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Series GSE37184 Query DataSets for GSE37184
Status Public on May 13, 2013
Title Dynamic binding of RBPJ is determined by Notch signalling status
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary Notch signalling plays crucial roles in mediating cell fate choices in all metazoans largely by specifying the transcriptional output of one cell in response to a neighbouring cell. The DNA-binding protein RBPJ is the principle effector of this pathway in mammals and together with the transcription factor moiety of Notch (NICD) it regulates the expression of target genes. The prevalent view presumes that RBPJ statically occupies consensus binding sites while exchanging repressors for activators in response to NICD. We present the first specific RBPJ chromatin immunoprecipitation and high-throughput sequencing study in mammalian cells. To dissect the mode of transcriptional regulation by RBPJ and identify its direct targets, whole genome binding profiles were generated for RBPJ, its coactivator p300, NICD and the histone H3 modifications H3K4me3, H3K4me1 and H3K27ac in myogenic cells under active or inhibitory Notch signalling conditions. Our results demonstrate dynamic binding of RBPJ in response to Notch activation at essentially all sites co-occupied by NICD. Additionally, we identify a distinct set of sites where RBPJ recruits neither NICD nor p300, and binds DNA statically, irrespective of Notch activity. These findings significantly modify our views on how RBPJ and Notch signalling mediate their activities and consequently impact on cell fate decisions.
Overall design ChIP (chromatin immunoprecipitation) is followed by deep sequencing to generate genome-wide patterns of RBP-J binding in mouse C2C12 cells under various conditions. Cells were either Notch activated by exposure to immobilized ligand or by overexpression of NICDGFP, or Notch inhibited by treatment with DAPT. Notch activation and inhibition treatments were applied for 6h and 24h. In addition to RBP-J, p300 and NICDGFP were profiled by ChIP-Seq and gene expression was assessed by RNA-Seq.
Contributor(s) Castel D, Mourikis P, Bartels SJ, Brinkman AB, Tajbakhsh S, Stunnenberg HG
Citation(s) 23651858, 29795344
Submission date Apr 11, 2012
Last update date May 21, 2019
Contact name Arjen Brinkman
Organization name Radboud University, Nijmegen Center for Molecular Life Sciences
Department Molecular Biology
Lab Stunnenberg
Street address NCMLS #274, Geert Grooteplein Zuid 30
City Nijmegen
ZIP/Postal code 6525 GA
Country Netherlands
Platforms (2)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (33)
GSM913281 Input_C2C12_6hDelta_repl1
GSM913282 ChIP_RBPj_1F1_C2C12_6hDelta_repl1
GSM913283 ChIP_RBPj_1F1_C2C12_6hDAPT_repl1
BioProject PRJNA158623
SRA SRP012155

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Supplementary file Size Download File type/resource
GSE37184_RAW.tar 6.7 Gb (http)(custom) TAR (of BED, RPKM, WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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