Profiling RNA Polymerase II Phosphorylation Genome-Wide in Fission Yeast

Kecman, Tea; Heo, Dong-Hyuk; Vasiljeva, Lidia

doi:10.1016/bs.mie.2018.07.009

Cited by 4 publications

(6 citation statements)

References 23 publications

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“…An untagged wild type was included as control. RNAPII-ChIP signal for an isogenic wild type is shown for reference (α-Rpb1, 8WG16) (Kecman et al, 2018; GEO: GSE111326). Positions of protein-coding genes and non-coding genes are indicated in black and grey, respectively.…”

Section: Resultsmentioning

confidence: 99%

“…Trendlines were fitted using linear regression. RNAPII ChIP data from Kecman et al, 2018; GEO: GSE111326 (n = 2). C Metagene analysis of mean ChIP-seq coverage of Dbp2-HTP and Srp2-HTP (n = 3), and total RNAPII (α-rpb1 (8WG16) in Dbp2-3myc; n = 2) (upper panel) across ribosomal protein genes (RPGs) including 200 bp upstream and 500 bp downstream of the annotated transcription units.…”

Section: Resultsmentioning

confidence: 99%

“…The coupling between 3’-end processing and transcription termination is further promoted by the activation of the CPAC-associated phosphatase Dis2/PNUTS-PP1 during PAS recognition. Dis2/PNUTS-PP1 then dephosphorylates the elongation factor Spt5 to slow down transcription in the termination zone, giving the torpedo nuclease an edge over RNAPII (Cortazar et al, 2019; Kecman, Kuś, et al, 2018; Parua et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

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DEAD-box ATPase Dbp2 mediates mRNA release after 3'-end formation

Aydin,

Boehme,

Keil

et al. 2024

Preprint

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mRNA biogenesis in the eukaryotic nucleus is a highly complex process. The numerous RNA processing steps are tightly coordinated to ensure that only fully processed transcripts are released from chromatin for export from the nucleus. Here, we present the hypothesis that fission yeast Dbp2, a ribonucleoprotein complex (RNP) remodelling ATPase of the DEAD-box family, is the key enzyme in an RNP assembly checkpoint at the 3'-end of genes. We show that Dbp2 interacts with the cleavage and polyadenylation complex (CPAC) and localizes to cleavage bodies, which are enriched for 3'-end processing factors and proteins involved in nuclear RNA surveillance. Upon loss of Dbp2, 3'-processed, polyadenylated RNAs accumulate on chromatin and in cleavage bodies, and CPAC components are depleted from the soluble pool. Under these conditions, cells display an increased likelihood to skip polyadenylation sites and a delayed transcription termination, suggesting that levels of free CPAC components are insufficient to maintain normal levels of 3'-end processing. Our data support a model in which Dbp2 is the active component of an mRNP remodelling checkpoint that licenses RNA export and is coupled to CPAC release.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

DEAD-box ATPase Dbp2 mediates mRNA release after 3'-end formation

Aydin,

Boehme,

Keil

et al. 2024

Preprint

View full text Add to dashboard Cite

show abstract

“…All ChIP-Seq experiments were carried out in duplicates except Ser7-P ChIP-Seq. Chromatin was prepared as previously described ( Kecman et al., 2018b ). Briefly, exponentially growing cells (200 ml) were crosslinked with 1% formaldehyde solution for 20 min at room temperature.…”

Section: Methodsmentioning

confidence: 99%

“…Chromatin immunoprecipitation (ChIP-Seq and ChIP-qPCR) All ChIP-Seq experiments were carried out in duplicates except Ser7-P ChIP-Seq. Chromatin was prepared as previously described (Kecman et al, 2018b Article ll…”

Section: Resource Availabilitymentioning

confidence: 99%

Transcription and chromatin-based surveillance mechanism controls suppression of cryptic antisense transcription

et al. 2021

Self Cite

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Phosphorylation of the RNA polymerase II C-terminal domain Y 1 S 2 P 3 T 4 S 5 P 6 S 7 consensus sequence coordinates key events during transcription, and its deregulation leads to defects in transcription and RNA processing. Here, we report that the histone deacetylase activity of the fission yeast Hos2/Set3 complex plays an important role in suppressing cryptic initiation of antisense transcription when RNA polymerase II phosphorylation is dysregulated due to the loss of Ssu72 phosphatase. Interestingly, although single Hos2 and Set3 mutants have little effect, loss of Hos2 or Set3 combined with ssu72D results in a synergistic increase in antisense transcription globally and correlates with elevated sensitivity to genotoxic agents. We demonstrate a key role for the Ssu72/Hos2/Set3 mechanism in the suppression of cryptic antisense transcription at the 3 0 end of convergent genes that are most susceptible to these defects, ensuring the fidelity of gene expression within dense genomes of simple eukaryotes.

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DEAD-box ATPase Dbp2 is the key enzyme in an mRNP assembly checkpoint at the 3’-end of genes and involved in the recycling of cleavage factors

Aydin,

Schreiner,

Böhme

et al. 2024

Nat Commun

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AbstractmRNA biogenesis in the eukaryotic nucleus is a highly complex process. The numerous RNA processing steps are tightly coordinated to ensure that only fully processed transcripts are released from chromatin for export from the nucleus. Here, we present the hypothesis that fission yeast Dbp2, a ribonucleoprotein complex (RNP) remodelling ATPase of the DEAD-box family, is the key enzyme in an RNP assembly checkpoint at the 3’-end of genes. We show that Dbp2 interacts with the cleavage and polyadenylation complex (CPAC) and localises to cleavage bodies, which are enriched for 3’-end processing factors and proteins involved in nuclear RNA surveillance. Upon loss of Dbp2, 3’-processed, polyadenylated RNAs accumulate on chromatin and in cleavage bodies, and CPAC components are depleted from the soluble pool. Under these conditions, cells display an increased likelihood to skip polyadenylation sites and a delayed transcription termination, suggesting that levels of free CPAC components are insufficient to maintain normal levels of 3’-end processing. Our data support a model in which Dbp2 is the active component of an mRNP remodelling checkpoint that licenses RNA export and is coupled to CPAC release.

show abstract

Profiling RNA Polymerase II Phosphorylation Genome-Wide in Fission Yeast

Cited by 4 publications

References 23 publications

DEAD-box ATPase Dbp2 mediates mRNA release after 3'-end formation

DEAD-box ATPase Dbp2 mediates mRNA release after 3'-end formation

Transcription and chromatin-based surveillance mechanism controls suppression of cryptic antisense transcription

DEAD-box ATPase Dbp2 is the key enzyme in an mRNP assembly checkpoint at the 3’-end of genes and involved in the recycling of cleavage factors

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