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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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CK2 regulates transcriptional elongation

ABSTRACT: CK2 binds to actively transcribed regions in the genome and regulates transcriptional elongation. Identification of genome-wide binding sites of CK2?, and examination of the effect of Pol II binding upon CK2 inhibition in LNCaP cells

ORGANISM(S): Homo sapiens

SUBMITTER: Yuliang Tan

PROVIDER: E-GEOD-58607 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Tyrosine phosphorylation of histone H2A by CK2 regulates transcriptional elongation.

Basnet Harihar H Su Xue B XB Tan Yuliang Y Meisenhelder Jill J Merkurjev Daria D Ohgi Kenneth A KA Hunter Tony T Pillus Lorraine L Rosenfeld Michael G MG

Nature 20140924 7530

Post-translational histone modifications have a critical role in regulating transcription, the cell cycle, DNA replication and DNA damage repair. The identification of new histone modifications critical for transcriptional regulation at initiation, elongation or termination is of particular interest. Here we report a new layer of regulation in transcriptional elongation that is conserved from yeast to mammals. This regulation is based on the phosphorylation of a highly conserved tyrosine residue ...[more]

PMID: 25252977

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Project description:LSD1n regulates transcriptional elongation by removing H4K20 methylation. Identification of genome-wide binding sites of LSD1, and examination of the histone modifications upon LSD1n deletion in primary cortical neurons

2015-07-27 | E-GEOD-63271 | biostudies-arrayexpress

ATAC-seq in control compared to ZEB1 knock-down MDA-MB-231 cells

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Substrate selectivity for semisynthetic CK2 proteins

Project description:This SuperSeries is composed of the following subset Series: GSE33149: Substrate selectivity for semisynthetic CK2 proteins with various posttranslational modifications GSE33150: Substrate selectivity for semisynthetic CK2 proteins with Pin1 Refer to individual Series

2011-10-24 | E-GEOD-33151 | biostudies-arrayexpress

CK2 regulates transcriptional elongation

Project description:CK2 binds to actively transcribed regions in the genome and regulates transcriptional elongation.

2014-09-30 | GSE58607 | GEO

Dynamics of H3K4me2 during cardiac lineage reprogramming

Project description:During reprogramming of fibroblasts into cardiomyocyte-like cells by overexpression of transcription factors, GATA4, Hand2, Mef2C and Tbx5 (GHMT), H3K4Me2, an active histone code, shifts from fibroblast-exclusive peaks to cardiomyocyte-exclusive peaks. Important cardiac genes are gradually marked by this active histone marker. Mouse embryonic fibroblasts (MEFs) and neonatal mouse ventricular cardiomyocytes (NMVMs) represent fibroblasts and cardiomyocytes, respectively. Chromatins harvested from MEFs infected with retroviruses carrying GHMT at day 3, day 5, day 7 post-viral infection were prepared for immunoprecipitation.

2015-07-28 | E-GEOD-71392 | biostudies-arrayexpress

Substrate selectivity for semisynthetic CK2 proteins with various posttranslational modifications

Project description:Protein Ser/Thr kinase CK2 is involved in a myriad of cellular processes including cell growth and proliferation by phosphorylating hundreds of substrates, yet the regulation process of CK2 function is poorly understood. The CK2 catalytic subunit, CK2α, is modified by O-GlcNAc on Ser347 proximal to a Cdk1 phosphorylation site at Thr344 on the same protein. The substrate selectivity for protein kinase CK2 was examined by performing kinase assays on protein microarrays spotted with 17,000 human proteins. Semisynthetic CK2α proteins were prepared to contain an unmodified C-terminal tail, S-GlcNAc-Serine at S347, or Pfa (non-hyrdolyzeable phosphomimic) at T344. These semisynthetic proteins were used to determine if the posttranslational modifications on CK2 alpha modulate the substrate selectivity for this pleiotropic kinase. The different semisynthetic CK2α proteins were tested alone and in the presence of the regulatory subunit CK2β since it is known that the CK2α subunit is active both in its isolated state and in the heterotetrameric state formed in the presence of the regulatory beta subunit. The CK2β subunit has been shown to modulate CK2 activity with some substrates and not others. In the study presented here, kinase assays were performed using three different semisynthetic CK2 alpha proteins: unmodified C-terminal tail; S-GlcNAc-Ser at 347; and Pfa (phosphomimic) at 344. The semisynthetic proteins were each tested alone and in the presence of the regualatory CK2 beta subunit. There were six different kinase conditions and each condition was performed in duplicate and one no kinase control was performed to eliminate autophorylated proteins.

2011-10-24 | E-GEOD-33149 | biostudies-arrayexpress

Regulation of DNA methylation by CK2-mediated phosphorylation of DNMT3A (Beadchip)

Project description:DNA methylation is a central epigenetic modification that has essential roles in cellular processes including chromatin structure, gene regulation, development and disease. The de novo DNA methyltransferases are responsible for the generation of genomic methylation patterns, but the underlying mechanisms are still poorly understood. Here, we show that phosphorylation of DNMT3A by the CK2 protein kinase regulates the establishment of DNA methylation patterns. We find that DNMT3A is phosphorylated by CK2 at two key residues located near its PWWP domain. We observed that, through phosphorylation of these residues, CK2 negatively regulates DNMT3A’s ability to methylate DNA and consistent with this, CK2 was found to decrease overall genomic level of 5-methylcytosine. Further, genome-wide DNA methylation analysis in CK2-depleted cells revealed that CK2 affects primarily CpG methylation of several heterochromatin repeats as well as Alu elements. Along these lines, we found that CK2-mediated phosphorylation of DNMT3A was required for its proper heterochromatin localization. Our results define phosphorylation as a new mode of regulation of de novo DNA methyltransferase function. These findings further uncover a previously unrecognized mechanism for the regulation of methylation at repetitive elements. They shed new light into the origin of DNA methylation patterns.

2014-07-17 | GSE26164 | GEO

Substrate selectivity for semisynthetic CK2 proteins with various posttranslational modifications

2011-10-25 | GSE33149 | GEO

Regulation of DNA methylation by CK2-mediated phosphorylation of DNMT3A (Beadchip)

Project description:DNA methylation is a central epigenetic modification that has essential roles in cellular processes including chromatin structure, gene regulation, development and disease. The de novo DNA methyltransferases are responsible for the generation of genomic methylation patterns, but the underlying mechanisms are still poorly understood. Here, we show that phosphorylation of DNMT3A by the CK2 protein kinase regulates the establishment of DNA methylation patterns. We find that DNMT3A is phosphorylated by CK2 at two key residues located near its PWWP domain. We observed that, through phosphorylation of these residues, CK2 negatively regulates DNMT3AM-bM-^@M-^Ys ability to methylate DNA and consistent with this, CK2 was found to decrease overall genomic level of 5-methylcytosine. Further, genome-wide DNA methylation analysis in CK2-depleted cells revealed that CK2 affects primarily CpG methylation of several heterochromatin repeats as well as Alu elements. Along these lines, we found that CK2-mediated phosphorylation of DNMT3A was required for its proper heterochromatin localization. Our results define phosphorylation as a new mode of regulation of de novo DNA methyltransferase function. These findings further uncover a previously unrecognized mechanism for the regulation of methylation at repetitive elements. They shed new light into the origin of DNA methylation patterns. Bisulphite converted DNA from 6 samples were hybridised to the Illumina Infinium 27K Human Methylation Beadchip v1.2

2014-07-17 | E-GEOD-26164 | biostudies-arrayexpress

Substrate selectivity for semisynthetic CK2 proteins with Pin1

2011-10-25 | GSE33150 | GEO

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