2022
DOI: 10.15252/embr.202254762
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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… Show more

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Cited by 7 publications
(8 citation statements)
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“…( B ) Significantly enriched (FDR < 0.05) mirDB gene sets associated with the miR-290-295 cluster in TR-differentiated cells compared to parental EC cell lines with normalized enrichment scores (NES) as determined by GSEA. ( C ) Volcano plots showing differential gene expression of the 106 candidate target genes of the miR-290-295 cluster from Schaefer et al 40 Gene names of experimentally determined direct targets of the miR-290-295 cluster are labelled. Genes that were significantly upregulated in TR-differentiated cells are in red, genes that were significantly downregulated in TR-differentiated cells are in blue, and genes that were not significantly differentially expressed are in grey.…”
Section: Resultsmentioning
confidence: 99%
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“…( B ) Significantly enriched (FDR < 0.05) mirDB gene sets associated with the miR-290-295 cluster in TR-differentiated cells compared to parental EC cell lines with normalized enrichment scores (NES) as determined by GSEA. ( C ) Volcano plots showing differential gene expression of the 106 candidate target genes of the miR-290-295 cluster from Schaefer et al 40 Gene names of experimentally determined direct targets of the miR-290-295 cluster are labelled. Genes that were significantly upregulated in TR-differentiated cells are in red, genes that were significantly downregulated in TR-differentiated cells are in blue, and genes that were not significantly differentially expressed are in grey.…”
Section: Resultsmentioning
confidence: 99%
“…Data were visualized using GraphPad Prism. 40 Gene names of experimentally determined direct targets of the miR-290-295 cluster are labelled. Genes that were significantly upregulated in TR-differentiated cells are in red, genes that were significantly downregulated in TR-differentiated cells are in blue, and genes that were not significantly differentially expressed are in grey.…”
Section: Methodsmentioning
confidence: 99%
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“…This widespread regulation has spurred their popularity, driven further by their potential use as diagnostic biomarkers owing to their considerable variety and extracellular stability [ 3 ]. miRNAs are expressed within a wide range of plants and animals, including mammalian preimplantation embryos [ 4 , 5 ] wherein miRNAs regulate developmentally critical features such as inner cell mass pluripotency and proliferation [ 6 , 7 ]. Extracellular miRNAs found within the surrounding spent culture media are also finding application as accessible biomarkers indicative of the developmental state [ 8 ].…”
Section: Introductionmentioning
confidence: 99%