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Series GSE15188 Query DataSets for GSE15188
Status Public on Jul 15, 2009
Title Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo
Organisms Escherichia coli; Saccharomyces cerevisiae
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary We assess the role of intrinsic histone-DNA interactions by mapping nucleosomes assembled in vitro on genomic DNA. Nucleosomes strongly prefer yeast DNA over E. coli DNA, indicating that the yeast genome evolved to favor nucleosome formation. Many yeast promoter and terminator regions intrinsically disfavor nucleosome formation, and nucleosomes assembled in vitro display strong rotational positioning. Nucleosome arrays generated by the ACF assembly factor display fewer nucleosome-free regions, reduced rotational positioning, and less translational positioning than obtained by intrinsic histone-DNA interactions. Importantly, in vitro assembled nucleosomes display only a limited preference for specific translational positions and do not show the pattern observed in vivo. Our results argue against a genomic code for nucleosome positioning, and they suggest that the nucleosomal pattern in coding regions arises primarily from statistical positioning from a barrier near the promoter that involves some aspect of transcriptional initiation by RNA polymerase II.
 
Overall design This data series consists of two experimental samples, "Nucleosomes assembled on yeast and E. coli DNA by salt dialysis" and "Nucleosomes assembled on yeast and E. coli DNA by ACF" plus one control sample, "Yeast-Ecoli control, sonicated".
 
Contributor(s) Zhang Y, Moqtaderi Z, Rattner B, Euskirchen G, Snyder M, Kadonaga JT, Liu XS, Struhl K
Citation(s) 19620965
Submission date Mar 11, 2009
Last update date May 15, 2019
Contact name Ghia Euskirchen
E-mail(s) ghia.euskirchen@stanford.edu
Organization name Stanford University
Department Genetics
Lab Snyder
Street address 1501 S. California Ave.
City Palo Alto
State/province CA
ZIP/Postal code 94304
Country USA
 
Platforms (1)
GPL10839 Illumina Genome Analyzer (Escherichia coli; Saccharomyces cerevisiae)
Samples (3)
GSM379239 Nucleosomes assembled on yeast and E. coli DNA by salt dialysis
GSM379240 Nucleosomes assembled on yeast and E. coli DNA by ACF
GSM379241 Yeast-E. coli control, sonicated
Relations
SRA SRP001302
BioProject PRJNA116403

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
GSE15188_RAW.tar 561.5 Mb (http)(custom) TAR (of TXT, WIG)
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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