MiRLog and dbmiR: Prioritization and functional annotation tools to study human microRNA sequence variants.

Base Sequence Computational Biology / methods Genome, Human / genetics Humans MicroRNAs / genetics Molecular Sequence Annotation Nucleotides Polymorphism, Single Nucleotide
functional annotation machine learning microRNA noncoding element single nucleotide variants

Journal

Human mutation
ISSN: 1098-1004
Titre abrégé: Hum Mutat
Pays: United States
ID NLM: 9215429

Informations de publication

Date de publication:
09 2022
Historique:
revised: 03 05 2022
received: 27 01 2022
accepted: 11 05 2022
pubmed: 19 5 2022
medline: 5 8 2022
entrez: 18 5 2022
Statut: ppublish

Résumé

The recent identification of noncoding variants with pathogenic effects suggests that these variations could underlie a significant number of undiagnosed cases. Several computational methods have been developed to predict the functional impact of noncoding variants, but they exhibit only partial concordance and are not integrated with functional annotation resources, making the interpretation of these variants still challenging. MicroRNAs (miRNAs) are small noncoding RNA molecules that act as fine regulators of gene expression and play crucial functions in several biological processes, such as cell proliferation and differentiation. An increasing number of studies demonstrate a significant impact of miRNA single nucleotide variants (SNVs) both in Mendelian diseases and complex traits. To predict the functional effect of miRNA SNVs, we implemented a new meta-predictor, MiRLog, and we integrated it into a comprehensive database, dbmiR, which includes a precompiled list of all possible miRNA allelic SNVs, providing their biological annotations at nucleotide and miRNA levels. MiRLog and dbmiR were used to explore the genetic variability of miRNAs in 15,708 human genomes included in the gnomAD project, finding several ultra-rare SNVs with a potentially deleterious effect on miRNA biogenesis and function representing putative contributors to human phenotypes.

Identifiants

DOI: 10.1002/humu.24399 PMID: 35583122 PMC: PMC9546175
pubmed: 35583122
doi: 10.1002/humu.24399
pmc: PMC9546175
doi:

Substances chimiques

MicroRNAs 0
Nucleotides 0

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

1201-1215

Informations de copyright

© 2022 The Authors. Human Mutation published by Wiley Periodicals LLC.

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Auteurs

Agnese Giovannetti (A)

Laboratory of Clinical Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy.
ORCID: 0000-0001-5207-7243

Salvatore Daniele Bianco (SD)

Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy.
Unit of Bioinformatics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy.
ORCID: 0000-0001-7466-9741

Alice Traversa (A)

Laboratory of Clinical Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy.
ORCID: 0000-0001-6138-6179

Noemi Panzironi (N)

Laboratory of Clinical Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy.

Alessandro Bruselles (A)

Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy.

Sara Lazzari (S)

Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy.

Niccolò Liorni (N)

Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy.
Unit of Bioinformatics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy.
ORCID: 0000-0003-0472-5693

Marco Tartaglia (M)

Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy.
ORCID: 0000-0001-7736-9672

Massimo Carella (M)

Medical Genetics Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy.

Antonio Pizzuti (A)

Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy.

Tommaso Mazza (T)

Unit of Bioinformatics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy.
ORCID: 0000-0003-0434-8533

Viviana Caputo (V)

Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy.
ORCID: 0000-0001-6753-1234

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Classifications MeSH

questionsmedicales.fr › Sciences de l'information › Sources d'information › Services d'information › Documentation › Données de séquences moléculaires › Séquence nucléotidique › MiRLog and dbmiR: Prioritization and...
questionsmedicales.fr › Sciences de l'information › Informatique › Biologie informatique › MiRLog and dbmiR: Prioritization and...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Génome humain › MiRLog and dbmiR: Prioritization and...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › MiRLog and dbmiR: Prioritization and...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ARN › ARN non traduit › Petit ARN non traduit › microARN › MiRLog and dbmiR: Prioritization and...
questionsmedicales.fr › Sciences de l'information › Sources d'information › Services d'information › Documentation › Données de séquences moléculaires › Annotation de séquence moléculaire › MiRLog and dbmiR: Prioritization and...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Nucléotides › MiRLog and dbmiR: Prioritization and...
questionsmedicales.fr › Phénomènes génétiques › Variation génétique › Polymorphisme génétique › Polymorphisme de nucléotide simple › MiRLog and dbmiR: Prioritization and...