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Series GSE38496 Query DataSets for GSE38496
Status Public on Jun 08, 2012
Title A Key Role for Chd1 in Histone H3 Dynamics at the 3' Ends of Long Genes in Yeast (gene expression)
Organism Saccharomyces cerevisiae
Experiment type Expression profiling by array
Summary Chd proteins are ATP-dependent chromatin remodeling enzymes implicated in biological functions from transcriptional elongation to control of pluripotency. Here, we examine roles of Chd1 in replication- independent dynamics of histone H3 in yeast. Using genome-wide ChIP on chip analysis, we find that Chd1 influences histone turnover at the 5’ and 3’ ends of genes, accelerating H3 replacement at the 5’ ends of genes while protecting the 3’ ends of genes from excessive H3 turnover. Although consistent with a direct role for Chd1 in exchange, these results may indicate that Chd1 stabilizes nucleosomes perturbed by transcription. Curiously, we observe a strong effect of gene length on Chd1’s effects on H3 turnover. Finally, we show that Chd1 also affects histone H3K4 and H3K36 methylation patterns over genes, likely as a consequence of its effects on histone replacement. In control experiments, we measure effects of deletion of CHD1 on RNA polymerase II distribution across the genome and on gene expression. We also examine the effect of deleting the TOP1 gene, alone and in combination with deletion of CHD1, on histone replacement. Taken together, our results emphasize a role for Chd1 in histone replacement in both budding yeast and Drosophila, and surprisingly show that the major effects of Chd1 on turnover occur at the 3’ ends of genes.
 
Overall design This series compares gene expession in wild type to that in chd1 mutant cells. Two biological replicates with dye swaps.
 
Contributor(s) Radman-Livaja M, Quan TK, Valenzuela L, Armstrong J, van Welsem T, Kim T, Lee LJ, Buratowski S, van Leeuwen F, Rando OJ, Hartzog GA
Citation(s) 22807688
Submission date Jun 05, 2012
Last update date Nov 21, 2014
Contact name Grant A Hartzog
E-mail(s) hartzog@ucsc.edu
Phone 8314595826
Fax 8314593139
Organization name UC Santa Cruz
Department MCD Biology
Street address 349 Sinsheimer Labs
City Santa Cruz
State/province CA
ZIP/Postal code 95064
Country USA
 
Platforms (1)
GPL11043 Yeast Splicing/Expression Chip v6.2-6.3
Samples (2)
GSM943588 chd1D_WT (1)
GSM943589 chd1D_WT (2)
This SubSeries is part of SuperSeries:
GSE38540 A Key Role for Chd1 in Histone H3 Dynamics at the 3' Ends of Long Genes in Yeast
Relations
BioProject PRJNA168233

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
GSE38496_RAW.tar 7.7 Mb (http)(custom) TAR (of GPR)
Processed data included within Sample table

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