E-GEOD-51766 - Nucleosome organization in mouse embryonic stem cells

Status
Released on 29 October 2013, last updated on 3 May 2014
Organism
Mus musculus
Samples (1)
Protocols (3)
Description
The position of nucleosomes influences DNA accessibility to DNA-binding proteins. Genome-wide nucleosome profiles often report the observation of a canonical nucleosome organization at gene promoters where arrays of well-positioned nucleosomes emanate from nucleosome-depleted regions. It is unclear how this canonical promoter nucleosome organization forms and how it is related to transcription activation and the establishment of histone marks during development. Here we report the genome-wide organization of nucleosomes during zebrafish embryogenesis and show that well-positioned nucleosome arrays appear in thousands of promoters during the activation of the zygotic genome. The formation of canonical promoter nucleosome organization cannot be explained by DNA sequence preference, and is independent of transcription and the presence of RNA polymerase II, but strongly correlates with the presence of Histone H3 Lysine 4 trimethylation (H3K4me3). Our study further suggests that promoter nucleosome structure primes genes to future transcription activation. To determine whether the occlusions are consistent in mammalian pluripotent cells, we performed the same analyses in mouse embryonic stem cells and found similar relationships. MNase-seq to generate nucleosome organization in mouse embryonic stem cell (J1)
Experiment type
ChIP-seq 
Contacts
Jianxing Feng, Ying Ge, Yong Zhang
MINSEQE
Exp. designProtocolsFactorsProcessedSeq. reads
Files
Investigation descriptionE-GEOD-51766.idf.txt
Sample and data relationshipE-GEOD-51766.sdrf.txt
Processed data (1)E-GEOD-51766.processed.1.zip
Links