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Arabidopsis thaliana

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

PROVIDER: PRJNA383812 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5464550_1.fastq.gz	Fastqsanger.gz
	SRR5464550_2.fastq.gz	Fastqsanger.gz
	SRR5464551_1.fastq.gz	Fastqsanger.gz
	SRR5464551_2.fastq.gz	Fastqsanger.gz
	SRR5464546_1.fastq.gz	Fastqsanger.gz

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E-GEOD-98045

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

2020-04-15 | E-GEOD-98045 | ExpressionAtlas

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

Project description:Salt-stress and CTD phosphatase-like 4 mediate switching of snRNA to mRNA transcription in Arabidopsis thaliana

| PRJNA383803 | ENA

Arabidopsis thaliana

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

| PRJNA383872 | ENA

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

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

2018-02-16 | GSE98045 | GEO

RNA biotype-associated molecular classification in hepatitis B-related hepatocellular carcinoma

Project description:Recent advance of RNA-seq technology enabled us to profile the diverse variations of RNA transcripts precisely, including the variants from alternative splicing as well as non-coding transcripts. Here, by performing transcriptome profiling including coding and noncoding transcripts, we identify four molecular subtypes of hepatitis B-related hepatocellular carcinoma (HCC) patients that are characterized by enriched expression of the RNA biotypes of noncoding (NC) and immune-related transcripts (IM) (i.e., IM+NC+, IM-NC+, IM+NC-, IM-NC-). The subtype IM+NC+ shows better prognostic outcome, while the subtype IM+NC- shows the worst prognostic outcome, respectively. Further interrogation of the subtypes identifies long noncoding transcripts (i.e., LINC00844, C3P1, and TRPG1-AS1) as well as an alternatively spliced event of USO1 that play pivotal roles in HCC progression. In addition, we report an oncogenic fusion transcript SLC39A14-PIWIL2 that promotes an aggressive phenotype of HCC. Our comprehensive and systematic analysis of HCC transcriptome identify RNA biotype-based molecular classification, revealing novel driver transcriptome variants that can be potential biomarkers and/or therapeutic targets for precision medicine.

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Arabidopsis thaliana

Project description:A CTD phosphatase modulates eIF4AIII nucleocytoplasmic shuttling and nonsense-mediated mRNA decay

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Phospho-site mutants of the RNA Polymerase II C-terminal domain alter subtelomeric gene expression and chromatin modification state in fission yeast

Project description:Eukaryotic gene expression requires that RNA Polymerase II (RNAP II) gain access to DNA in the context of chromatin. The C-terminal domain (CTD) of RNAP II recruits chromatin modifying enzymes to promoters, allowing for transcription initiation or repression. Specific CTD phosphorylation marks facilitate recruitment of chromatin modifiers, transcriptional regulators, and RNA processing factors during the transcription cycle. However, the readable code for recruiting such factors is still not fully defined and how CTD modifications affect related families of genes or regional gene expression is not well understood. Here we examine the effects of manipulating the Y1S2P3T4S5P6S7 heptapeptide repeat of the CTD of RNAP II in Schizosaccharomyces pombe by substituting non-phosphorylatable alanines for Ser2 and/or Ser7 and the phosphomimetic glutamic acid for Ser7. Global gene expression analyses were conducted using splicing-sensitive microarrays and validated via RT-qPCR. The CTD mutations did not affect pre-mRNA splicing or snRNA levels. Rather, the data revealed upregulation of subtelomeric genes and alteration of the repressive histone H3 lysine 9 methylation (HeK9me) landscape. The data further indicate that H3K9me and expression status are not fully correlated, suggestive of CTD-dependent subtelomeric repression mechansims that act independently of H3K9me levels. Splicing sensitive S. pombe microarrays (Agilent-027365) were used to compare the splicing and expression profile of four mutant strains relative to WT control with 3-5 biological replicates and dye flipped samples

2016-08-10 | E-GEOD-83426 | biostudies-arrayexpress

A Universal RNA Polymerase II CTD Cycle Is Orchestrated by Complex Interplays Between Kinase, Phosphatase and Isomerase Enzymes Along Genes

Project description:Transcription by RNA polymerase II (RNAPII) is coupled to mRNA processing and chromatin modifications via the C-terminal domain (CTD) of its largest subunit, consisting of multiple repeats of the heptapeptide YSPTSPS. Pioneering studies showed that CTD serines are differentially phosphorylated along genes in a prescribed pattern during the transcription cycle. Genome-wide analyses challenged this idea, suggesting that this cycle is non-uniform among different genes. Moreover, the respective role of enzymes responsible for CTD modifications remains controversial. Here, we systematically profiled the location of the RNAPII phospho-isoforms in wild type cells and mutants for most CTD modifying enzymes. Together with results of in vitro assays, these data reveal a complex interplay between the modifying enzymes, and provide evidence that the CTD cycle is uniform across genes. We also identify Ssu72 as the Ser7 phosphatase and show that proline isomerization is a key regulator of CTD dephosphorylation at the end of genes.

2012-02-01 | GSE29403 | 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

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