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E-GEOD-67912 - Bas1 and Ino4 ChIP-seq

Status
Released on 21 August 2015, last updated on 29 August 2015
Organism
Saccharomyces cerevisiae
Samples (4)
Protocols (3)
Description
Meiotic recombination is initiated by developmentally programmed DNA double-strand breaks (DSBs). In S. cerevisiae, the vast majority of DSBs occur in the nucleosome-depleted regions at gene promoters, where transcription factors (TFs) bind. It has been proposed that TF binding can stimulate DSB formation nearby by modulating local chromatin structure. However, a prior study in TF bas1 mutant suggested that the role of TF binding in determining break formation is complex. Here, we examined fine-scale DSB distributions in TF mutant (bas1Δ and ino4Δ) strains. In bas1Δ mutants, 239 out of the 2468 hotspots showed reduced DSB activity, whereas 87 hotspots showed increased DSB activity. Similarly, in ino4Δ mutant, 415 out of the 2468 hotspots showed reduced DSB activity, whereas 322 hotspots showed increased DSB activity. We also mapped Bas1 and Ino4 binding sites in meiosis and found that only a small portion of the affected hotspots contained TF binding sites. This indicates that TF can influence DSB distribution both directly and indirectly. Surprisingly, these DSB changes in TF mutants did not correlate with change in chromatin structure and histone H3K4me3 modification, suggesting that the role of TF on DSB distribution cannot be simply explained by affecting local chromatin status. Four samples total: Bas1-Myc (ChIP and input samples), Ino4-Myc (ChIP and input samples)
Experiment type
ChIP-seq 
Contacts
Jeffrey Zhao <zhaoy@mskcc.org>, Scott Keeney, Xuan Zhu
Citation
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-67912.idf.txt
Sample and data relationshipE-GEOD-67912.sdrf.txt
Processed data (2)E-GEOD-67912.processed.1.zip, E-GEOD-67912.processed.2.zip
Links