Distinct and redundant roles of nuclear RNA exosome targeting complexes
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA566003 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10134312.fastq.gz | Fastqsanger.gz | |||
| SRR10134313.fastq.gz | Fastqsanger.gz | |||
| SRR10134314.fastq.gz | Fastqsanger.gz | |||
| SRR10134315.fastq.gz | Fastqsanger.gz | |||
| SRR10134316.fastq.gz | Fastqsanger.gz |
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Project description:Degradation of transcripts in mammalian nuclei is primarily facilitated by the RNA exosome. To obtain substrate specificity, the exosome is aided by adaptors; in the nucleoplasm, the Nuclear EXosome Targeting (NEXT) complex and the PolyA (pA) eXsome Targeting (PAXT) connection. However, how exact targeting is achieved remains enigmatic. Employing high-resolution 3’end sequencing of both steady state and newly produced pA+ and pA- RNA, we demonstrate that NEXT substrates arise from heterogenous and predominantly pA- 3’ends often covering kb-wide genomic regions. In contrast, PAXT targets harbor well-defined pA+ 3’ends defined by canonical pA site usage. Irrespective this clear division, NEXT and PAXT act redundantly in two ways: i) Regional redundancy: The majority of exosome-targeted transcription units produce both NEXT- and PAXT-sensitive RNA isoforms; and ii) Isoform redundancy: The PAXT connection ensures the fail-safe decay of post-transcriptionally polyadenylated NEXT targets. In conjunction, this provides for the efficient nuclear removal of superfluous RNA.
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Project description:Cryptic unstable transcripts (CUTs) are rapidly degraded by the nuclear exosome, however, the way they are recognized and targeted to the exosome is not fully understood. The recently identified Schizosaccharomyces pombe MTREC complex has been shown to promote degradation of meiotic mRNAs and regulatory ncRNAs. Here, we report that the MTREC complex is also the major nuclear exosome targeting complex for CUTs and unspliced mRNAs. MTREC complex specifically binds to CUTs, meiotic mRNAs and unspliced mRNA transcripts and targets these RNAs for degradation by the nuclear exosome, while the TRAMP complex has only a minor role in this process. The MTREC complex physically interacts with the nuclear exosome and with various RNA-binding and -processing complexes, coupling RNA processing to the RNA degradation machinery. Our study reveals the central role of the evolutionarily conserved MTREC complex in RNA quality control, and in the recognition and elimination of aberrant, cryptic transcripts. All experiments were performed twice in biological replicates.
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