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Series GSE13622 Query DataSets for GSE13622
Status Public on Dec 18, 2008
Title The DNA-Encoded Nucleosome Organization of a Eukaryotic Genome
Platform organisms Saccharomyces cerevisiae; Homo sapiens; Mus musculus; synthetic construct
Sample organisms Saccharomyces cerevisiae; synthetic construct
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by array
Summary Nucleosome organization is critical for gene regulation. In living cells, this organization is determined by multiple factors, including the action of chromatin remodelers, competition with site-specific DNA-binding proteins, and the DNA sequence preferences of the nucleosomes themselves. However, it has been difficult to estimate the relative importance of each of these mechanisms in vivo, because in vivo nucleosome maps reflect the combined action of all influencing factors. Here, we determine the importance of DNA sequence preferences experimentally by measuring the genome-wide occupancy of nucleosomes assembled on purified yeast genomic DNA. The resulting map, in which nucleosome occupancy is governed only by the intrinsic sequence preferences of nucleosomes, is remarkably similar to in vivo nucleosome maps generated in three different growth conditions. In vitro, nucleosome depletion is evident at many transcription factor binding sites and around gene start and end sites, suggesting that nucleosome depletion at these sites in vivo is partially encoded in the genome. We confirm these results with a micrococcal nuclease-independent experiment that measures the relative affinity of nucleosomes for ~40,000 double-stranded 150bp oligonucleotides. Using our in vitro data, we devise a computational model of nucleosome sequence preferences that is significantly correlated with in vivo nucleosome occupancy in C. elegans. Our results indicate that the intrinsic DNA sequence preferences of nucleosomes play a central role in determining the organization of nucleosomes in vivo.
Overall design Solexa/Illumina sequencing of in vivo and in vitro mononucleosomes. In vitro: 2 biological replicates; YPD: 6 biological replicates (4 non-crosslinked, 2 crosslinked); YPEthanol: 4 replicates (2 non-crosslinked, 2 crosslinked); YPGalactose: 3 replicates (2 non-crosslinked, 1 crosslinked).
Microarray hybridization (GPL7641) of in vitro reconstitution on synthetic sequences: Three technical replicates, pool 1 (DT sequences), pool 2 (ES sequences), pool 3 (DT and ES sequences combined).
Sequencing of in vitro reconstituted nucleosomes on synthetic sequences. Input pool 1 (DT sequences, 3 technical replicates), Input pool 2 (ES sequences, 2 technical replicates), reconstituted pool 1 (3 technical replicates), reconstituted pool 2 (3 technical replicates)
Contributor(s) Kaplan N, Moore I, Fondufe-Mittendorf Y, Gossett A, Tillo D, Field Y, LeProust EM, Hughes TR, Lieb JD, Widom J, Segal E
Citation(s) 19092803, 26330564
Submission date Nov 17, 2008
Last update date May 15, 2019
Contact name Desiree Tillo
Phone +1-240-760-7289
Organization name NIH/NCI
Street address 41 Center Dr, Room D310
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
Platforms (3)
GPL7641 Long oligo 44K tracking array
GPL9377 Illumina Genome Analyzer II (Saccharomyces cerevisiae)
GPL9423 Illumina Genome Analyzer II (synthetic construct)
Samples (8)
GSM343272 long_oligo_array_hyb1
GSM343273 long_oligo_array_hyb2
GSM343274 long_oligo_array_hyb3
BioProject PRJNA110649
SRA SRP001116

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Supplementary file Size Download File type/resource
GSE13622_RAW.tar 362.3 Mb (http)(custom) TAR (of TAB, TXT)
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA
Processed data included within Sample table

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