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MKRN2 physically interacts with GLE1 to regulate mRNA export and zebrafish retinal development (RNA-Seq)

ABSTRACT: MKRN2 physically interacts with GLE1 to regulate mRNA export and zebrafish retinal development (RNA-Seq)

PROVIDER: PRJNA562527 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10025741.fastq.gz	Fastqsanger.gz
	SRR10025742.fastq.gz	Fastqsanger.gz
	SRR10025743.fastq.gz	Fastqsanger.gz
	SRR10025744.fastq.gz	Fastqsanger.gz
	SRR10025745.fastq.gz	Fastqsanger.gz

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MKRN2 physically interacts with GLE1 to regulate mRNA export and zebrafish retinal development

Project description:The canonical mammalian mRNA export process is thought to terminate at the cytoplasmic face of the nuclear pore complex through mRNP remodeling. We conducted a stringent affinity-purification mass-spectrometry-based screen of the physical interactions of human RNA-binding E3 ubiquitin ligases. The resulting protein-interaction network revealed unexpected interactions between the RNA-binding E3 ubiquitin ligase MKRN2 and GLE1, a DEAD-box helicase activator implicated in mRNA export termination. We assessed MKRN2 epistasis with GLE1 in a genetically tractable zebrafish model. Strikingly, morpholino-mediated knockdown or CRISPR/Cas9-based knockout of MKRN2 partially rescued retinal developmental defects seen upon GLE1 depletion. Next, using iCLIP, we showed that MKRN2 binds preferentially to the 3'UTR of a diverse subset of mRNAs. Next-generation sequencing of fractionated cell extracts revealed that nuclear export of MKRN2-associated mRNAs is enhanced upon knockdown of MKRN2. Taken together, these results indicate that MKRN2 selectively interacts with GLE1 to regulate mRNA nuclear export and retinal development.

2020-05-19 | GSE136399 | GEO

MKRN2 physically interacts with GLE1 to regulate mRNA export and zebrafish retinal development (RNA-Seq)

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MKRN2 physically interacts with GLE1 to regulate mRNA export and zebrafish retinal development

Project description:MKRN2 physically interacts with GLE1 to regulate mRNA export and zebrafish retinal development

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Human RNA-binding protein E3 ubiquitin ligase AP-MS

Project description:The canonical mammalian mRNA nuclear export process is thought to terminate at the cytoplasmic face of the nuclear pore complex through ribonucleoprotein remodeling. We conducted a stringent affinity-purification mass-spectrometry-based screen of the physical interactions of human RNA-binding E3 ubiquitin ligases. The resulting protein-interaction network revealed interactions between the RNA-binding E3 ubiquitin ligase MKRN2 and GLE1, a DEAD-box helicase activator implicated in mRNA export termination. We assessed MKRN2 epistasis with GLE1 in a genetically tractable zebrafish model. Morpholino-mediated knockdown or CRISPR/Cas9-based knockout of MKRN2 partially rescued retinal developmental defects seen upon GLE1 depletion, consistent with a functional association between GLE1 and MKRN2. Using ribonomic approaches, we showed that MKRN2 binds selectively to the 3'UTR of a diverse subset of mRNAs and that nuclear export of MKRN2-associated mRNAs is enhanced upon knockdown of MKRN2. Taken together, we suggest that MKRN2 interacts with GLE1 to selectively regulate mRNA nuclear export and retinal development.

2020-05-29 | PXD017541 | Pride

Profiling of CSDE1-bound RNAs under MKRN2-mediated ubiquitination

Project description:This study aims to elucidate how MKRN2-mediated ubiquitination regulates the RNA-binding capacity of CSDE1. By overexpressing CSDE1 in MKRN2 knockout (KO) SHSY5Y cells and complementing with MKRN2 for comparison, we systematically analyzed the alterations in the RNA-binding repertoire of CSDE1 upon its interaction with MKRN2.

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Identifying cellular RNA-binding proteins during infection uncovers a role for MKRN2 in influenza mRNA trafficking.

Project description:Utilisation of RNA-binding proteins (RBPs) is an important aspect of post-transcriptional regulation of viral RNA. Viruses such as influenza A viruses (IAV) interact with RBPs to regulate processes including splicing, nuclear export and trafficking, while also encoding RBPs within their genomes, such as NP and NS1. But with almost 1000 RBPs encoded within the human genome it is still unclear what role, if any, many of these proteins play during viral replication. Using the RNA interactome capture (RIC) technique, we isolated RBPs from IAV infected cells to unravel the RBPome of mRNAs from IAV infected human cells. This led to the identification of one particular RBP, MKRN2, that associates with and positively regulates IAV mRNA. Through further validation, we determined that MKRN2 is involved in the nuclear-cytoplasmic trafficking of IAV mRNA likely through an association with the RNA export mediator GLE1. In the absence of MKRN2, IAV mRNAs accumulate in the nucleus of infected cells, which we suspect leads to their degradation by the nuclear RNA exosome complex. MKRN2, therefore, appears to be required for the efficient nuclear export of IAV mRNAs in human cells.

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The RNA-binding E3 ligase MKRN2 selectively disrupts IL-6 translation to restrain inflammation

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The RNA-binding E3 ligase MKRN2 selectively disrupts IL-6 translation to restrain inflammation [RNA-seq]

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Epstein-Barr Virus episome physically interacts with active regions of the host genome in lymphoblastoid cells

Project description:Epstein-Barr Virus episome physically interacts with active regions of the host genome in lymphoblastoid cells

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Identification of RNAs that are physically and functionally associated with RNase P

Project description:Numerous RNAs copurify with RNase P and are affected by temperture sensitive mutations in conserved residues with the essential RNA and protein subunits. Specifically, RNase P physically interacts with ribosomal protein mRNAS and the intron-encoded box C/D snoRNAs. Keywords: RNA copurification, temperature sensitive mutants ORF and intergenic regions were analyzed in order to determine which RNAs were affected in RNase P strains.

2008-06-01 | E-GEOD-10514 | biostudies-arrayexpress

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