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Salt-stress and CTD phosphatase-like 4 mediate switching of snRNA to mRNA transcription in Arabidopsis thaliana [CPL4(Oto)]

ABSTRACT: RNA polymerase II C-terminal domain (CTD) phosphorylation regulates transcription of both protein-coding mRNAs and non-coding RNAs (ncRNAs). However, understanding about CTD-phosphoregulation in plant ncRNA transcription is still obscure. Here we used Arabidopsis CTD phosphatase-like 4 knock-down lines (CPL4RNAi) and show that CPL4 functions in a genome-wide, conditional 3'-extensions of small nuclear RNA (snRNA) and biogenesis of novel snR-DPGs, which are protein-coding snRNA-mRNA fusion transcripts (snR-Downstream Protein-coding Gene). Production of snR-DPG is dependent on pol II snRNA promoter (PIIsnR), and CPL4RNAi promotes readthrough of snRNA 3’-end processing signal and pol II transcription downstream of snRNA. Also discovered was a novel unstable ncRNASSP14, which is driven by a PIIsnR and is conditionally 3'-extended to produce mRNA. In wild type, the snRNA-to-snR-DPG switching is induced by salt stress, and is associated with alteration of CTD phosphorylation status in the transcribing pol II complex. The snR-DPG transcripts occur widely in plants, suggesting that the transcriptional snRNA-to-snR-DPG switching is a previously unknown mechanism ubiquitous in plants to regulate gene expression in response to environmental stresses.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE98045 | GEO | 2018/02/16

REPOSITORIES: GEO

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Salt-stress and CTD phosphatase-like 4 mediate switching of snRNA to mRNA transcription in Arabidopsis thaliana [im-nc]

Project description:RNA polymerase II C-terminal domain (CTD) phosphorylation regulates transcription of both protein-coding mRNAs and non-coding RNAs (ncRNAs). However, understanding about CTD-phosphoregulation in plant ncRNA transcription is still obscure. Here we used Arabidopsis CTD phosphatase-like 4 knock-down lines (CPL4RNAi) and show that CPL4 functions in a genome-wide, conditional 3'-extensions of small nuclear RNA (snRNA) and biogenesis of novel snR-DPGs, which are protein-coding snRNA-mRNA fusion transcripts (snR-Downstream Protein-coding Gene). Production of snR-DPG is dependent on pol II snRNA promoter (PIIsnR), and CPL4RNAi promotes readthrough of snRNA 3’-end processing signal and pol II transcription downstream of snRNA. Also discovered was a novel unstable ncRNASSP14, which is driven by a PIIsnR and is conditionally 3'-extended to produce mRNA. In wild type, the snRNA-to-snR-DPG switching is induced by salt stress, and is associated with alteration of CTD phosphorylation status in the transcribing pol II complex. The snR-DPG transcripts occur widely in plants, suggesting that the transcriptional snRNA-to-snR-DPG switching is a previously unknown mechanism ubiquitous in plants to regulate gene expression in response to environmental stresses.

2018-02-16 | GSE98046 | GEO

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2018-10-05 | PXD008197 | Pride

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Project description:RNA Polymerase II (Pol II) carries out transcription of both protein-coding and non-coding genes. Whereas Pol II initiation at protein-coding genes has been studied in detail, Pol II initiation at non-coding genes such as small nuclear RNA (snRNA) genes is not understood at the structural level. Here we study Pol II initiation at snRNA gene promoters and show that the snRNA-activating protein complex (SNAPc) enables DNA opening and transcription initiation independent of TFIIE and TFIIH in vitro. We then resolve cryo-EM structures of the SNAPc-containing Pol II preinitiation complex (PIC) assembled on U1 and U5 snRNA promoters. The core of SNAPc binds two turns of DNA and recognizes the snRNA promoter-specific proximal sequence element (PSE) located upstream of the TATA box-binding protein TBP. Two extensions of SNAPc called wing-1 and wing-2 bind TFIIA and TFIIB, respectively, explaining how SNAPc directs Pol II to snRNA promoters. Comparison of structures of closed and open promoter complexes elucidates TFIIH-independent DNA opening. These results provide the structural basis of Pol II initiation at non-coding RNA gene promoters.

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Spliceosome specifically associates with RNA polymerase II CTD Ser5-P isoform to promote co-transcriptional splicing

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Pol II Ser7phospho ChIP-seq in mES cells

