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Early effects of cdkf;1 RNAPII CTD Serine-7 kinase mutation on regulation of transcription in 7 days old Arabidopsis seedlings

ABSTRACT: Serine phosphorylation of conserved Y1S2P3T4S5P6S7 repeats of RNA polymerase II carboxy-terminal domain (RNAPII CTD) plays a central role in the regulation of transcription and co-transcriptional RNA processing. Maintenance of CTD phosphoserine-7 mark in Arabidopsis requires the CDKF;1 kinase, which mediates in vivo activation of downstream-acting CDKD CTD kinase family. Knockout mutations of CDKF;1 lead to over 50% reduction of RNAPII CTD Ser-7 phosphorylation as early as 7 days after germination in seedlings. The transcript profiling experiment aimed at determining how early changes in CTD Ser-7 phosphorylation affect global regulation of transcription. We used Affymetrix ATH1-121501 Genome Array to compare global transcript levels in wild type and cdkf;1-2 mutant seedlings 7 days after germination.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE27687 | GEO | 2011/09/01

SECONDARY ACCESSION(S): PRJNA138167

REPOSITORIES: GEO

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Early effects of cdkf;1 RNAPII CTD Serine-7 kinase mutation on regulation of transcription in 7 days old Arabidopsis seedlings

Project description:Serine phosphorylation of conserved Y1S2P3T4S5P6S7 repeats of RNA polymerase II carboxy-terminal domain (RNAPII CTD) plays a central role in the regulation of transcription and co-transcriptional RNA processing. Maintenance of CTD phosphoserine-7 mark in Arabidopsis requires the CDKF;1 kinase, which mediates in vivo activation of downstream-acting CDKD CTD kinase family. Knockout mutations of CDKF;1 lead to over 50% reduction of RNAPII CTD Ser-7 phosphorylation as early as 7 days after germination in seedlings. The transcript profiling experiment aimed at determining how early changes in CTD Ser-7 phosphorylation affect global regulation of transcription. We used Affymetrix ATH1-121501 Genome Array to compare global transcript levels in wild type and cdkf;1-2 mutant seedlings 7 days after germination. Wild type and cdkf;1-2 mutant Arabidopsis (Col-0) seedlings were grown in solid MSAR medium (Koncz, C., Martini, N., Szabados, L., Hrouda, M., Bachmair, A., and Schell, J. (1994). Specialized vectors for gene tagging and expression studies. In: Plant Molecular Biology Manual, Gelvin,S., and Schilperoort, B. (eds.), Kluwer Academic Publishers, Dordrecht-Boston-London, B2, 1-22.) containing ½ concentration of macro elements and 0.5% sucrose in Petri-dishes at 22°C, 120 mol/m2s light intensity and 8h light/16h dark period. Seedling were collected at 4h after the start of the light period in liquid nitrogen for RNA preparation.

2011-08-31 | E-GEOD-27687 | biostudies-arrayexpress

Distribution of RNA polymerase II and changes of carbo-terminal phosphorylation sites after INTS11 knockdown

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2023-07-25 | GSE207269 | GEO

The C-Terminal Domain of RNA Polymerase II is Modified by Site-Specific Methylation

Project description:The Carboxy-terminal domain (CTD) of RNA Polymerase II (RNAPII) in mammals undergoes extensive post-translational modification, which is essential for transcriptional initiation and elongation. Here, we show that the CTD of RNAPII is methylated at a single arginine (R1810) by the transcriptional co-activator CARM1. Although methylation at R1810 is present on the hyper-phosphorylated form of RNAPII in vivo, Ser-2 or Ser-5 phosphorylation inhibit CARM1 activity towards this site in vitro, suggesting that methylation occurs before transcription initiation. Mutation of R1810 results in the mis-expression of a variety of snRNAs and snoRNAs, an effect that is also observed in Carm1-/- MEFs. These results demonstrate that CTD methylation facilitates the expression of select RNAs, perhaps serving to discriminate the RNAPII-associated machinery recruited to distinct gene types. To address the function of RNAPII methylation, we generated Raji cell lines expressing an RNA Polymerase II resistant to Î±-amanitin and carrying either wild-type R1810 or an arginine to alanine substitution at that same residue, abolishing R1810 methylation of the CTD. In cells cultured in Î±-amanitin, the Î±-amanitin-resistant mutants fully replaced the functions of endogenous RNAPII, allowing us to study if gene-expression is affected by the absence of R1810me

2011-04-01 | E-GEOD-27315 | biostudies-arrayexpress

The C-Terminal Domain of RNA Polymerase II is Modified by Site-Specific Methylation

2011-04-01 | GSE27315 | GEO

Expression profiling of rpb1-12XWTCTD and rpb1-12XS2ACTD fission yeast strains.

