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Splicing of nascent RNA coincides with intron exit from RNA polymerase II

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

ORGANISM(S): Saccharomyces cerevisiae Schizosaccharomyces pombe

PROVIDER: GSE70908 | GEO | 2016/03/24

SECONDARY ACCESSION(S): PRJNA289900

REPOSITORIES: GEO

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Splicing of nascent RNA coincides with intron exit from RNA polymerase II

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-03-24 | E-GEOD-70908 | biostudies-arrayexpress

Splicing of Nascent RNA Coincides with Intron Exit from RNA Polymerase II.

Project description:Protein-coding genes in eukaryotes are transcribed by RNA polymerase II (Pol II) and introns are removed from pre-mRNA by the spliceosome. Understanding the time lag between Pol II progression and splicing could provide mechanistic insights into the regulation of gene expression. Here, we present two single-molecule nascent RNA sequencing methods that directly determine the progress of splicing catalysis as a function of Pol II position. Endogenous genes were analyzed on a global scale in budding yeast. We show that splicing is 50% complete when Pol II is only 45 nt downstream of introns, with the first spliced products observed as introns emerge from Pol II. Perturbations that slow the rate of spliceosome assembly or speed up the rate of transcription caused splicing delays, showing that regulation of both processes determines in vivo splicing profiles. We propose that matched rates streamline the gene expression pathway, while allowing regulation through kinetic competition.

| S-EPMC4826323 | biostudies-literature

Splicing of nascent RNA coincides with intron exit from RNA polymerase II

Project description:Splicing of nascent RNA coincides with intron exit from RNA polymerase II

| PRJNA289900 | ENA

Intron looping is mediated by U1 snRNP and RNA polymerase II co-transcriptionally

Project description:This SuperSeries is composed of the SubSeries listed below.

2021-06-16 | GSE145092 | GEO

RNA polymerase II is necessary for spatial chromatin reorganization following exit from mitosis

Project description:This SuperSeries is composed of the SubSeries listed below.

2021-06-18 | GSE160321 | GEO

Mapping RNA exit channel on transcribing RNA polymerase II by FRET analysis.

Project description:A simple genetic tag-based labeling method that permits specific attachment of a fluorescence probe near the C terminus of virtually any subunit of a protein complex is implemented. Its immediate application to yeast RNA polymerase II (pol II) enables us to test various hypotheses of RNA exit channel by using fluorescence resonance energy transfer (FRET) analysis. The donor dye is labeled on a site near subunit Rpb3 or Rpb4, and the acceptor dye is attached to the 5' end of RNA transcript in the pol II elongation complex. Both in-gel and single-molecule FRET analysis show that the growing RNA is leading toward Rpb4, not Rpb3, supporting the notion that RNA exits through the proposed channel 1. Distance constraints derived from our FRET results, in conjunction with triangulation, reveal the exit track of RNA transcript on core pol II by identifying amino acids in the vicinity of the 5' end of RNA and show that the extending RNA forms contacts with the Rpb7 subunit. The significance of RNA exit route in promoter escape and that in cotranscriptional mRNA processing is discussed.

| S-EPMC2610012 | biostudies-literature

RNA polymerase II collision interrupts convergent transcription

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2012-11-30 | E-GEOD-38384 | biostudies-arrayexpress

Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation

Project description:This SuperSeries is composed of the SubSeries listed below.

2010-12-09 | GSE25495 | GEO

The conserved protein Seb1 drives transcription termination by binding RNA polymerase II and nascent RNA.

Project description:Termination of RNA polymerase II (Pol II) transcription is an important step in the transcription cycle, which involves the dislodgement of polymerase from DNA, leading to release of a functional transcript. Recent studies have identified the key players required for this process and showed that a common feature of these proteins is a conserved domain that interacts with the phosphorylated C-terminus of Pol II (CTD-interacting domain, CID). However, the mechanism by which transcription termination is achieved is not understood. Using genome-wide methods, here we show that the fission yeast CID-protein Seb1 is essential for termination of protein-coding and non-coding genes through interaction with S2-phosphorylated Pol II and nascent RNA. Furthermore, we present the crystal structures of the Seb1 CTD- and RNA-binding modules. Unexpectedly, the latter reveals an intertwined two-domain arrangement of a canonical RRM and second domain. These results provide important insights into the mechanism underlying eukaryotic transcription termination.

| S-EPMC5382271 | biostudies-literature

Do DEAD-box proteins promote group II intron splicing without unwinding RNA?

Project description:The DEAD-box protein Mss116p promotes group II intron splicing in vivo and in vitro. Here we explore two hypotheses for how Mss116p promotes group II intron splicing: by using its RNA unwinding activity to act as an RNA chaperone or by stabilizing RNA folding intermediates. We show that an Mss116p mutant in helicase motif III (SAT/AAA), which was reported to stimulate splicing without unwinding RNA, retains ATP-dependent unwinding activity and promotes unfolding of a structured RNA. Its unwinding activity increases sharply with decreasing duplex length and correlates with group II intron splicing activity in quantitative assays. Additionally, we show that Mss116p can promote ATP-independent RNA unwinding, presumably via single-strand capture, also potentially contributing to DEAD-box protein RNA chaperone activity. Our findings favor the hypothesis that DEAD-box proteins function in group II intron splicing as in other processes by using their unwinding activity to act as RNA chaperones.

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