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MicroRNAs are negative and positive post-transcriptional regulators of BRAF-X1 mRNA [miRNA]

ABSTRACT: microRNAs are negative and positive post-transcriptional regulators of BRAF-X1 mRNA [miRNA]

PROVIDER: PRJNA482819 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7591172.fastq.gz	Fastqsanger.gz
	SRR7591173.fastq.gz	Fastqsanger.gz

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microRNAs are negative and positive post-transcriptional regulators of BRAF-X1 mRNA [miRNA]

Project description:X1 is the most abundant transcript variant of BRAF mRNA and has a long 3’UTR, but its involvement in post-transcriptional regulatory circuits has not been investigated yet. Here, we describe 20 microRNAs that bind directly to the X1 3’UTR. They were identified in BRAFV600E mutant A375 melanoma cells using miR-CATCHv2.0, an implemented experimental method that combines RNA affinity purification with small RNA sequencing and an ad hoc analytical workflow. X1-targeting microRNAs fall into 4 classes, according to the effect that they exert (decrease/increase in BRAFV600E mRNA and protein levels) and on the mechanism they use to achieve it (destabilization/stabilization of X1 mRNA or decrease/increase in its translation). In many cases, the microRNA-induced variations in BRAFV600E protein levels are coupled to consistent variations in pMEK levels and, in turn, to melanoma cell proliferation and sensitivity to the BRAF inhibitor vemurafenib. However, examples exist of microRNAs that uncouple the degree of activation of the ERK pathway from the levels of BRAFV600E protein. Our study describes miR-CATCHv2.0 as an effective tool for the identification of direct microRNA-target interactions and unveils the complexity of the post-transcriptional regulation to which BRAFV600E and the ERK pathway are subjected in melanoma cells.

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microRNAs are negative and positive post-transcriptional regulators of BRAF-X1 mRNA [miR-CATCH]

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microRNAs are negative and positive post-transcriptional regulators of BRAF-X1 mRNA

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microRNAs are negative and positive post-transcriptional regulators of BRAF-X1 mRNA [miR-CATCH]

Project description:microRNAs are negative and positive post-transcriptional regulators of BRAF-X1 mRNA [miR-CATCH]

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microRNAs are negative and positive post-transcriptional regulators of BRAF-X1 mRNA

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-03-31 | GSE117642 | GEO

Systematic evaluation of the microRNAome through miR-CATCHv2.0 identifies positive and negative regulators of BRAF-X1 mRNA.

Project description:Here we present miR-CATCHv2.0, an implemented experimental method that allows the identification of the microRNA species directly bound to an RNA of interest. After cross-linking of microRNA::RNA::Ago2 complexes using formaldehyde, the RNA is fragmented using sonication and then subjected to affinity purification using two sets of biotinylated tiling probes (ODD and EVEN). Finally, enriched microRNA species are retrieved by means of small RNA sequencing coupled with an ad hoc analytical workflow. In BRAFV600E mutant A375 melanoma cells, miR-CATCHv2.0 allowed us to identify 20 microRNAs that target X1, the most abundant isoform of BRAF mRNA. These microRNAs fall into different functional classes, according to the effect that they exert (decrease/increase in BRAFV600E mRNA and protein levels) and to the mechanism they use to achieve it (destabilization/stabilization of X1 mRNA or decrease/increase in its translation). microRNA-induced variations in BRAFV600E protein levels are most of the times coupled to consistent variations in pMEK levels, in melanoma cell proliferation in vitro and in sensitivity to the BRAF inhibitor vemurafenib in a xenograft model in zebrafish. However, microRNAs exist that uncouple the degree of activation of the ERK pathway from the levels of BRAFV600E protein. Our study proposes miR-CATCHv2.0 as an effective tool for the identification of direct microRNA-target interactions and, by using such a tool, unveils the complexity of the post-transcriptional regulation to which BRAFV600E and the ERK pathway are subjected in melanoma cells.

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Project description:Bacillus sp. X1(2014) strain:X1 Genome sequencing

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Project description:Salmonella enterica subsp. enterica strain:H3-X1 | isolate:H3-X1 Genome sequencing

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