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ProteomicsHuman chromatin platforms for the study of transcription and RNA regulation
Here we describe tools to study the step-wise assembly of protein complexes on chromatin in a highly-controlled manner using reconstituted chromatin platforms and quantitative proteomic profiling. We profile the early steps in transcriptional activation and highlight the potential for understanding...
ORGANISM(S): Saccharomyces Cerevisiae (ncbitaxon:4932) 
2018-05-15 | MSV000082363 | MassIVE
TranscriptomicsExtensive promoter-centered chromatin interactions provide a topological basis for transcription regulation
Higher-order chromosomal organization for transcription regulation is poorly understood in eukaryotes. Using genome-wide Chromatin Interaction Analysis with Paired-End-Tag sequencing (ChIA-PET), we mapped long-range chromatin interactions associated with RNA polymerase II in human cells and uncovere...
ORGANISM(S): Homo sapiens 
2012-01-20 | E-GEOD-33664 | biostudies-arrayexpress
GenomicsTissue-specific regulation of chromatin insulator function
Chromatin insulators organize the genome into distinct transcriptional domains and contribute to cell type-specific chromatin organization. However, factors regulating tissue-specific insulator function have not yet been discovered. Here we identify the RNA recognition motif-containing protein, Shep...
ORGANISM(S): Drosophila melanogaster 
2012-11-30 | E-GEOD-40797 | biostudies-arrayexpress
GenomicsThe RNA-binding protein Rumpelstiltskin antagonizes gypsy chromatin insulator function in a tissue-specific manner
Chromatin insulators are DNA-protein complexes situated throughout the genome that contribute to higher order organization and demarcation into distinct transcriptional domains. Mounting evidence in different species implicates RNA and RNA-binding proteins as regulators of chromatin insulator activ...
ORGANISM(S): Drosophila melanogaster 
2014-04-18 | E-GEOD-51462 | biostudies-arrayexpress
GenomicsChromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants (ChIP-seq)
Chromatin-based functional genomic analyses and genomewide association studies (GWASs) together implicate enhancers as critical elements influencing gene expression and risk for common diseases. Here, we performed systematic chromatin and transcriptome pro- filing in human pancreatic islets. Integra...
ORGANISM(S): Homo sapiens 
2013-11-08 | E-GEOD-51311 | biostudies-arrayexpress
ProteomicsChromatin capture links the metabolic enzyme AHCY to stem cell proliferation
Profiling the chromatin-bound proteome (chromatome) in a simple, direct, and reliable manner might be key to uncovering the role of yet uncharacterized chromatin factors in physiology and disease. Here, we have design an experimental strategy to survey the chromatome of proliferating cells by using ...
ORGANISM(S): Mus musculus (Mouse) 
2019-03-13 | PXD011670 | Pride
Chromatin Proteomics Stem cells Ahcy 
TranscriptomicsMolecular basis for chromatin binding and regulation of MLL5
The human mixed lineage leukemia 5 (MLL5) protein mediates hematopoietic cell homeostasis, cell cycle and survival, however, the molecular basis underlying MLL5 activities remains unknown. Here, we show that MLL5 is recruited to gene-rich euchromatic regions via the interaction of its PHD finger wit...
ORGANISM(S): Mus musculus 
2013-07-01 | E-GEOD-47100 | biostudies-arrayexpress
ProteomicsThe proteomics data for Increased matrix stiffness promotes fibrogenesis of hepatic stellate cells through AP-1-induced chromatin priming
Matrix stiffness has significant effects on cell behavior, however, less is known regarding the epigenomic and transcriptional regulation underling the effect of matrix stiffness on cells. In this study, we use an in vitro system to assess the phenotypic shifts of hepatic stellate cells (HSCs) follo...
ORGANISM(S): Homo Sapiens 
2025-04-19 | PXD063173 |
GenomicsOpen chromatin maps of genetically different yeast strains
Open chromatin provides access to a wide spectrum of DNA binding proteins for DNA metabolism processes such as transcription, repair, recombination, and replication. In this regard, open chromatin profiling has been widely used to identify the location of regulatory regions, including promoters, enh...
ORGANISM(S): Saccharomyces cerevisiae 
2012-11-02 | E-GEOD-33466 | 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
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