GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE75684 Query DataSets for GSE75684
Status Public on Jan 12, 2017
Title RNA binds to a CBP regulatory motif to stimulate histone acetylation and transcription
Organism Mus musculus
Experiment type Other
Non-coding RNA profiling by high throughput sequencing
Summary CBP/p300 are transcription co-activators whose binding is a signature of enhancers, cis-regulatory elements that control patterns of gene expression in multicellular organisms. Active enhancers produce bi-directional enhancer RNAs (eRNAs) and display CBP/p300 dependent histone acetylation. Here, we demonstrate that CBP binds directly to RNAs in vivo and in vitro. RNAs bound to CBP in vivo include a large number of eRNAs. Using steady-state histone acetyltransferase (HAT) assays we show that an RNA binding region in the HAT domain of CBP—a regulatory motif unique to CBP/p300—allows RNA to stimulate CBP’s HAT activity. At enhancers where CBP interacts with eRNAs, stimulation manifests in RNA-dependent changes in the histone acetylation mediated by CBP, such as H3K27ac, and by corresponding changes in gene expression. By interacting directly with CBP, eRNAs contribute to the unique chromatin structure at active enhancers, which in turn is required for regulation of target genes.
Overall design MEFs were treated with 4-thiouridine for 16h, irradiated with 365nm UV and CBP immunopreciptated. RNA species cross-linked to CBP were purified and sequenced. The series contains 2 biological replicates for CBP PAR-CLIP seq, and negative controls for background PAR-CLIP binding: nuclear flag-tagged GFP (nGFP) and the DNA binding domain of yeast protein Gal4p (Gal4-DBD) (two replicates each)
Contributor(s) Bose DA, Donahue G, Berger SL
Citation(s) 28086087
Submission date Dec 03, 2015
Last update date May 15, 2019
Contact name Daniel Bose
Organization name University of Pennsylvania
Department Cell and Developmental Biology
Lab Berger Lab
Street address 3400 Civic Center Blvd., 9th floor
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (6)
GSM1963687 CBP PAR-CLIP (Replicate 1)
GSM1963688 CBP PAR-CLIP (Replicate 2)
GSM1963689 nGFP background control (Replicate 1)
BioProject PRJNA305043
SRA SRP066981

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE75684_RAW.tar 18.9 Mb (http)(custom) TAR (of BIGWIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap