Comment[ArrayExpressAccession] E-GEOD-6667
Investigation Title PolII occupancy
Comment[Submitted Name] PolII occupancy
Publication Title Dynamics of replication-independent histone turnover in budding yeast.
Publication Author List Dion MF, Kaplan T, Kim M, Buratowski S, Friedman N, Rando OJ
Publication DOI
PubMed ID 17347438
Experimental Design ChIP-chip by tiling array
Experimental Design Term Source REF EFO
Public Release Date 2007-05-16
Experiment Description Chromatin plays roles in processes governed by different time scales. To assay the dynamic behaviour of chromatin in living cells, we used genomic tiling arrays to measure histone H3 turnover in G1-arrested S. cerevisiae at single-nucleosome resolution over 4% of the genome, and over the entire genome at lower (~265 bp) resolution. We find that nucleosomes at promoters are replaced more rapidly than at coding regions, and that replacement rates over coding regions correlate with polymerase density. In addition, rapid histone turnover is found at known chromatin boundary elements. These results suggest that rapid histone turnover serves to functionally separate chromatin domains and prevent spread of histone states. Keywords: Chip-chip, PolII ChIP-chip for RNA polymerase II (vs genomic DNA).
Date of Experiment
Term Source Name EFO
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Term Source File
Person Last Name Kaplan Dion Kaplan Kim Buratowski Friedman Rando
Person First Name Tommy Michael Tommy Minkyu Stephen Nir Oliver
Person Mid Initials F J
Person Email tommy@cs.huji.ac.il
Person Affiliation Hebrew University
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Person Address School of Computer Science, Hebrew University, Ross bldg, Jerusalem, Israel
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Protocol Name P-GSE6667-2 P-GSE6667-1 P-GSE6667-3 P-GSE6667-4 P-GSE6667-9 P-GSE6667-8 P-GSE6667-11 P-GSE6667-5 P-GSE6667-6 P-GSE6667-7 P-GSE6667-10
Protocol Description ID_REF =
VALUE = log2(Pol II IP/Genomic) t0 rep2
t0-PolII-rep2-Int = PolII IP t0 rep2
t0-Genomic-rep2-Int = Genomic t0 rep1 ID_REF =
VALUE = log2(Pol II IP/Genomic) t0 rep1
t0-PolII-rep1-Int = PolII IP t0 rep1
t0-Genomic-rep1-Int = Genomic t0 rep1 ID_REF =
VALUE = log2(Pol II IP/Genomic) t60 rep1
t60-PolII-rep1-Int = PolII IP t60 rep1
t60-Genomic-rep1-Int = Genomic t60 rep1 ID_REF =
VALUE = log2(Pol II IP/Genomic) t60 rep2
t60-PolII-rep2-Int = PolII IP t60 rep2
t60-Genomic-rep2-Int = Genomic t60 rep2 was scanned according to Agilent protocol was hybridized according to Agilent protocol t=60 (3 hours of alpha factor, 60 minutes after galactose shift) t=0 (3 hours of alpha factor, no galactose) See [Kim et al, Nature 432(7016):517-22 (2004)] See [Kim et al, Nature 432(7016):517-22 (2004)] log2(Cy5/Cy3)
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Protocol Type bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation bioassay_data_transformation image_aquisition hybridization specified_biomaterial_action specified_biomaterial_action nucleic_acid_extraction labeling feature_extraction
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Comment[SecondaryAccession] GSE6667
Comment[GEOLastUpdateDate] 2009-03-15
Comment[GEOReleaseDate] 2007-05-15
Comment[ArrayExpressSubmissionDate] 2007-01-06
SDRF File E-GEOD-6667.sdrf.txt