communications · 2025Article
- Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing.bioRxiv : the preprint server for biology · 2024Article
- Gene Self-Expressive Networks as a Generalization-Aware Tool to Model Gene Regulatory Networks.Biomolecules · 2023Article
- EpisomiR, a New Family of miRNAs, and Its Possible Roles in Human Diseases.Biomedicines · 2022Review
- A comparison of transcriptome analysis methods with reference genome.BMC genomics · 2022Article
- Novel Indel Variation of NPC1 Gene Associates With Risk of Sudden Cardiac Death.Frontiers in genetics · 2022Article
- A Functional Indel Polymorphism Within MIR155HG Is Associated With Sudden Cardiac Death Risk in a Chinese Population.Frontiers in cardiovascular medicine · 2021Article
- Population-scale study of eRNA transcription reveals bipartite functional enhancer architecture.Nature communications · 2020Article
- A molecular-level perspective on the frequency, distribution, and consequences of messenger RNA modifications.Wiley interdisciplinary reviews. RNA · 2020Review
- A novel splice site indel alteration in the EIF2AK3 gene is responsible for the first cases of Wolcott-Rallison syndrome in Hungary.BMC medical genetics · 2020Article
- Pathogenicity and selective constraint on variation near splice sites.Genome research · 2019Article
- The Length of the Expressed 3' UTR Is an Intermediate Molecular Phenotype Linking Genetic Variants to Complex Diseases.Frontiers in genetics · 2019Article
- Trans-Ethnic Mapping ofInternational journal of molecular sciences · 2018Article
- Targeting the Polyadenylation Signal of Pre-mRNA: A New Gene Silencing Approach for Facioscapulohumeral Dystrophy.International journal of molecular sciences · 2018Review
- Structure-mediated modulation of mRNA abundance by A-to-I editing.Nature communications · 2017Article
- A to I editing in disease is not fake news.RNA biology · 2017Review
- Article
Corrections and comments
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Authors and funding
14 authors at 20 institutions in 9 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent advances in the cost-efficiency of sequencing technologies enabled the combined DNA- and RNA-sequencing of human individuals at the population-scale, making genome-wide investigations of the inter-individual genetic impact on gene expression viable. Employing mRNA-sequencing data from the Geuvadis Project and genome sequencing data from the 1000 Genomes Project we show that the computational analysis of DNA sequences around splice sites and poly-A signals is able to explain several observations in the phenotype data. In contrast to widespread assessments of statistically significant associations between DNA polymorphisms and quantitative traits, we developed a computational tool to pinpoint the molecular mechanisms by which genetic markers drive variation in RNA-processing, cataloguing and classifying alleles that change the affinity of core RNA elements to their recognizing factors. The in silico models we employ further suggest RNA editing can moonlight as a splicing-modulator, albeit less frequently than genomic sequence diversity. Beyond existing annotations, we demonstrate that the ultra-high resolution of RNA-Seq combined from 462 individuals also provides evidence for thousands of bona fide novel elements of RNA processing-alternative splice sites, introns, and cleavage sites-which are often rare and lowly expressed but in other characteristics similar to their annotated counterparts.
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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.