Comment[ArrayExpressAccession] E-GEOD-51766 MAGE-TAB Version 1.1 Public Release Date 2013-10-29 Investigation Title Nucleosome organization in mouse embryonic stem cells Comment[Submitted Name] Nucleosome organization in mouse embryonic stem cells Experiment 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) Term Source Name ArrayExpress EFO Term Source File http://www.ebi.ac.uk/arrayexpress/ http://www.ebi.ac.uk/efo/efo.owl Person Last Name Zhang Zhang Ge Feng Person First Name Yong Yong Ying Jianxing Person Email geo@ncbi.nlm.nih.gov Person Affiliation Tongji University Person Address Tongji University, 1239 Siping Road, Shanghai, China Person Roles submitter Protocol Name P-GSE51766-3 P-GSE51766-2 P-GSE51766-1 Protocol Description All sequenced reads were aligned using bowtie version 4.1.2. Uniquely mapped reads with a maximum of two mismatches were kept. All mapped reads were extended to 147 bp in their 3M-bM-^@M-^Y direction, and the middle 73 bp were piled up to generate wig files. Genome_build: mm9 Supplementary_files_format_and_content: wig format Collect 10ml cells in a 15ml BD tube, and fix in 1% formaldehyde for 1 minute at room temperature. Formaldehyde was quenched by adding 1ml 1.25M glycine. Cells were rinsed 3 times in ice-cold PBS, immediately resuspended in cell lysis buffer (10mM Tris-HCl pH7.5/10mM NaCl/0.5%NP40) and lysed for 5 min on ice. Nuclei were collected by centrifugation, washed with ice-cold PBS, collected by centrifugation again and resuspended in digestion buffer (50mM Tris-HCl pH7.5/1mM CaCl2/0.2%Triton X-100). Samples were divided into 200M-NM-