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

ABSTRACT: 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 < 10% of expressed genes are functionally and directly regulated by miRNAs in mESCs. In addition, analyses of the stem cell-specific miR-290-295 cluster target genes identify TFAP4 as an important transcription factor for early development. The extensive datasets developed in this study will support the development of improved predictive models for miRNA-mRNA functional interactions.

SUBMITTER: Schaefer M

PROVIDER: S-EPMC9442311 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature

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

Schaefer Moritz M Nabih Amena A Spies Daniel D Hermes Victoria V Bodak Maxime M Wischnewski Harry H Stalder Patrick P Ngondo Richard Patryk RP Liechti Luz Angelica LA Sajic Tatjana T Aebersold Ruedi R Gatfield David D Ciaudo Constance C

EMBO reports 20220728 9

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 ...[more]

PMID: 35899551

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Dataset Information

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

Publications

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

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