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A nuclear export block triggers the decay of newly synthesized polyadenylated RNA

ABSTRACT: A nuclear export block triggers the decay of newly synthesized polyadenylated RNA

PROVIDER: PRJNA427344 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6413660.fastq.gz	Fastqsanger.gz
	SRR6413670.fastq.gz	Fastqsanger.gz
	SRR6413651.fastq.gz	Fastqsanger.gz
	SRR6413661.fastq.gz	Fastqsanger.gz
	SRR6413671.fastq.gz	Fastqsanger.gz

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A nuclear export block triggers the decay of newly synthesized polyadenylated RNA

Project description:Genomes are promiscuously transcribed, necessitating mechanisms that facilitate the sorting of RNA for function or destruction. The polyA (pA) tail is one such distinguishing feature, which in the S. cerevisiae nucleus is bound by the Nab2p protein, yielding transcript protection. As Nab2p also contacts the main nuclear export factor Mex67p, we asked whether transport kinetics contributes to RNA sorting. Indeed, 3’end sequencing of newly transcribed pA+ RNAs demonstrates that nuclear depletion of Mex67p elicits their instant and global decay. A similar phenotype is evident upon inactivation of other export factors and proportional to the amount of nuclear pA+ RNA. Since RNA production is partially rescued by Nab2p over-expression, we propose that an export-block out-titrates Nab2p onto nuclear retained pA+ RNA, reducing the pool of Nab2p free to protect new transcripts. More generally, we suggest that nuclear RNA decay, negotiated by Nab2p availability, aids in balancing cellular transcript supply with demand.

2018-08-28 | GSE108477 | GEO

A Nuclear Export Block Triggers the Decay of Newly Synthesized Polyadenylated RNA.

Project description:Genomes are promiscuously transcribed, necessitating mechanisms that facilitate the sorting of RNA for function or destruction. The polyA (pA) tail is one such distinguishing feature, which in the Saccharomyces cerevisiae nucleus is bound by the Nab2p protein, yielding transcript protection. As Nab2p also contacts the main nuclear export factor Mex67p, we asked whether transport kinetics contributes to RNA sorting. Indeed, 3' end sequencing of newly transcribed pA+ RNAs demonstrates that nuclear depletion of Mex67p elicits their instant and global decay. A similar phenotype is evident upon inactivation of other export factors and proportional to the amount of nuclear pA+ RNA. As RNA expression is partially rescued by Nab2p overexpression, we propose that an export block out-titrates Nab2p onto nuclear-retained pA+ RNA, reducing the pool of Nab2p available to protect new transcripts. More generally, we suggest that nuclear RNA decay, negotiated by Nab2p availability, aids in balancing cellular transcript supply with demand.

| S-EPMC6130047 | biostudies-literature

ALYREF is shared by polyadenylated and nonpolyadenylated mRNA processing and export pathways [iCLIP-seq]

Project description:we try to investigate the binding of ALYREF and NXF1 on histone mRNA when the cell treated with indicated siRNAs. ALYREF plays key roles in nuclear export of polyadenylated mRNAs and also modulates their 3' processing, but whether it is involved in regulating RNAs beyond polyadenylated mRNAs is unknown. The replication-dependent (RD) histone mRNAs are not polyadenylated, but end in a stem-loop (SL) structure. Here we demonstrate that ALYREF prevalently binds a region next to the SL on RD histone mRNAs. SL-binding protein (SLBP) directly interacts with ALYREF and ensures this binding. To examine how SLBP KD impact ALYREF distribution on the histone mRNA, we carried out ALYREF iCLIP in control and SLBP KD cells. To investigate the functional consequence for ALYREF binding on histone mRNAs, we isolated polyA+ and polyA- RNAs from control and ALYREF KD cells, and carried out RNA-seq separately.

2019-02-27 | GSE124735 | GEO

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ALYREF is shared by polyadenylated and nonpolyadenylated mRNA processing and export pathways

Project description:ALYREF is shared by polyadenylated and nonpolyadenylated mRNA processing and export pathways

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Project description:To analyse the genome-wide impact of inactivation of the ATAC or SAGA coactivator complexes on RNA polymerase II (Pol II) transcription, we purified newly synthesized RNA from mutant mouse embryonic stem (ES) cell lines in which subunits of ATAC (Yeats2, Zzz3) or SAGA (Supt7l) are inactivated or depleted. We also performed this analysis in mutant cell lines in which a subunit (Tada3) of the shared histone acetyltransferase activity of these two complexes is depleted. Newly synthesized RNA was purified following the 4sU labelling method (more details in extract protocol). For two wildtype samples, the total RNA input was also analysed.

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Project description:Influenza viruses (IV) exploit a variety of signaling pathways. Previous studies showed that the Raf/MEK/ERK pathway is functionally linked to nuclear export of viral ribonucleoprotein (vRNP) complexes, suggesting that vRNP export is a signaling induced event. However, the underlying mechanism remained completely enigmatic. Here we have dissected the unknown molecular steps of signaling-driven vRNP export. We identified RSK1 as downstream target of virus-activated ERK signaling. While RSK2 displays an antiviral role, we demonstrate for the first time a virus-supportive function of RSK1, migrating to the nucleus to phosphorylate NP, the major constituent of vRNPs. This drives association with viral M1 at the chromatin, important for vRNP export. Inhibition or knockdown of MEK, ERK or RSK1 caused impaired vRNP export actions of different RSK isoforms.

2020-06-18 | PXD016638 | Pride

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