E-TABM-260 - Chromatin immunoprecipitation of wild type, SET2 deletion, Rco1 PHD domain deletion and Eaf3 chromodomain deletion yeast using anti-acetyl-histone H4

Submitted on 16 April 2007, released on 16 May 2007, last updated on 2 May 2014
Saccharomyces cerevisiae
Samples (8)
Array (1)
Protocols (8)
Nucleosomes must be deacetylated behind elongating RNA polymerase II to prevent cryptic initiation of transcription within the coding region. RNA polymerase II signals for deacetylation through methylation of histone H3 lysine 36 (H3K36) which provides the recruitment signal for the Rpd3S deacetylase complex. Recognition of methyl-H3K36 by Rpd3S requires the chromodomain of its Eaf3 subunit. Paradoxically, Eaf3 is also a subunit of the NuA4 acetyltransferase complex yet NuA4 does not recognize methyl H3K36 nucleosomes. We found that methyl H3K36 nucleosome recognition by Rpd3S also requires the PHD domain of its Rco1 subunit. Thus, the coupled chromo and PHD domains of Rpd3S specifies recognition of the methyl H3K36 mark; demonstrating the first combinatorial domain requirement within a protein complex to read a specific histone code.
Experiment types
ChIP-chip by array, binding site identification, individual genetic characteristics
Combined Action of PHD and Chromo Domains Directs the Rpd3S HDAC to Transcribed Chromatin. Li, Bing; Gogol, Madelaine; Carey, Mike; Lee, Daeyoup; Seidel, Chris; Workman, Jerry L. Science 316(5827):1050 (2007), Europe PMC 17510366
Infrequently transcribed long genes depend on the Set2/Rpd3S pathway for accurate transcription. Li, Bing; Gogol, Madelaine; Carey, Mike; Pattenden, Samantha G.; Seidel, Chris; Workman, Jerry L. Genes Dev 21(11):1422 (2007), Europe PMC 17545470
Investigation descriptionE-TABM-260.idf.txt
Sample and data relationshipE-TABM-260.sdrf.txt
Raw data (1)E-TABM-260.raw.1.zip
Processed data (1)E-TABM-260.processed.1.zip
Array designA-AGIL-29.adf.txt
R ExpressionSetE-TABM-260.eSet.r