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Series GSE112578 Query DataSets for GSE112578
Status Public on Jun 26, 2018
Title Endogenous transcripts control miRNA levels and activity in mammalian cells by a target-dependent miRNA degradation mechanism [RNA-Seq_2]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Little is known about how miRNAs are turned over, in particular in mammalian cells. A target-dependent miRNA degradation mechanism (TDMD) has been recently suggested, in which RNA targets may induce miRNA degradation. However, endogenous RNA targets involved in TDMD have not been yet identified. During serum stimulation of quiescent fibroblasts, a deep change of miRNA expression occurs in few hours. We scanned the mammalian genome for targets eligible for TDMD and found a dominant miRNA:target pair, consisting of a target (SerpinE1) extraordinarily induced upon serum stimulation and two matched miRNAs (miR-30b/c) quickly downregulated. We verified directly the occurrence of TDMD by interfering specifically with the miR-:target interaction, keeping target and miRNA expression at endogenous levels, using CRISPR/cas9 mediated deletion of the miR-30 responsive element (MRE) of SerpinE1. In MRE-KO cells, we observed the stabilization of the predicted miRNAs, with no evidence of alterations in precursors or unrelated miRNAs, suggesting that TDMD is occurring and has been disrupted by a single MRE deletion. At molecular level miRNA degradation occurs within physiological ranges of target expression (upon 1000 copies per cells) and is accompanied by modification on 3’ends (tailing, mostly through adenylation). TDMD suppression was sufficient to shift the activity of miR-30b/c towards other shared targets, modulate significantly gene expression and, thus, influence cellular functions, including cell proliferation, apoptosis, and adhesion. In conclusion, these data strongly support the existence of a novel and sophisticated regulatory layer of miRNA and gene expression mediated by specific endogenous targets in mammalian cells.
Overall design mRNA regulation in wild type and MRE_KO cells (where the miR-30 microRNA responsive element within Serpine1 3'UTR was deleted by CRISPR/Cas9 genome editing) in quiescence and upon serum-stimulation.
Contributor(s) Ghini F, Marzi MJ, Nicassio F
Citation(s) 30087332
Submission date Apr 01, 2018
Last update date Mar 08, 2019
Contact name Francesco Nicassio
Organization name Istituto Italiano di Tecnologia
Department Center for genomic science
Street address Via Adamello 16
City Milano
ZIP/Postal code 20139
Country Italy
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (9)
GSM3073176 Parental_3T9_0h
GSM3073177 MRE_KO1_3T9_0h
GSM3073178 MRE_KO2_3T9_0h
This SubSeries is part of SuperSeries:
GSE104650 Endogenous transcripts control miRNA levels and activity in mammalian cells by a target-dependent miRNA degradation mechanism
BioProject PRJNA448326
SRA SRP136884

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Supplementary file Size Download File type/resource
GSE112578_GEO_fghini_3T9_serum_RNAseq_TPM.xls.gz 1.4 Mb (ftp)(http) XLS
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