Global and precise identification of functional miRNA targets in mESCs by integrative analysis

MicroRNA (miRNA) loaded Argonaute (AGO) complexes regulate gene expression via direct base pairing with their mRNA targets. Previous works suggest that up to 60% of mammalian transcripts might be subject to miRNA‐mediated regulation, but it remains largely unknown which fraction of these interaction...

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Published in:EMBO reports 2022-09, Vol.23 (9), p.e54762-n/a
Main Authors: Schaefer, Moritz, Nabih, Amena, Spies, Daniel, Hermes, Victoria, Bodak, Maxime, Wischnewski, Harry, Stalder, Patrick, Ngondo, Richard Patryk, Liechti, Luz Angelica, Sajic, Tatjana, Aebersold, Ruedi, Gatfield, David, Ciaudo, Constance
Format: Article
Language:English
Subjects:
Algorithms
Binding
Depletion
EMBO09
EMBO34
EMBO36
Gene expression
Genes
integrative analysis
microRNA
MicroRNAs
miRNA
miR‐290‐295 cluster
mouse embryonic stem cells
Phenotypes
Prediction models
Ribonucleic acid
RNA
Stem cells
Target recognition
Tfap4
Transcriptomes
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Summary:MicroRNA (miRNA) loaded Argonaute (AGO) complexes regulate gene expression via direct base pairing with their mRNA targets. Previous works suggest that up to 60% of mammalian transcripts might be subject to miRNA‐mediated regulation, but it remains largely unknown which fraction of these interactions are functional in a specific cellular context. Here, we integrate transcriptome data from a set of miRNA‐depleted mouse embryonic stem cell (mESC) lines with published miRNA interaction predictions and AGO‐binding profiles. Using this integrative approach, combined with molecular validation data, we present evidence that
ISSN:1469-221X
1469-3178
DOI:10.15252/embr.202254762