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TranscriptomicsDivergent transcription from active promoters
Here we describe a novel class of short RNAs that indicate widespread divergent transcription at mammalian promoters Small RNA cloning and deep sequencing from human embryonic stem cells, derived neural progenitors and neurons
ORGANISM(S): Homo sapiens 
2008-11-06 | E-GEOD-13483 | biostudies-arrayexpress
GenomicsRecurrent epimutations activate gene body promoters in primary glioblastoma
Aberrant DNA hypomethylation may play an important role in the growth rate of glioblastoma (GBM), but the functional impact on transcription remains poorly understood. We assayed the GBM methylome with MeDIP-seq and MRE-seq, adjusting for copy number differences, in a small set of non-glioma CpG isl...
EGAS00001000685 | EGA
ProteomicsHerpesvirus infection reduces Pol II occupancy of host promoters but spares viral promoters
In mammalian cells, widespread acceleration of cytoplasmic mRNA degradation is linked to impaired RNA polymerase II (Pol II) transcription. This mRNA decay-induced transcriptional repression occurs during infection with gammaherpesviruses including Kaposi’s sarcoma associated herpesvirus (KSHV) and ...
ORGANISM(S): Mus musculus (Mouse) 
2019-12-10 | PXD015786 | Pride
Mhv68 Infection Tmt Herpesvirus Rna pol ii 
GenomicsSystematic Interrogation of Human Promoters
Systematic Interrogation of Human Promoters
PRJNA484949 | ENA
TranscriptomicsInferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters
Despite extensive research, our understanding of the rules according to which cis-regulatory sequences are converted into gene expression is limited We devised a method for obtaining parallel, highly accurate gene expression measurements from thousands of designed promoters and applied it to measure...
ORGANISM(S): Saccharomyces cerevisiae 
2012-05-20 | E-GEOD-37851 | biostudies-arrayexpress
GenomicsDivergent transcription from active promoters
Here we describe a novel class of short RNAs and high-resolution ChIP-Seq data that together indicate widespread divergent transcription at mammalian promoters and suggest the existence of novel regulatory mechanisms concerning both initiation and elongation by RNA polymerase II. ChIP-seq in murine ...
ORGANISM(S): Mus musculus 
2008-12-01 | E-GEOD-12680 | biostudies-arrayexpress
ProteomicsThe SPARC complex defines RNAPII promoters in Trypanosoma brucei
Kinetoplastids are a highly divergent lineage of eukaryotes with unusual mechanisms for regulating gene expression. We previously surveyed 65 putative chromatin factors in the kinetoplastid Trypanosoma brucei. Our analyses revealed that the predicted histone methyltransferase SET27 and the Chromodom...
ORGANISM(S): Trypanosoma brucei 
2023-03-11 | PXD036454 | Pride
Set27 promoter-associated regulatory complex (sparc) Chromodomain protein crd1 Trypanosoma brucei Histone methyltransferase set27 
TranscriptomicsA high-resolution map of active promoters in the human genome
Our ability to understand the control logic embedded in the human genome is limited by a lack of accurate information of the promoter sequences for most genes. Promoters are a unique class of control sequences, serving as the binding sites for both sequence-specific factors and the general transcri...
ORGANISM(S): Homo sapiens 
2010-07-01 | E-GEOD-2672 | biostudies-arrayexpress
ProteomicsMulti-omic analysis of gametogenesis reveals a novel signature at the promoters and distal enhancers of active genes
Epigenetic regulation of gene expression is tightly controlled by the dynamic modification of histones by chemical groups, the diversity of which has largely expanded over the past decade with the discovery of lysine acylations, catalyzed from acyl-coenzymes A. Here, we investigated the dynamics of ...
ORGANISM(S): Mus musculus (Mouse) Saccharomyces cerevisiae (Baker's yeast) 
2020-03-26 | PXD015380 | Pride
Promoters and enhancers Omics data integration Crotonylation Mouse spermatogenesis Histones 
ProteomicsReduction of ZFX levels decreases histone H4 acetylation and increases the pause ratio at target promoters
The ZFX transcriptional activator binds to CpG island promoters, with a major peak at ~200-250bp downstream from transcription start sites. Because ZFX binds within the transcribed region, we investigated whether it regulates transcriptional elongation. We used GRO-seq to show that loss or reduction...
ORGANISM(S): Homo sapiens (Human) 
2024-08-09 | PXD044709 | Pride
Elongation Turboid Pol2 pausing Zfx Transcription 
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