학술논문
Looking for a needle in a haystack: de novo phenotypic target identification reveals Hippo pathway-mediated miR-202 regulation of egg production.
Document Type
Academic Journal
Author
Janati-Idrissi S; INRAE, UR1037, LPGP, Rennes, France.; de Abreu MR; INRAE, UR1037, LPGP, Rennes, France.; Guyomar C; Sigenae, GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France.; de Mello F; INRAE, UR1037, LPGP, Rennes, France.; Nguyen T; INRAE, UR1037, LPGP, Rennes, France.; Mechkouri N; Institut de Génétique Humaine, UMR 9002 CNRS and University of Montpellier, Montpellier, France.; Gay S; INRAE, UR1037, LPGP, Rennes, France.; Montfort J; INRAE, UR1037, LPGP, Rennes, France.; Gonzalez AA; MGX-Montpellier GenomiX, University of Montpellier, CNRS, INSERM, Montpellier, France.; Abbasi M; INRAE, UR1037, LPGP, Rennes, France.; Bugeon J; INRAE, UR1037, LPGP, Rennes, France.; Thermes V; INRAE, UR1037, LPGP, Rennes, France.; Seitz H; Institut de Génétique Humaine, UMR 9002 CNRS and University of Montpellier, Montpellier, France.; Bobe J; INRAE, UR1037, LPGP, Rennes, France.
Source
Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE
Subject
Language
English
Abstract
Understanding microRNA (miRNA) functions has been hampered by major difficulties in identifying their biological target(s). Currently, the main limitation is the lack of a suitable strategy to identify biologically relevant targets among a high number of putative targets. Here we provide a proof of concept of successful de novo (i.e. without prior knowledge of its identity) miRNA phenotypic target (i.e. target whose de-repression contributes to the phenotypic outcomes) identification from RNA-seq data. Using the medaka mir-202 knock-out (KO) model in which inactivation leads to a major organism-level reproductive phenotype, including reduced egg production, we introduced novel criteria including limited fold-change in KO and low interindividual variability in gene expression to reduce the list of 2853 putative targets to a short list of 5. We selected tead3b, a member of the evolutionarily-conserved Hippo pathway, known to regulate ovarian functions, due to its remarkably strong and evolutionarily conserved binding affinity for miR-202-5p. Deleting the miR-202-5p binding site in the 3' UTR of tead3b, but not of other Hippo pathway members sav1 and vgll4b, triggered a reduced egg production phenotype. This is one of the few successful examples of de novo functional assignment of a miRNA phenotypic target in vivo in vertebrates.
(© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.)
(© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.)