Tamaki Suganuma

Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription

Yeast Rpd3 histone deacetylase plays an important role at actively transcribed genes. We characterized two distinct Rpd3 complexes, Rpd3L and Rpd3S, by MudPIT analysis. Both complexes shared a three subunit core and Rpd3L contains unique subunits consistent with being a promoter targeted corepressor. Rco1 and Eaf3 were subunits specific to Rpd3S. Mutants of RCO1 and EAF3 exhibited increased acetylation in the FLO8 and STE11 open reading frames (ORFs) and the appearance of aberrant transcripts initiating within the body of these ORFs. Mutants in the RNA polymerase II-associated SET2 histone methyltransferase also displayed these defects. Set2 functioned upstream of Rpd3S and the Eaf3 methyl-histone binding chromodomain was important for recruitment of Rpd3S and for deacetylation within the STE11 ORF. These data indicate that Pol II-associated Set2 methylates H3 providing a transcriptional memory which signals for deacetylation of ORFs by Rpd3S. This erases transcription elongation-associated acetylation to suppress intragenic transcription initiation.

Signals and Combinatorial Functions of Histone Modifications

Alterations of chromatin structure have been shown to be crucial for response to cell signaling and for programmed gene expression in development. Posttranslational histone modifications influence changes in chromatin structure both directly and by targeting or activating chromatin-remodeling complexes. Histone modifications intersect with cell signaling pathways to control gene expression and can act combinatorially to enforce or reverse epigenetic marks in chromatin. Through their recognition by protein complexes with enzymatic activities cross talk is established between different modifications and with other epigenetic pathways, including noncoding RNAs (ncRNAs) and DNA methylation. Here, we review the functions of histone modifications and their exploitation in the programming of gene expression during several events in development.

Crosstalk among Histone Modifications

Histone modifications play a complex role in the regulation of transcription. Recent studies (Duncan et al., 2008; Lee et al., 2007; Li et al., 2008) reveal that regulation of histone modifications can be functionally linked to reinforce the activation or repression of gene expression.

ATAC is a double histone acetyltransferase complex that stimulates nucleosome sliding

The Ada2a-containing (ATAC) complex is an essential Drosophila melanogaster histone acetyltransferase (HAT) complex that contains the transcriptional cofactors Gcn5 (KAT2), Ada3, Ada2a, Atac1 and Hcf. We have analyzed the complex by MudPIT (multidimensional protein identification technology) and found eight previously unidentified subunits. These include the WD40 repeat protein WDS, the PHD and HAT domain protein CG10414 (herein renamed Atac2/KAT14), the YEATS family member D12, the histone fold proteins CHRAC14 and NC2β, CG30390, CG32343 (Atac3) and CG10238. The presence of CG10414 (Atac2) suggests that it acts as a second acetyltransferase enzyme in ATAC in addition to Gcn5. Indeed, recombinant Atac2 displays HAT activity in vitro with a preference for acetylating histone H4, and mutation of Atac2 abrogated H4 lysine 16 acetylation in D. melanogaster embryos. Furthermore, although ATAC does not show nucleosome-remodeling activity itself, it stimulates nucleosome sliding by the ISWI, SWI–SNF and RSC complexes.

Host Cell Factor and an Uncharacterized SANT Domain Protein Are Stable Components of ATAC, a Novel dAda2A/dGcn5-Containing Histone Acetyltransferase Complex in Drosophila

ABSTRACT Gcn5 is a conserved histone acetyltransferase (HAT) found in a number of multisubunit complexes from Saccharomyces cerevisiae, mammals, and flies. We previously identified Drosophila melanogaster homologues of the yeast proteins Ada2, Ada3, Spt3, and Tra1 and showed that they associate with dGcn5 to form at least two distinct HAT complexes. There are two different Ada2 homologues in Drosophila named dAda2A and dAda2B. dAda2B functions within the Drosophila version of the SAGA complex (dSAGA). To gain insight into dAda2A function, we sought to identify novel components of the complex containing this protein, ATAC (Ada two A containing) complex. Affinity purification and mass spectrometry revealed that, in addition to dAda3 and dGcn5, host cell factor (dHCF) and a novel SANT domain protein, named Atac1 (ATAC component 1), copurify with this complex. Coimmunoprecipitation experiments confirmed that these proteins associate with dGcn5 and dAda2A, but not with dSAGA-specific components such as dAda2B and dSpt3. Biochemical fractionation revealed that ATAC has an apparent molecular mass of 700 kDa and contains dAda2A, dGcn5, dAda3, dHCF, and Atac1 as stable subunits. Thus, ATAC represents a novel histone acetyltransferase complex that is distinct from previously purified Gcn5/Pcaf-containing complexes from yeast and mammalian cells.

