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ProteomicsMIR sequences recruit zinc finger protein ZNF768 to expressed genes
Mammalian-wide interspersed repeats (MIRs) are retrotransposed elements of mammalian genomes. Here we report the specific binding of zinc finger protein ZNF768 to the sequence motif GCTGTGTG (N20) CCTCTCTG in the core region of MIRs. ZNF768 binding is preferentially associated with euchromatin and p...
ORGANISM(S): Homo sapiens (Human) 
2018-10-29 | PXD010831 | Pride
Heptad-repeats Elongator Mammalian interspersed repeats Gene regulation Zinc finger protein Placentalia 
ProteomicsIdentification of cellular CDK9 substrates using an analog-sensitive cell line
Analog-sensitive kinase technology allows for specific inhibition of a given kinase. Here we utilize an analog-sensitive CDK9 cell line to determine the impact of CDK9 inhibition on the phospho-proteome of human cells. Specifically, we aim to identify substrates of CDK9 in a quantitative way using s...
ORGANISM(S): Homo sapiens (Human) 
2019-11-11 | PXD014825 | Pride
Analog-sensitive Mass spectrometry P-tefb Protein phosphorylation 
ProteomicsTyrosine-1 of RNA polymerase II CTD controls global termination of gene transcription in mammals
The aim of the project was to analyse the functional role of Tyrosine-1 of mammalian RNA polymerase II CTD in the regulation of transcription-coupled processes. We studied mammalian CTD mutants to analyze the function of tyrosine1 residues. Mutation of 3/4 of the tyrosine residues in a mutant YFFF ...
ORGANISM(S): Homo sapiens (Human) 
2018-01-09 | PXD008270 | Pride
Tyrosine1 Transcription termination Promoter-proximal pausing Read-through transcription Divergent transcription. Ctd Rna polymerase ii 
GenomicsPol II Ser7phospho ChIP-seq in mES cells
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 ...
ORGANISM(S): Mus musculus 
2010-05-20 | E-GEOD-21917 | biostudies-arrayexpress
TranscriptomicsEstrogen-dependent gene expression in human breast cancer cells relies upon proteosome-dependent monoubiquitination of histone H2B
The estrogen receptor-alpha (ERα) determines breast cancer cell phenotype and is a prognostic indicator. A better understanding of the mechanisms controlling ERα function may uncover improved strategies for the treatment of breast cancer. Proteasome inhibition was previously reported to regulate e...
ORGANISM(S): Homo sapiens 
2011-11-22 | E-GEOD-31118 | biostudies-arrayexpress
TranscriptomicsProteasome inhibition blocks estrogen-dependent gene transcription by decreasing histone H2B monoubiquitination in human breast cancer cells
The estrogen receptor-alpha (ERα) determines breast cancer cell phenotype and is a prognostic indicator. A better understanding of the mechanisms controlling ERα function may uncover improved strategies for the treatment of breast cancer. Proteasome inhibition was previously reported to regulate est...
ORGANISM(S): Homo sapiens 
2011-11-22 | E-GEOD-30931 | biostudies-arrayexpress
GenomicsTyrosine phosphorylation of RNA Polymerase II CTD is associated with antisense promoter transcription and active enhancers in mammalian cells
In mammals, the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II consists of 52 conserved heptapeptide repeats containing the consensus sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. Post-translational modifications of the CTD coordinate the transcription cycle and various steps of mRNA matura...
ORGANISM(S): Homo sapiens 
2014-06-01 | E-GEOD-52914 | biostudies-arrayexpress
TranscriptomicsChromatin immunoprecipitation of yeast to assess changes in RNA Polymerase II, Ser5-P, and Ser7-P occupancy upon chemical inhibition of Kin28
Chromatin Immunoprecipitation to assess changes in RNA Polymerase II, Ser5-P, and Ser7-P occupancy in S. cerevisiae upon chemical inhibition of Kin28
ORGANISM(S): Saccharomyces cerevisiae 
2009-07-01 | E-TABM-689 | biostudies-arrayexpress
GenomicsIn vivo live imaging of RNA polymerase II transcription factories in primary cells
Transcription steps are marked by different modifications of the C-terminal domain of RNA polymerase II (RNAPII). Phosphorylation of Ser5 and Ser7 by cyclin-dependent kinase 7 (CDK7) as part of TFIIH marks initiation, whereas phosphorylation of Ser2 by CDK9 marks elongation. These processes are thou...
ORGANISM(S): Mus musculus 
2013-05-13 | E-GEOD-46849 | biostudies-arrayexpress
GenomicsThreonine-4 of Mammalian RNA Polymerase II CTD is Targeted by Polo-like Kinase-3 and Required for Transcriptional Elongation
Eukaryotic RNA polymerase II (Pol II) has evolved an array of heptad repeats with the consensus sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7 at the carboxy-terminal domain (CTD) of the large subunit (Rpb1). Differential phosphorylation of Ser2, Ser5, and Ser7 in the 5M-bM-^@M-^Y and 3M-bM-^@M-^Y regi...
ORGANISM(S): Homo sapiens 
2012-06-04 | E-GEOD-37519 | biostudies-arrayexpress
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