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TranscriptomicsA combined genomic approach unveils the transcriptional basis of heterogeneity of human pancreatic ductal adenocarcinoma [RNA-seq]
The histological grade of carcinomas describes the ability of tumor cells to organize differentiated epithelial structures and has prognostic impact. Molecular control of differentiation in normal and cancer cells relies on lineage-determining transcription factors (TFs) that activate the repertoire...
ORGANISM(S): Homo sapiens 
2016-01-18 | E-GEOD-64558 | biostudies-arrayexpress
ProteomicsRestrictor synergizes with Symplekin and PNUTS to terminate extragenic transcription
Transcription termination pathways mitigate the detrimental consequences of unscheduled promiscuous initiation occurring at hundreds of thousands of genomic cis-regulatory elements. The Restrictor complex, composed of the Pol II-interacting protein WDR82 and the RNA-binding protein ZC3H4, suppresses...
ORGANISM(S): Homo sapiens (Human) 
2024-05-23 | PXD043638 | Pride
Ranscription termination Zc3h4 
ProteomicsAcetyl-CoA production by Mediator-bound 2-ketoacid dehydrogenases boosts de novo histone acetylation and is regulated by nitric oxide
Histone modifying enzymes depend on the availability of cofactors, with acetyl-CoA being required for histone acetyltransferase (HAT) activity. The discovery that mitochondrial acyl-CoA producing enzymes are also delivered to the nucleus suggests that high concentrations of metabolites generated loc...
ORGANISM(S): Mus musculus (Mouse) 
2025-05-06 | PXD040979 | Pride
Mediator  pyruvate dehydrogenase  2-ketoacid dehydrogenases  acetylation  chromatin  transcription 
TranscriptomicsTrap-80-dependence of TNF-alpha-induced genes
In fibroblasts, p65-dependent genes can be sub-divided, depending on whether they are Trap-80-dependent or -independent. To examine the generality of this grouping, we performed a microarray analysis of wild-type and Trap-80 knock-down fibroblasts, before and after stimulation of NF-kappaB activity...
ORGANISM(S): Mus musculus 
2010-04-09 | E-GEOD-12697 | biostudies-arrayexpress
GenomicsCo-regulation of transcription factor binding and nucleosome occupancy through DNA features of mammalian enhancers
In mammalian cells transcription factors (TFs) preferentially bind sites contained in regions of high nucleosomal occupancy, as determined by nucleotide-dependent computational analysis. This observation suggests that nucleosomes may act as gatekeepers of TF binding sites. We hypothesized that in ma...
ORGANISM(S): Mus musculus 
2014-05-08 | E-GEOD-50762 | biostudies-arrayexpress
GenomicsThe Histone Methyltransferase Wbp7 Controls Macrophage Function through GPI Glycolipid Anchor Synthesis. [ChIP_seq]
Histone methyltransferases catalyze site-specific deposition of methyl groups, enabling recruitment of transcriptional regulators. In mammals, trimethylation of lysine 4 in histone H3, a modification localized at the transcription start sites of active genes, is catalyzed by six enzymes (SET1a and S...
ORGANISM(S): Mus musculus 
2012-04-09 | E-GEOD-30972 | biostudies-arrayexpress
GenomicsA large fraction of extragenic RNA Pol II transcription sites overlap enhancers (2)
Mammalian genomes are pervasively transcribed outside mapped protein-coding genes. One class of extragenic transcription products is represented by long non-coding RNAs (lncRNAs), some of which result from Pol_II transcription of bona-fide RNA genes. Whether all lncRNAs described insofar are product...
ORGANISM(S): Mus musculus 
2010-05-21 | E-GEOD-19991 | biostudies-arrayexpress
GenomicsIdentification and Characterization of Enhancers Controlling the Inflammatory Gene Expression Program in Macrophages
Enhancers determine tissue-specific gene expression programs. Enhancers are marked by high histone H3 lysine 4 mono-methylation (H3K4me1) and by the acetyl-transferase p300, which has allowed genome-wide enhancer identification. However, the regulatory principles by which subsets of enhancers become...
ORGANISM(S): Mus musculus 
2010-03-05 | E-GEOD-19553 | biostudies-arrayexpress
TranscriptomicsA large fraction of extragenic RNA Pol II transcription sites overlap enhancers
Mammalian genomes are pervasively transcribed outside mapped protein-coding genes. One class of extragenic transcription products is represented by long non-coding RNAs (lncRNAs), some of which result from Pol_II transcription of bona-fide RNA genes. Whether all lncRNAs described insofar are product...
ORGANISM(S): Mus musculus 
2010-05-21 | E-GEOD-20370 | biostudies-arrayexpress
GenomicsMus musculus
TET2 Regulates Mast Cell Differentiation and Proliferation through Catalytic and Non-catalytic Activities.
PRJNA314899 | ENA
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