Diverse functions of WD40 repeat proteins in histone recognition

WD40 repeat proteins have been shown to bind the histone H3 tail at the center of their beta-propeller structure. In contrast, in this issue of Genes & Development, Song and colleagues (pp. 1313-1318) demonstrate that the WD40 repeat protein p55 binds a structured region of H4 through a novel binding pocket on the side of beta-propeller, illustrating a diversity of histone recognition by WD40 repeat proteins.

Serine and SAM Responsive Complex SESAME Regulates Histone Modification Crosstalk by Sensing Cellular Metabolism

Pyruvate kinase M2 (PKM2) is a key enzyme for glycolysis and catalyzes the conversion of phosphoenolpyruvate (PEP) to pyruvate, which supplies cellular energy. PKM2 also phosphorylates histone H3 threonine 11 (H3T11); however, it is largely unknown how PKM2 links cellular metabolism to chromatin regulation. Here, we show that the yeast PKM2 homolog, Pyk1, is a part of a novel protein complex named SESAME (Serine-responsive SAM-containing Metabolic Enzyme complex), which contains serine metabolic enzymes, SAM (S-adenosylmethionine) synthetases, and an acetyl-CoA synthetase. SESAME interacts with the Set1 H3K4 methyltransferase complex, which requires SAM synthesized from SESAME, and recruits SESAME to target genes, resulting in phosphorylation of H3T11. SESAME regulates the crosstalk between H3K4 methylation and H3T11 phosphorylation by sensing glycolysis and glucose-derived serine metabolism. This leads to auto-regulation of PYK1 expression. Thus, our study provides insights into the mechanism of regulating gene expression, responding to cellular metabolism via chromatin modifications.

The ATAC Acetyltransferase Complex Coordinates MAP Kinases to Regulate JNK Target Genes

In response to extracellular cues, signal transduction activates downstream transcription factors like c-Jun to induce expression of target genes. We demonstrate that the ATAC (Ada two A containing) histone acetyltransferase (HAT) complex serves as a transcriptional cofactor for c-Jun at the Jun N-terminal kinase (JNK) target genes Jra and chickadee. ATAC subunits are required for c-Jun occupancy of these genes and for H4K16 acetylation at the Jra enhancer, promoter, and transcribed sequences. Under conditions of osmotic stress, ATAC colocalizes with c-Jun, recruits the upstream kinases Misshapen, MKK4, and JNK, and suppresses further activation of JNK. Relocalization of these MAPKs and suppression of JNK activation by ATAC are dependent on the CG10238 subunit of ATAC. Thus, ATAC governs the transcriptional response to MAP kinase signaling by serving as both a coactivator of transcription and as a suppressor of upstream signaling.

Chromatin and signaling.

Signaling involves the coordinated action of multiple molecules including stimuli, receptors and enzymes part of which interact with the transcriptional machinery and target chromatin. Signaling systems regulate the cell events responsible for survival, development and homeostasis. Many of the signaling pathways induce target gene activation through interaction with the transcription machinery, including RNA polymerase II, and with histone modifying complexes. These studies are having a broad impact on chromatin biology. Recent studies suggest that chromatin itself receives the signals. Increasing examples are illustrating novel regulatory mechanisms that promote our understanding of development and disease.

MAP kinases and histone modification

Signal transduction pathways alter the gene expression program in response to extracellular or intracellular cues. Mitogen-activated protein kinases (MAPKs) govern numerous cellular processes including cell growth, stress response, apoptosis, and differentiation. In the past decade, MAPKs have been shown to regulate the transcription machinery and associate with chromatin-modifying complexes. Moreover, recent studies demonstrate that several MAPKs bind directly to chromatin at target genes. This review highlights the recent discoveries of MAPK signaling in regard to histone modifications and chromatin regulation. Evidence suggesting that further unknown mechanisms integrate signal transduction with chromatin biology is discussed.