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MetabolomicsA multi-omics dataset of heat-shock response in the yeast RNA binding protein Mip6 (NMR assay)

Gene expression is a biological process regulated at different molecular levels, including chromatin accessibility, transcription, and RNA maturation and transport. In addition, these regulatory mechanisms have strong links with cellular metabolism. Here we present a multi-omics dataset that capt...

2020-02-14 | MTBLS1320 | MetaboLights
GenomicsHigh-resolution mapping of transcription factor binding sites on native chromatin
Sequence-specific DNA-binding proteins including transcription factors (TFs) are key determinants of gene regulation and chromatin architecture. Formaldehyde cross-linking and sonication followed by Chromatin ImmunoPrecipitation (X-ChIP) and sequencing is widely used for genome-wide profiling of pro...
ORGANISM(S): Drosophila melanogaster 
2013-12-14 | E-GEOD-45672 | biostudies-arrayexpress
ProteomicsDNA binding reorganizes the intrinsically disordered C-terminal region of PSC in Drosophila PRC1
Polycomb Group (PcG) proteins regulate gene expression by modifying chromatin. A key PcG complex, PRC1, has two activities: a ubiquitin ligase activity for histone H2A, and a chromatin compacting/nucleosome bridging activity that can inhibit transcription and chromatin remodeling. In Drosophila, the...
ORGANISM(S): Drosophila Melanogaster (ncbitaxon:7227) 
2020-05-15 | MSV000085418 | MassIVE
TranscriptomicsCTCF binding polarity determines chromatin looping [4C]
CCCTC-binding factor (CTCF) is an architectural protein involved in the three-dimensional organization of chromatin. In this study, we systematically assayed the 3D genomic contact profiles of hundreds of CTCF binding sites in multiple tissues with high-resolution 4C-seq. We find both developmentall...
ORGANISM(S): Mus musculus 
2015-10-29 | E-GEOD-72539 | biostudies-arrayexpress
TranscriptomicsChromatin modifications induced by PML-RARalpha repress critical targets in leukemogenesis as analyzed by ChIP-Chip.
A global view of PML-RAR? transcriptional functions was obtained by genome-wide binding and chromatin modification analyses, combined with genome wide expression data. Complete Abstract: The translocation t(15;17) generates the chimeric PML-RAR? transcription factor that is the initiating event of ...
ORGANISM(S): Homo sapiens 
2008-09-06 | E-GEOD-12641 | biostudies-arrayexpress
GenomicsCTCF demarcates chromatin domains
Insulators are DNA elements, which prevent inappropriate interactions between the neighboring regions of the genome. They can be functionally classified as either enhancer blockers or domain barriers. CTCF (CCCTC binding factor) is the only known major insulator binding protein in the vertebrates a...
ORGANISM(S): Homo sapiens 
2008-10-20 | E-GEOD-12889 | biostudies-arrayexpress
ProteomicsA quantitative proteomic analysis of in vitro assembled chromatin
The structure of chromatin is critical for many aspects of cellular physiology and is considered to be the primary medium to store epigenetic information. It is defined by the histone molecules that constitute the nucleosome, the positioning of the nucleosomes along the DNA and the non-histone prote...
ORGANISM(S): Drosophila melanogaster (Fruit fly) 
2016-01-27 | PXD002537 | Pride
Acetylation  affinity proteomics  chromatin function or biology  label-free quantification   macromolecular assemblages 
GenomicsCombining transcription factor binding affinities with open chromatin data for accurate gene expression prediction
The binding and contribution of transcription factors (TF) to cell specific gene expression is often deduced from open-chromatin measurements to avoid cost and labour intensive TF ChIP-seq assays.It is important to develop reliable and fast computational methods for accurate TF binding prediction in...
EGAS00001002073 | EGA
TranscriptomicsGenome-wide profiling of PRC1 and PRC2 Polycomb chromatin binding in Drosophila
Polycomb group (PcG) proteins maintain transcriptional repression of developmentally important genes and have been implicated in cell proliferation and stem-cell self-renewal. We used a genome-wide approach to map binding patterns of PcG proteins (Pc, esc and Sce) in Drosophila Kc cells. We found th...
ORGANISM(S): Drosophila melanogaster 
2010-06-11 | E-GEOD-4564 | biostudies-arrayexpress
GenomicsOverexpression of androgen receptor enhances the binding of the receptor to the chromatin in prostate cancer
Androgen receptor (AR) is overexpressed in the majority of castration-resistant prostate cancers (CRPCs). Our goal was to study the effect of AR overexpression on the chromatin binding of the receptor and to identify AR target genes that may be important in the emergence of CRPC. We have established...
ORGANISM(S): Homo sapiens 
2013-06-27 | E-GEOD-48308 | biostudies-arrayexpress
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