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TranscriptomicsThe mRNA-bound proteome and its global occupancy profile on protein-coding transcripts [protein occupancy profiling]
Protein-RNA interactions are fundamental to core biological processes, such as mRNA splicing, localization, degradation and translation. We developed a photoreactive nucleotide-enhanced UV crosslinking and oligo(dT) purification approach to identify the mRNA-bound proteome using quantitative proteom...
ORGANISM(S): Homo sapiens 
2012-06-01 | E-GEOD-38355 | biostudies-arrayexpress
TranscriptomicsRSC and ISW1 Chromatin Remodelers Display Functional and Chromatin-based Promoter Antagonism [nucleosome occupancy]
ISWI-family chromatin remodelers organize nucleosome arrays, while SWI/SNF-family remodelers (RSC) disorganize and eject nucleosomes, implying an antagonism that is largely unexplored in vivo. Here, we describe two independent genetic screens for rsc suppressors that yielded mutations in the promote...
ORGANISM(S): Saccharomyces cerevisiae 
2015-04-01 | E-GEOD-65590 | biostudies-arrayexpress
TranscriptomicsCoupling p53 binding and nucleosome occupancy measurements at p53 binding sites
We were interested to explain why p53 binds some high affinity sites in contrast to other high affinity sites that are not bound by p53. p53 binding was measured using p53 ChIP-CHIP and in parallel nucleosome occupancy was measured on these same sites Comparison between p53 binding and nucleosome oc...
ORGANISM(S): Homo sapiens 
2010-08-09 | E-GEOD-22783 | biostudies-arrayexpress
TranscriptomicsThe mRNA-bound proteome and its global occupancy profile on protein-coding transcripts [RNA-seq]
Protein-RNA interactions are fundamental to core biological processes, such as mRNA splicing, localization, degradation and translation. We developed a photoreactive nucleotide-enhanced UV crosslinking and oligo(dT) purification approach to identify the mRNA-bound proteome using quantitative proteom...
ORGANISM(S): Homo sapiens 
2012-06-01 | E-GEOD-38356 | biostudies-arrayexpress
ProteomicsPhosphorylation of Hsp90β on serine residues in the charged linker modulates binding to interacting proteins and has implications for overall Hsp90β conformation (Occupancy and phospho-modulation data)
Human Hsp90β is constitutively phosphorylated in vivo on two serine residues in the charged linker region, S226 and S255. We developed a targeted method to measure the phosphorylation occupancy (the extent of phosphorylation) of both phosphosites in a range of cultured cell lines and consistently fo...
ORGANISM(S): Homo sapiens (Human) 
2021-07-07 | PXD025888 | Pride
Hsp90 Heat shock Tio Stress Hsp90 inhibitors Phosphorylation Occupancy 
ProteomicsGlobal, site-resolved analysis of ubiquitylation occupancy and turnover rate reveals systems properties
Ubiquitylation regulates most proteins and biological processes in a eukaryotic cell. However, the site-specific occupancy (stoichiometry) and turnover rate of ubiquitylation have not been quantified. Here we present an integrated picture of the global ubiquitylation site occupancy and half-life. Ub...
ORGANISM(S): Homo sapiens (Human) 
2024-04-15 | PXD037009 | Pride
Human Ubiquitylation Dynamics Ptms Stoichiometry Half-life 
TranscriptomicsDeterminants of nucleosome positioning and their influence on plant gene expression
We report the global nuclesome posiitons to study the relationship between nucleosome occupancy and gene expression in response to Coronatine in Arabidopsis We examined nucleosome occupancy and mRNA abundance in response to Coronatine in Arabidopsis rosette leaves
ORGANISM(S): Arabidopsis thaliana 
2015-05-27 | E-GEOD-64397 | biostudies-arrayexpress
GenomicsIntegrated genome-wide analysis of transcription factor occupancy, RNA polymerase II binding and steady-state RNA levels identify differentially regulated functional gene classes
Routine methods for assaying steady-state mRNA levels such as RNA-seq and micro-arrays are commonly used as readouts to study the role of transcription factors (TFs) in gene expression regulation. However, cellular RNA levels do not solely depend on activity of TFs and subsequent transcription by RN...
ORGANISM(S): Homo sapiens 
2012-03-09 | E-GEOD-36349 | biostudies-arrayexpress
GenomicsBAF250a regulates nucleosome occupancy and histone modification in priming embryonic stem cell differentiation
BAF complex is one major group of chromatin remodeling factors in mammals. However, how BAF regulated nucleosomes and other histone modifications is not clear. Here we delete BAF250a, a major component in esBAF to study the nucleosome and histone changes in ESCs. We find that deletion of BAF250a lea...
ORGANISM(S): Mus musculus 
2015-08-03 | E-GEOD-59082 | biostudies-arrayexpress
ProteomicsPEPseq Quantifies Transcriptome-Wide Changes in Protein Occupancy and Reveals Selective Translational Repression After Translational Stress
Post-transcriptional gene regulation is accomplished by the interplay of the transcriptome with RNA-binding proteins, which occurs in a dynamic manner in response to altered cellular conditions. Recording the combined occupancy of all proteins binding to the transcriptome offers the opportunity to i...
ORGANISM(S): Homo sapiens (Human) 
2023-10-24 | PXD042395 | Pride
Nascent proteome enrichment Protein-rna crosslinking Aha Protein occupancy on rna Arsenite washout Recovery from translational arrest Silac 
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