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Cotranscriptional RNA cleavage by Drosha homolog Pac1 triggers transcription termination in fission yeast.

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Schizosaccharomyces pombe

PROVIDER: GSE167065 | GEO | 2021/02/19

REPOSITORIES: GEO

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Co-transcriptional RNA cleavage by Drosha homolog Pac1 triggers transcription termination in fission yeast.

Project description:Transcription termination of protein-coding genes in eukaryotic cells usually relies on a tight coordination between the cleavage and polyadenylation of the pre-mRNA, and 5'-3' degradation of the downstream nascent transcript. Here we investigated the contribution of the essential fission yeast endonuclease Pac1, a homolog of human Drosha that cleaves hairpin RNA structures, in triggering polyadenylation-independent transcription termination. Using ChIP-sequencing in Pac1-deficient cells, we found that Pac1 triggers transcription termination at snRNA and snoRNA genes as well as at specific protein-coding genes. Notably, we found that Pac1-dependent premature termination occurred at two genes encoding conserved transmembrane transporters whose expression were strongly repressed by Pac1. Analysis by genome editing indicated that a stem-loop structure in the nascent transcript directs Pac1-mediated cleavage and that the regions upstream and downstream of the Pac1 cleavage site in the targeted mRNAs were stabilized by mutation of nuclear 3'-5' and 5'-3' exonucleases, respectively. Our findings unveil a premature transcription termination pathway that uncouples co-transcriptional RNA cleavage from polyadenylation, triggering rapid nuclear RNA degradation.

| S-EPMC8421224 | biostudies-literature

Cotranscriptional RNA cleavage by Drosha homolog Pac1 triggers transcription termination in fission yeast. [RNA-Seq]

Project description:RNAse III is an evolutionarily conserved family of endoribonuclease that cleaves dsRNA structures. Here we studied RNAse III homolog Pac1 In fission yeast to shed light on underappreciated roles of Drosha. We found that Pac1 co-transcriptional cleavage of nascent hairpin RNA structures trigger transcriptional termination by creating an entry point for “torpedo” exonucleases – that is, exonuclease that degrade the nascent RNA until they bump into the transcribing polymerases. As such termination pathway decouple termination from pre-mRNA polyadenylation, the nascent transcript are destabilized upon Pac1 cleavage, therefore expending the paradigm of post-transcriptional regulation of gene expression.

2021-02-19 | GSE167041 | GEO

Cotranscriptional RNA cleavage by Drosha homolog Pac1 triggers transcription termination in fission yeast. [ChIP-Seq]

2021-02-19 | GSE167040 | GEO

Cotranscriptional RNA cleavage by Drosha homolog Pac1 triggers transcription termination in fission yeast.

Project description:Cotranscriptional RNA cleavage by Drosha homolog Pac1 triggers transcription termination in fission yeast.

| PRJNA702813 | ENA

Cotranscriptional RNA cleavage by Drosha homolog Pac1 triggers transcription termination in fission yeast. [RNA-Seq]

Project description:Cotranscriptional RNA cleavage by Drosha homolog Pac1 triggers transcription termination in fission yeast. [RNA-Seq]

| PRJNA702776 | ENA

Cotranscriptional RNA cleavage by Drosha homolog Pac1 triggers transcription termination in fission yeast. [ChIP-Seq]

Project description:Cotranscriptional RNA cleavage by Drosha homolog Pac1 triggers transcription termination in fission yeast. [ChIP-Seq]

| PRJNA702775 | ENA

Common mechanism of transcription termination at coding and noncoding RNA genes in fission yeast.

Project description:Termination of RNA polymerase II (RNAPII) transcription is a fundamental step of gene expression that is critical for determining the borders between genes. In budding yeast, termination at protein-coding genes is initiated by the cleavage/polyadenylation machinery, whereas termination of most noncoding RNA (ncRNA) genes occurs via the Nrd1-Nab3-Sen1 (NNS) pathway. Here, we find that NNS-like transcription termination is not conserved in fission yeast. Rather, genome-wide analyses show global recruitment of mRNA 3' end processing factors at the end of ncRNA genes, including snoRNAs and snRNAs, and that this recruitment coincides with high levels of Ser2 and Tyr1 phosphorylation on the RNAPII C-terminal domain. We also find that termination of mRNA and ncRNA transcription requires the conserved Ysh1/CPSF-73 and Dhp1/XRN2 nucleases, supporting widespread cleavage-dependent transcription termination in fission yeast. Our findings thus reveal that a common mode of transcription termination can produce functionally and structurally distinct types of polyadenylated and non-polyadenylated RNAs.

