Dataset Information

Identification of functional miRNA gene interactions in mESC by computational data integration approaches.

ABSTRACT: miRNAs are short regulatory single stranded RNA sequences that upon complementary binding to mRNAs lead to the inhibition or degradation of their targets. This regulatory mechanisms has been shown to play crucial roles throughout the whole life cycle of animals and plants as well as in disease. While a plethora of methods exist to predict targets of miRNA, which suggest that up to 80% of the genome is miRNA regulated, it has recently been reported that many of these predictions are false positives, cell type specific or represent non-functional binding. In order to identify the subset of real functional miRNAs and their targets, we established miRNA pathway mutants in mouse embryonic stem cells (mESC), allowing the dissection of canonical and non-canonical functions of pathway members. Additional data integration of downstream regulatory layers (CLIP-seq, ribosome profiling and MS) enabled us to follow and track down real functional miRNA-gene interactions, which reduced the miRNA genome regulation to approximately 1%.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Embryo, Endosperm, Embryonic Stem Cell

SUBMITTER: Tatjana Sajic

LAB HEAD: Prof. Dr. Rudolf Aebersold

PROVIDER: PXD014484 | Pride | 2022-08-31

REPOSITORIES: pride

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Dataset's files

Source:

			Action	DRS
	ConvertTSVToTraML.TraML	Other
	E1712181522_feature_alignment_requant.tsv.gz	Tabular
	SAJICTMITO_EPFL_LIVERE1712141542.prot.xml	Xml
	iprophet.pep.xml	Pepxml
	sajict_L171021_SW_1.zip	Other

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Publications

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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