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Homo sapiens

ABSTRACT: hMTR4 plays a central role in creating balanced nuclear RNA pools for degradation and export IV

PROVIDER: PRJNA350323 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR4448040_1.fastq.gz	Fastqsanger.gz
	SRR4448040_2.fastq.gz	Fastqsanger.gz
	SRR4448041_1.fastq.gz	Fastqsanger.gz
	SRR4448041_2.fastq.gz	Fastqsanger.gz
	SRR4448033_1.fastq.gz	Fastqsanger.gz

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hMTR4 plays a central role in creating balanced nuclear RNA pools for degradation and export

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Project description:hMTR4 plays a central role in creating balanced nuclear RNA pools for degradation and export I

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Identification of a nuclear exosome decay pathway for processed transcripts

Project description:The RNA exosome is fundamental for the degradation of RNA in eukaryotic nuclei. Substrate targeting is facilitated by its co-factor Mtr4p/hMTR4, which links to RNA-binding protein adaptors. One such activity is the human Nuclear EXosome Targeting (NEXT) complex, composed of hMTR4, the Zn-finger protein ZCCHC8 and the RNA-binding factor RBM7. NEXT primarily targets early and unprocessed transcripts, demanding a rationale for how the nuclear exosome recognizes processed RNAs. Here, we describe the PolyA tail eXosome Targeting (PAXT) connection, comprising the hitherto uncharacterized ZFC3H1 Zn-knuckle protein as a central link between hMTR4 and the nuclear polyA binding protein PABPN1. Individual depletion of ZFC3H1 and PABPN1 results in the accumulation of common transcripts, that are generally both longer and more 3’polyadenylated than NEXT substrates. Importantly, ZFC3H1/PABPN1 and ZCCHC8/RBM7 contact hMTR4 in a mutually exclusive manner, revealing that the exosome targets nuclear transcripts of different maturation status by substituting its hMTR4-associating adaptors.

2016-11-03 | GSE84172 | GEO

NRDE2 acts as a negative regulator of the exosome complex by disrupting hMTR4 interactome

Project description:The RNA exosome complex is the most versatile RNA-degradation machine in eukaryotes that requires MTR4 for every aspect of its nuclear functions. To date, how exosome functions are negatively regulated remains largely unknown. Here, we report the identification of NRDE2 as an inhibitory regulator of exosome functions. NRDE2 tightly and directly interacts with human MTR4 (hMTR4) via its N-terminal domain, resulting in their mutual stabilization. Overexpression of NRDE2 attenuates associations of hMTR4 with the exosome, CBC, TRAMP and NEXT components, resulting in accumulation of exosome target RNAs as well as 3’ extended 5.8S rRNAs. Conversely, in NRDE2 knockdown cells, the association of hMTR4 with CBC, TRAMP or NEXT components are significantly enhanced, accompanied by promoted RNA degradation. Together, our work uncovers NRDE2 as a direct negative regulator of exosome functions that prevents hMTR4 from associating with its interacting partners.

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Nuclear export is a limiting factor in eukaryotic mRNA metabolism

Project description:The eukaryotic mRNA life cycle includes transcription, nuclear mRNA export and degradation. To quantify all these processes simultaneously, we perform thiol-linked alkylation after metabolic labeling of RNA with 4-thiouridine (4sU), followed by sequencing of RNA (SLAM-seq) in the nuclear and cytosolic compartments. We develop a model that reliably quantifies mRNA synthesis, nuclear export, and nuclear and cytosolic degradation rates on a genome-wide scale. We find that nuclear degradation of polyadenylated mRNA is negligible and nuclear mRNA export is slow, while cytosolic mRNA degradation is comparatively fast. Consequently, an mRNA molecule generally spends most of its life in the nucleus. We also observe large differences in the nuclear export rates of different 3’UTR transcript isoforms. Furthermore, we identify genes whose expression is abruptly induced upon metabolic labeling. These transcripts are exported substantially faster than average mRNAs, suggesting the existence of alternative export pathways. Our results highlight nuclear mRNA export as a limiting factor in mRNA metabolism and gene regulation.

2024-04-23 | GSE233546 | GEO

The RNA exosome adaptor protein ZFC3H1 functionally competes with nuclear export activity to retain target transcripts

Project description:Mammalian genomes are promiscuously transcribed, yielding protein-coding and non-coding products. Many transcripts are short-lived due to their nuclear degradation by the ribonucleolytic RNA exosome. Here, we show that abolished nuclear exosome function causes the formation of distinct nuclear foci, containing polyadenylated (pA+) RNA secluded from nucleocytoplasmic export. We asked whether exosome co-factors could serve such nuclear retention. Co-localization studies revealed the enrichment of pA+ RNA foci with ‘pA-tail exosome targeting (PAXT) connection’ components MTR4, ZFC3H1 and PABPN1, but no overlap with known nuclear structures, such as Cajal bodies, speckles, paraspeckles or nucleoli. Interestingly, ZFC3H1 is required for foci formation, and in its absence selected pA+ RNAs, including coding and non-coding transcripts, are exported to the cytoplasm in a process dependent on the mRNA export factor AlyREF. Our results establish ZFC3H1 as a central nuclear RNA retention factor, counteracting nuclear export activity.

2018-05-14 | GSE108197 | GEO

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