Project description:RNA Polymerase II transcribes protein-coding and many non-coding RNA genes in eukaryotes. The largest subunit of RNA Polymerase II, Rpb1, contains a hepta-peptide repeat on its C-terminal tail with three potential phosphorylation sites (Serine 2, Serine 5 and Serine 7). Mammalian Rpb1 contains 52 repeats. The phosphorylation events are catalyzed by specific protein kinases where the phosphorylation of specific residues is coupled to the transcription cycle. For example, the Cdk7 subunit of TFIIH phosphorylates both Serine 5 and Serine 7 during intiation and the Cdk9 subunit of P-TEFb phosphorylates Serine 2 during the transition into productive elongation. The dataset presented here is the genome-wide distribution of RNA Pol II with Serine 7 of the CTD phosphorylated in murine embryonic stem cells. This data, in addition to phospho-specific datasets generated in the same cell type in Rahl et al. Cell 2010 and Seila et al. Science 2008, represents the genome-wide distribution of multiple RNA Pol II isoforms in murine embryonic stem cells: total Pol II, hypophosphorylated CTD Pol II, Serine 2 phosphorylated CTD Pol II, Serine 5 phosphorylated CTD Pol II and Serine 7 phosphorylated CTD Pol II. An antibody specific to RNA Pol II Serine 7 phosphorylated CTD (gift of Dirk Eick; Chapman et al. Science 2008) was used to enrich for DNA fragments associated with this Pol II isoform in murine embryonic stem cells. DNA was purified and prepared for Illumina/Solexa sequencing following their standard protocol. This is a single dataset but together with datasets from Rahl et al. Cell 2010 and Seila et al. Science 2008, these datasets represent the genome-wide distribution of multiple RNA Pol II isoforms in murine embryonic stem cells: total Pol II, hypophosphorylated CTD Pol II, Serine 2 phosphorylated CTD Pol II, Serine 5 phosphorylated CTD Pol II and Serine 7 phosphorylated CTD Pol II.

2010-05-20 | E-GEOD-21917 | biostudies-arrayexpress

Pol II Ser7phospho ChIP-seq in mES cells

2010-05-20 | GSE21917 | GEO

RNA polymerase II Immunoprecipitation from Arabidopsis LC-MSMS

Project description:RNA polymerase II (Pol II) was immunoprecipitated from Arabidopsis thaliana seedlings, using antibodies that specifically recognize: 1) C’ terminal Domain (CTD), 2) CTD Serine 5 Phosphorylation and 3) CTD Serine 2 Phosphorylation. Proteins that co-immunoprecipitate with different Pol II pools were analysed.

2018-10-17 | PXD006004 | Pride

RNA polymerase II activity revealed by GRO-seq and pNET-seq in Arabidopsis

Project description:RNA polymerase II (Pol II) play an essential role in gene expression. Here, we adapted mammalian Native Elongation Transcript sequencing and Global Run On sequencing to profile nascent RNA genome wide in Arabidopsis. We found Pol II tends to accumulate downstream of transcription start site and pausing at proximal promoter is an important regulatory step for Pol II transcription although loosely controlled. Furthermore, the Pol II with unphosphorylated carboxyl-terminal domain (CTD) mainly accumulates downstream the TSS, while the Ser5P CTD Pol II associates with spliceosome, and the Ser2P CTD Pol II presents a sharp peak 250 base pair downstream of polyadenylation site indicating a stringent control of termination for protein coding genes; whilst the termination of noncoding genes is not. Active expressed genes can be classified into three clusters according to the distribution patterns of different Pol II isoforms. In summary, we demonstrated the modified plant GRO-seq and mNET-seq are suitable to study RNA Pol II dynamics in planta. Although transcription is conserved among high eukaryotes, Pol II has its feature in Arabidopsis.

2018-09-30 | GSE109974 | GEO

RNA polymerase II activity revealed by GRO-seq and pNET-seq in Arabidopsis

Project description:RNA polymerase II (Pol II) play an essential role in gene expression. Here, we adapted plant Native Elongation Transcript sequencing and Global Run On sequencing to profile nascent RNA genome wide in Arabidopsis. We found Pol II tends to accumulate downstream of transcription start site and pausing at proximal promoter is an important regulatory step for Pol II transcription although loosely controlled. Furthermore, the Pol II with unphosphorylated carboxyl-terminal domain (CTD) mainly accumulates downstream the TSS, while the Ser5P CTD Pol II associates with spliceosome, and the Ser2P CTD Pol II presents a sharp peak 250 base pair downstream of polyadenylation site indicating a stringent control of termination for protein coding genes; whilst the termination of noncoding genes is not. Active expressed genes can be classified into three clusters according to the distribution patterns of different Pol II isoforms. In summary, we demonstrated the modified plant GRO-seq and pNET-seq are suitable to study RNA Pol II dynamics in planta. Although transcription is conserved among high eukaryotes, Pol II has its feature in Arabidopsis.

2018-09-30 | GSE117014 | GEO

Pol II chromatin immunoprecipitation in S. cerevisiae

Project description:In Saccharomyces cerevisiae short non-coding RNA (ncRNA) generated by RNA Polymerase II (Pol II) are terminated by the NRD complex consisting of Nrd1, Nab3 and Sen1. We now show that Pcf11, a component of the cleavage and polyadenylation complex (CPAC), is generally required for NRD-dependent transcription termination through the action of its CTD interacting domain (CID). Pcf11 localizes downstream of Nrd1 on NRD terminators, and its recruitment depends on Nrd1. Furthermore mutation of the Pcf11 CID results in Nrd1 retention on chromatin, delayed degradation of ncRNA and restricts Pol II CTD Ser2 phosphorylation and Sen1-Pol II interaction. Finally, the pcf11-13 and sen1-1 mutant phenotypes are very similar as both accumulate RNA:DNA hybrids and display Pol II pausing downstream of NRD terminators. We predict a mechanism whereby Nrd1 and Pcf11 exchange on chromatin facilitates Pol II pausing and CTD Ser2-P phosphorylation. This in turn promotes Sen1 activity that is required for NRD-dependent transcription termination in vivo. ChIP-seq with antibody against pol II in wild type and Pcf11 mutants: Pcf11-2, Pcf11-9 and Pcf11-13 grown at 25C and 37C along with input samples

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