ArticleNucleic acids research2018
A screen for deeply conserved non-coding GWAS SNPs uncovers a MIR-9-2 functional mutation associated to retinal vasculature defects in human.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 40 citations in OpenAlex.
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- Genetic effects of sequence-conserved enhancer-like elements on human complex traits.Genome biology · 2024Article
- Zebrafish as a Model for Osteoporosis: Functional Validations of Genome-Wide Association Studies.Current osteoporosis reports · 2023Review
- Genetic predisposition to neuroblastoma results from a regulatory polymorphism that promotes the adrenergic cell state.The Journal of clinical investigation · 2023Article
- Cell-specific cis-regulatory elements and mechanisms of non-coding genetic disease in human retina and retinal organoids.Developmental cell · 2022Article
- Exploring the effects of genetic variation on gene regulation in cancer in the context of 3D genome structure.BMC genomic data · 2022Article
- Tubulin-folding cofactor E deficiency promotes vascular dysfunction by increased endoplasmic reticulum stress.European heart journal · 2022Article
- Mutational Landscape Screening Through Comprehensive In Silico Analysis for Polycystic Ovarian Syndrome-Related Genes.Reproductive sciences (Thousand Oaks, Calif.) · 2022Article
- Review
- Conceptualization of functional single nucleotide polymorphisms of polycystic ovarian syndrome genes: an in silico approach.Journal of endocrinological investigation · 2021Article
- dbCNS: A New Database for Conserved Noncoding Sequences.Molecular biology and evolution · 2021Article
- Genetic disruption of serine biosynthesis is a key driver of macular telangiectasia type 2 aetiology and progression.Genome medicine · 2021Article
- Identification of genetic factors influencing metabolic dysregulation and retinal support for MacTel, a retinal disorder.Communications biology · 2021Article
- Mapping theProceedings of the National Academy of Sciences of the United States of America · 2020Article
- Zebrafish models of sarcopenia.Disease models & mechanisms · 2020Review
- Using zebrafish to study skeletal genomics.Bone · 2019Review
- GTRD: a database on gene transcription regulation-2019 update.Nucleic acids research · 2019Article
- Genetics of Cardiovascular Disease: Fishing for Causality.Frontiers in cardiovascular medicine · 2018Review
Corrections and comments
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Authors and funding
7 authors at 1 institution in 2 countries.
Funding
Abstract
Thousands of human disease-associated single nucleotide polymorphisms (SNPs) lie in the non-coding genome, but only a handful have been demonstrated to affect gene expression and human biology. We computationally identified risk-associated SNPs in deeply conserved non-exonic elements (CNEs) potentially contributing to 45 human diseases. We further demonstrated that human CNE1/rs17421627 associated with retinal vasculature defects showed transcriptional activity in the zebrafish retina, while introducing the risk-associated allele completely abolished CNE1 enhancer activity. Furthermore, deletion of CNE1 led to retinal vasculature defects and to a specific downregulation of microRNA-9, rather than MEF2C as predicted by the original genome-wide association studies. Consistent with these results, miR-9 depletion affects retinal vasculature formation, demonstrating MIR-9-2 as a critical gene underpinning the associated trait. Importantly, we validated that other CNEs act as transcriptional enhancers that can be disrupted by conserved non-coding SNPs. This study uncovers disease-associated non-coding mutations that are deeply conserved, providing a path for in vivo testing to reveal their cis-regulated genes and biological roles.
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Registered trials
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