| S-EPMC6195540 | biostudies-literature

Yeast RNase III triggers polyadenylation independent transcription termination

Project description:Transcription termination of messenger RNA (mRNA) is normally achieved by polyadenylation followed by Rat1p dependent 5’-3’ exoribonuleolytic degradation of the downstream transcript. Here we show that the yeast orthologue of the dsRNA-specific ribonuclease III (Rnt1p) may trigger Rat1p dependent termination of RNA transcripts that fail to terminate near polyadenylation signals. Rnt1p cleavage sites were found downstream of several genes and the deletion of RNT1 resulted in transcription read-through. Inactivation of Rat1p impaired Rnt1p dependent termination and resulted in the accumulation of 3’ end cleavage products. These results support a new model for transcription termination in which co-transcriptional cleavage by Rnt1p provides access for exoribonucleases in the absence of polyadenylation signals.

2009-10-09 | GSE16784 | GEO

The conserved ribonuclease aCPSF1 triggers genome-wide transcription termination of Archaea via a 3'-end cleavage mode.

Project description:Transcription termination defines accurate transcript 3'-ends and ensures programmed transcriptomes, making it critical to life. However, transcription termination mechanisms remain largely unknown in Archaea. Here, we reported the physiological significance of the newly identified general transcription termination factor of Archaea, the ribonuclease aCPSF1, and elucidated its 3'-end cleavage triggered termination mechanism. The depletion of Mmp-aCPSF1 in Methanococcus maripaludis caused a genome-wide transcription termination defect and disordered transcriptome. Transcript-3'end-sequencing revealed that transcriptions primarily terminate downstream of a uridine-rich motif where Mmp-aCPSF1 performed an endoribonucleolytic cleavage, and the endoribonuclease activity was determined to be essential to the in vivo transcription termination. Co-immunoprecipitation and chromatin-immunoprecipitation detected interactions of Mmp-aCPSF1 with RNA polymerase and chromosome. Phylogenetic analysis revealed that the aCPSF1 orthologs are ubiquitously distributed among the archaeal phyla, and two aCPSF1 orthologs from Lokiarchaeota and Thaumarchaeota could replace Mmp-aCPSF1 to terminate transcription of M. maripaludis. Therefore, the aCPSF1 dependent termination mechanism could be widely employed in Archaea, including Lokiarchaeota belonging to Asgard Archaea, the postulated archaeal ancestor of Eukaryotes. Strikingly, aCPSF1-dependent archaeal transcription termination reported here exposes a similar 3'-cleavage mode as the eukaryotic RNA polymerase II termination, thus would shed lights on understanding the evolutionary linking between archaeal and eukaryotic termination machineries.

| S-EPMC7515710 | biostudies-literature

Antisense-Mediated Transcript Knockdown Triggers Premature Transcription Termination.

Project description:Antisense oligonucleotides (ASOs) that trigger RNase-H-mediated cleavage are commonly used to knock down transcripts for experimental or therapeutic purposes. In particular, ASOs are frequently used to functionally interrogate long noncoding RNAs (lncRNAs) and discriminate lncRNA loci that produce functional RNAs from those whose activity is attributable to the act of transcription. Transcription termination is triggered by cleavage of nascent transcripts, generally during polyadenylation, resulting in degradation of the residual RNA polymerase II (Pol II)-associated RNA by XRN2 and dissociation of elongating Pol II. Here, we show that ASOs act upon nascent transcripts and, consequently, induce premature transcription termination downstream of the cleavage site in an XRN2-dependent manner. Targeting the transcript 3' end with ASOs, however, allows transcript knockdown while preserving Pol II association with the gene body. These results demonstrate that the effects of ASOs on transcription must be considered for appropriate experimental and therapeutic use of these reagents.

| S-EPMC7093083 | biostudies-literature

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