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Series GSE61888 Query DataSets for GSE61888
Status Public on Nov 29, 2014
Title High resolution chromatin dynamics during a yeast stress response
Organism Saccharomyces cerevisiae
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Covalent histone modifications are highly conserved and play multiple roles in eukaryotic transcription regulation. Because of extensive crosstalk between transcriptional processes and histone modifications, steady state observations are insufficient to fully disentangle histone modification networks. As transient perturbation of feedback mechanisms can reveal network structure, we mapped 26 histone modifications genome-wide over a time course following dramatic transcriptional reprogramming – response to diamide stress in yeast. Interestingly, while we observed limited combinatorial complexity in steady-state histone modification patterns, consistent with previous studies, the combinatorial complexity of histone modification space increased modestly during the stress response, resulting from roughly 3% of nucleosomes transiently populating rare histone modification states. We show that most of these short-lived histone mark combinations result from differences in histone modification dynamics that transiently uncouple highly correlated marks, with slow histone methylation changes often lagging the more rapid changes in acetylation. Together, our results provide the first detailed view of an epigenome in transition.
Overall design Mnase-ChIP-Seq with 26 antibodies, throuh a diamide stress response (0,4,8,15,30,60 minutes). Performed in batches, in each batch the MNase input is also sequenced in each time point.
Contributor(s) Weiner A, Hsieh TS, Appleboim A, Chen HV, Rahat A, Amit I, Rando OJ, Friedman N
Citation(s) 25801168
Submission date Sep 30, 2014
Last update date May 15, 2019
Contact name Alon Appleboim
Organization name Hebrew University of Jerusalem
Department Life Sciences
Lab Nir Friedman
Street address Hebrew University
City Jerusalem
ZIP/Postal code 9190501
Country Israel
Platforms (1)
GPL17582 Illumina HiSeq 1000 (Saccharomyces cerevisiae)
Samples (201)
GSM1516399 h2ak5ac_60
GSM1516400 h2ak5ac_30
GSM1516401 h2ak5ac_15
BioProject PRJNA262623
SRA SRP048526

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Supplementary file Size Download File type/resource
GSE61888_RAW.tar 3.8 Gb (http)(custom) TAR (of BW)
GSE61888_nucs_normed.csv.gz 20.2 Mb (ftp)(http) CSV
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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