ABSTRACT
Covalent modifications to histones are key epigenetic marks that control gene transcription. Multiple lysine residues on histone H3 are methylated (me), but their functions are unclear. Here, we demonstrate two phases of combinatorial and dynamic H3 methylation during induction of transcription at MET16 in yeast. K4me3 with K36me2/3 define a postinitiation regulatory phase and precede the appearance of K4me2 with K79me2 at the onset of transcript elongation. The Isw1 ATPase delays the release of initiated RNA polymerase II (RNAPII) into elongation to facilitate chromatin modifications. The Spp1 subunit of complex associated with Set1 (COMPASS) and Set2, determining K4me3 and K36me2/3, respectively, are required for transient NuA4-dependent H4K8ac. This releases RNAPII from Isw1 control and promotes controlled transcription elongation and termination. We propose that newly initiated RNAPII is under epigenetic control.
Subject(s)
Histones/metabolism , Lysine/metabolism , Oligonucleotide Array Sequence Analysis , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Transcription, Genetic , DNA, Fungal/genetics , Gene Expression Regulation , Kinetics , Methylation , Saccharomyces cerevisiae/growth & development , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolismABSTRACT
Set1p methylates lysine 4 (K4) of histone H3 and regulates the expression of many genes in yeast. Here we use a biochemical approach to identify a protein, Isw1p, which recognizes chromatin preferentially when it is di- and trimethylated at K4 H3. We show that on certain actively transcribed genes, the Isw1p chromatin remodeling ATPase requires K4 H3 methylation to associate with chromatin in vivo. Analysis of one such gene, MET16, shows that the enzymatic activities of Set1p and Isw1p are functionally connected: Set1p methylation and Isw1p ATPase generate specific chromatin changes at the 5' end of the gene, are necessary for the correct distribution of RNA polymerase II over the coding region, and are required for the recruitment of the cleavage and polyadenylation factor Rna15p. These results indicate that K4 H3 methylation and Isw1p ATPase activity are intimately linked in regulating transcription of certain genes in yeast.
Subject(s)
Adenosine Triphosphatases/metabolism , Chromatin/metabolism , DNA-Binding Proteins/metabolism , Histones/chemistry , Histones/metabolism , Lysine/metabolism , Adenosine Triphosphatases/genetics , Chromosomal Proteins, Non-Histone/metabolism , DNA-Binding Proteins/genetics , Gene Expression Regulation, Fungal , Humans , Methionine/metabolism , Methylation , Protein Binding , RNA Polymerase II/metabolism , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolism , mRNA Cleavage and Polyadenylation Factors/genetics , mRNA Cleavage and Polyadenylation Factors/metabolismABSTRACT
We demonstrate that distinct forms of the yeast chromatin-remodeling enzyme Isw1p sequentially regulate each stage of the transcription cycle. The Isw1a complex (Iswlp/Ioc3p) represses gene expression at initiation through specific positioning of a promoter proximal dinucleosome, whereas the Isw1b complex (Iswlp/Ioc2p/Ioc4p) acts within coding regions to control the amount of RNA polymerase (RNAPII) released into productive elongation and to coordinate elongation with termination and pre-mRNA processing. These effects of Isw1b are controlled via phosphorylation of the heptad repeat carboxy-terminal domain (CTD) of RNAPII and methylation of the chromatin template. The transcription elongation factor Spt4p antagonizes Isw1p and overcomes the Isw1p dependent pausing of RNAPII at the onset of the elongation cycle. Overall these studies establish the central role played by Isw1p in the coordination of transcription.