2011-09-01 | GSE31369 | GEO

Super-enhancer-associated oncogenes as novel therapeutic targets in osteosarcoma (Microarray gene expression data)

Project description:CDK7 is a component of the general transcription factor IIH, which regulates RNAPII initiation and elongation.THZ2, a new molecular inhibitor, can completely inhibit the phosphorylation of the established intracellular CDK7 substrate RNAPII CTD at Ser-2, -5 and -7 through irreversible covalent binding to CDK7. Gene expression profiling was then performed to investigate the THZ2-induced transcription effect, and search the subset of sensitive genes in these 2 osteosarcoma cell lines.

2019-12-27 | GSE134603 | GEO

Expression profiling of rpb1-12XWTCTD and rpb1-12XS2ACTD fission yeast strains.

Project description:In fission yeast, the nuclear-localized Lsk1p-Lsc1p-Lsg1p cyclin dependent kinase complex is required for the reliable execution of cytokinesis and is also required for Ser-2 phosphorylation RNA pol II carboxy terminal domain. To address whether alterations in CTD phosphorylation might selectively alter expression of cytokinesis genes, expression profiling of site-directed CTD mutants was performed. Strains bearing the rpb1-12XCTD and rpb1-12XS2ACTD mutations were grown to mid-log phase in YES media and treated with 0.5uM LatA (or the solvent control, DMSO) for three hours at 30C. Three biological replicates were performed.

2011-08-31 | E-GEOD-31369 | biostudies-arrayexpress

Kinetics of RNA polymerase 2 recruitment and H3K36me3 deposition after stimulation of murine T-cells

Project description:Activation of immune cells results in extremely rapid functional changes, yet it remains enigmatic how this is accomplished. By combining time-courses of RNA-polymerase-II (RNAPII) Chip-Seq, 4sU-Seq, RNA-Seq and ribosome profiling during Th1 activation we provide a genome-wide view on temporal dynamics for ~10.000 genes. Gene responses vary in time and magnitude and allow the identification of unknown immediate early (IEG) and posttranscriptionally regulated genes. However, >90% are regulated transcriptionally with coupled changes in translation. Surprisingly, not poised, but rather re-positioned RNAPII correlates with transcriptional changes and coincides with fluctuations in cotranscriptional splicing, which lags behind at first. Unspliced transcripts remain here at the chromatin, but are already poly-adenylated. Later splicing readjusts, correlating with progressive Ser-2 phosphorylation of the CTD domain of RNAPII and activation of the elongation-complex pTEFb. Thus, rapid re-positioning of RNAPII and regulating the phosphorylation state of its CTD dictates almost all events during immune responses, including post-transcriptional processes.

2017-03-31 | GSE94698 | GEO

Expanding the CTD code: methylation of non-consensus Lysine residues marks early transcription in mammalian cells

Project description:Dynamic post-translational modification of RNA polymerase II (RNAPII) coordinates the co-transcriptional recruitment of enzymatic complexes that regulate chromatin states and co-transcriptional processing of nascent RNA. Extensive phosphorylation of serine residues occurs at the structurally-disordered C-terminal domain (CTD) of the largest RNAPII subunit, which is composed of multiple heptapeptide repeats with consensus sequence Y1-S2-P3-T4-S5-P6-S7. Serine-5 and Serine-7 phosphorylation mark transcription initiation, whereas Serine-2 phosphorylation coincides with productive elongation. In vertebrates, the CTD has eight non-canonical substitutions of Serine-7 into Lysine-7, which can be acetylated (K7ac). Here, we describe for the first time mono- and di-methylation of CTD Lysine-7 residues (K7me1 and K7me2). K7me1 and K7me2 are observed during the earliest transcription stages and precede or accompany Serine-5 and Serine-7 phosphorylation. Genome wide mapping of 2 novel RNAPII post-translational modifications (CTD-K7me1 and CTD-K7me2) in mouse ES cells.

2015-12-22 | E-GEOD-72876 | biostudies-arrayexpress

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Project description:We report calibrated transcriptome of rpb1-CTD-S2A and WT of S. pombe cells. Phosphorylation of the RNA polymerase II (Pol II) C-terminal domain on heptad Y1S2P3T4S5P6S7 coordinates key events during transcription and when its deregulation leads to defects in transcription and RNA processing. Here we report that alanine substitution of all Ser2 in CTD result in increased antisense transcription.

2021-08-26 | GSE171307 | GEO

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