Ready, SET, Go: Post-translational regulation of the histone lysine methylation network in budding yeast

Abstract

Histone lysine methylation is a key epigenetic modification that regulates eukaryotic transcription. Here, we comprehensively review the function and regulation of the histone methylation network in the budding yeast and model eukaryote, Saccharomyces cerevisiae. First, we outline the lysine methylation sites that are found on histone proteins in yeast (H3K4me1/2/3, H3K36me1/2/3, H3K79me1/2/3, and H4K5/8/12me1) and discuss their biological and cellular roles. Next, we detail the reduced but evolutionarily conserved suite of methyltransferase (Set1p, Set2p, Dot1p, and Set5p) and demethylase (Jhd1p, Jhd2p, Rph1p, and Gis1p) enzymes that are known to control histone lysine methylation in budding yeast cells. Specifically, we illustrate the domain architecture of the methylation enzymes and highlight the structural features that are required for their respective functions and molecular interactions. Finally, we discuss the prevalence of post-translational modifications on yeast histone methylation enzymes and how phosphorylation, acetylation, and ubiquitination in particular are emerging as key regulators of enzyme function. We note that it will be possible to completely connect the histone methylation network to the cell's signaling system, given that all methylation sites and cognate enzymes are known, most phosphosites on the enzymes are known, and the mapping of kinases to phosphosites is tractable owing to the modest set of protein kinases in yeast. Moving forward, we expect that the rich variety of post-translational modifications that decorates the histone methylation machinery will explain many of the unresolved questions surrounding the function and dynamics of this intricate epigenetic network.

Keywords: Saccharomyces cerevisiae; chromatin; demethylase; epigenetics; histone methylation; kinase; methyltransferase; phosphorylation; post-translational modification; post-translational regulation.

Figure 1

Histone lysine methylation network in budding yeast. All histone lysine methylation sites in yeast are depicted along histone proteins as yellow diamonds. The upstream methyltransferase and demethylase enzymes that control these sites are shown in green and pink, respectively. Histone methyl marks are recognized by downstream effector proteins that harbor methyl-reader domains and are colored according to the key (bottom). Methylation can also inhibit binding of proteins to chromatin, notably the bromo-adjacent homology (BAH) domain of Sir3p (magenta), which is blocked by H3K79 methylation. The functional outcomes of histone methylation sites and the recruitment of specific effector proteins and complexes are shown in gray boxes. For ease of visualization, only a single copy of histones H3 and H4 has been illustrated, whereas both copies of histones H2A and H2B have been omitted.

Figure 2

Genomic distribution of histone lysine methylation sites in budding yeast and their regulation by other histone residues and modifications.A, the abundance of the mono-, di-, and trimethylated forms of H3K4 (top), H3K36 (middle), and H3K79 (bottom) along an active transcriptional unit is depicted by a color intensity gradient (indigo). B, regulation of budding yeast histone methylation sites by other histone residues and PTMs including acetylation (Ac; orange), ubiquitination (Ub; purple), and methylation (Me; yellow). The upstream modifying enzymes responsible for these PTMs are colored according to the key (bottom). The effects of these histone residues and PTMs are tabulated for each major lysine methylation site, where red arrows denote a stimulatory effect and blue arrows indicate an inhibitory effect. For both panels, histone H4 monomethylation sites at K5, K8, and K12 have been omitted given that little is known about the distribution of these modifications along genes and their cross talk with other features of the chromatin landscape. PTM, post-translational modification; TSS, transcription start site; TTS, transcription termination site.

Figure 3

Domain architecture and structural features of yeast histone methyltransferase and demethylase enzymes. Linear sequence maps of yeast histone methyltransferase (left panel) and demethylase (right panel) enzymes. Protein domains are displayed, to scale, for each enzyme. Methyltransferase and demethylase domains are shown in green and pink, respectively, whereas other regulatory and interaction domains are colored in blue. Amino acid (aa) residues that are critical for enzymatic activity are shown in crimson. To date, partial crystal structures have been resolved for the RNA recognition motif (RRM; Protein Data Bank [PDB] ID: 2J8A) and the SET methyltransferase domain (PDB ID: 6BX3) of Set1p, the tryptophan–tryptophan (WW; PDB ID: 1E0N) and Set2 Rbp1 interacting (SRI; PDB ID: 2C5Z) domains of Set2p, the DOT1 methyltransferase domain (PDB ID: 1U2Z) of Dot1p, and the JmjN and JmjC demethylase domains (PDB ID: 3OPW) of Rph1p. Structures are depicted as ribbon diagrams in inset boxes and colored according to the region of the linear sequence map to which they correspond. AID, autoinhibitory domain; AWS, associated with SET; C2H2, Cys2-His2; MYND, myeloid translocation protein, Nervy, Deaf; NLS, nuclear localization signal; PHD, plant homeodomain.

Figure 4

Post-translational modifications on yeast histone methylation enzymes. PTM sites were from a recent systematic characterization of yeast histone methyltransferases and demethylases (315) and high-throughput phosphoproteomic and acetylomic studies (246, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321). For each modification type, the number of residues within each protein that has been shown to be post-translationally modified in at least one study has been graphed as a bar chart. For phosphorylation (blue), this refers to the number of phosphorylated serine (S) and threonine (T) residues, whereas for acetylation (orange) and ubiquitination (purple), it refers to the number of modified lysine (K) residues. For all eight histone methylation enzymes, the average (mean) number of PTM sites was calculated and shown in the right panel. Proteome values were calculated based on a total of 6275 protein-coding yeast genes (345) and all known protein phosphorylation (87,703), acetylation (10,035), and ubiquitination (14,880) sites from the YAAM database (324). PTM, post-translational modification.

Figure 5

Post-translational regulation of yeast histone methylation enzymes. The functional effects of phosphorylation (blue), acetylation (orange), and ubiquitination (purple) sites on histone methyltransferase (green) and demethylase (pink) biology are shown. Where known, the amino acid residues that carry functional PTM sites are displayed above their cognate enzyme. For Set5p, its catalytic activity and chromatin association are regulated by a cluster of ten phosphosites corresponding to phosphorylation at S458, S461, S462, S466, S475, S476, T511, S512, S517, and S520. The upstream modifying enzymes responsible for PTM sites are shown if known and colored according to the key. Instances where the upstream enzyme is not known are denoted by question marks. For some PTMs, the environmental signals that trigger their deposition are illustrated in gray boxes. The downstream functional effects of PTM sites are also shown. Although the number of targeted studies into the post-translational regulation of yeast histone methylation enzymes is modest, it is apparent that PTMs can affect their catalytic activity, chromatin binding, genomic localization, and degradation. PTM, post-translational modification.

Figure 6

Feasibility of constructing a complete phosphoregulatory network of histone lysine methylation in yeast. A comparison of the histone methylation networks in budding yeast (Saccharomyces cerevisiae) and human (Homo sapiens). Yeast possesses almost the same number of histone lysine methylation sites (yellow) as human; however, they have substantially fewer methyltransferase (green) and demethylase (pink) enzymes responsible for their regulation. As a result, there is a much smaller number of phosphosites (blue) present on the histone methylation machinery to investigate experimentally. Systematic kinase mapping is also conceivable in yeast, given the relatively modest number of protein kinases (baby blue) encoded in their genome.