Whereas mono-, di- and trimethylation states of lysines on histones typically have specific functions, no specific functions have been attributed so far to the different methylation states of histone H3 Lysine 79 (H3K79) generated by Dot1. Here we show that Dot1, in contrast to other known histone methyltransferases, introduces multiple methyl groups via a nonprocessive mechanism. The kinetic mechanism implies that the H3K79 methylation states cannot be generated independently, suggesting functional redundancy. Indeed, gene silencing in yeast, which is dependent on Dot1, relied on global H3K79 methylation levels and not on one specific methylation state. Furthermore, our findings suggest that histone H2B ubiquitination affects H3K79 trimethylation by enhancing synthesis of all H3K79 methylation states. Our results suggest that multiple methylation of H3K79 leads to a binary code, which is expected to limit the possibilities for regulation by putative demethylases or binding proteins.

Bites byEnvenomation by Loxosceles spiders, endemic to temperate and (sub)tropical regions of the Americas, Africa, and Europe, can lead to local skin injury as well as to serious systemic toxicity, including thrombus formation, vascular leakage, hemolysis, and persistent inflammation (1-3). In severe cases, the hematologic complications can lead to renal failure and death, especially in children (2, 3). Treatment is difficult; antivenoms are not very effective, and the use of corticosteroids or anti-inflammatory medication is controversial (3). The toxin responsible for the local and systemic effects of Loxosceles venom is an unusual sphingomyelinase D (SMaseD) 1 that converts sphingomyelin (SM) in the outer leaflet of the plasma membrane to ceramide 1-phosphate (N-acylsphingosine 1-phosphate) (4 -7). Strikingly, while SMaseD is not found elsewhere in the animal kingdom, a similar enzyme is produced as an exotoxin by some pathogenic bacteria, notably Corynebacterium pseudotuberculosis, Corynebacterium ulcerans, and Arcanobacterium (formerly Corynebacterium) hemolyticum (8 -10). C. pseudotuberculosis causes lymphadenitis in animals but is also pathogenic for humans, while C. ulcerans and A. hemolyticum are pathogens of pharyngitis and other human infections (11); in no case is the molecular basis for virulence known (12). The SMaseD from C. pseudotuberculosis, also named SM-specific phospholipase D (PLD), is an essential virulence determinant that contributes to the persistence and spread of the bacteria within the host (13). The Loxosceles and C. pseudotuberculosis SMases D have the same molecular mass (31-32 kDa) and share about 30% sequence similarity (see "Results"). In model systems, the spider and bacterial enzymes provoke remarkably similar pathophysiological effects, including platelet aggregation, endothelial hyperpermeability, complement-dependent hemolysis, and neutrophil-dependent skin necrosis (4 -7, 9, 14 -16).Despite decades of study it remains unclear how SMaseD can elicit such a wide variety of biological effects, particularly, since ceramide 1-phosphate is not known as a signaling molecule. In contrast to ceramide, which may reorganize lipid microdomains and associated signaling complexes (17, 18), ceramide 1-phosphate is a bilayer-preferring phospholipid that is unlikely to significantly perturb membrane structure. Furthermore, mammalian cells treated with SMaseD from either Loxosceles deserta or C. pseudotuberculosis do not convert newly formed ceramide 1-phosphate to ceramide nor does SMaseD treatment affect membrane permeability or cell viability (19,20).Given the lack of understanding of SMaseD bioactivity, we set out to re-examine the substrate specificity and cellular effects of the enzyme. Our interest was stirred by a report of more than 30 years ago, showing that partially purified SMaseD from C. pseudotuberculosis (ovis) can catalyze the release of choline from lysophosphatidylcholine (LPC) but not from phosphatidylcholine (PC) (21). LPC is an abundant plasma component and removal ...

Post-translational modifications of histone proteins have a crucial role in regulating gene expression. If efficiently re-established after chromosome duplication, histone modifications could help propagate gene expression patterns in dividing cells by epigenetic mechanisms. We used an integrated approach to investigate the dynamics of the conserved methylation of histone H3 Lys 79 (H3K79) by Dot1. Our results show that methylation of H3K79 progressively changes after histone deposition, which is incompatible with a rapid copy mechanism. Instead, methylation accumulates on ageing histones, providing the cell with a timer mechanism to directly couple cell-cycle length to changes in chromatin modification on the nucleosome core. Keywords: cell cycle; chromatin; H3K79; H3K4; Set1 EMBO reports (2011) 12, 956-962.

Dot1 methylates histone H3 lysine 79 (H3K79) on the nucleosome core and is involved in Sir proteinmediated silencing. Previous studies suggested that H3K79 methylation within euchromatin prevents nonspecific binding of the Sir proteins, which in turn facilitates binding of the Sir proteins in unmethylated silent chromatin. However, the mechanism by which the Sir protein binding is influenced by this modification is unclear. We performed genome-wide synthetic genetic array (SGA) analysis and identified interactions of DOT1 with SIR1 and POL32. The synthetic growth defects found by SGA analysis were attributed to the loss of mating type identity caused by a synthetic silencing defect. By using epistasis analysis, DOT1, SIR1, and POL32 could be placed in different pathways of silencing. Dot1 shared its silencing phenotypes with the NatA N-terminal acetyltransferase complex and the conserved N-terminal bromo adjacent homology (BAH) domain of Sir3 (a substrate of NatA). We classified all of these as affecting a common silencing process, and we show that mutations in this process lead to nonspecific binding of Sir3 to chromatin. Our results suggest that the BAH domain of Sir3 binds to histone H3K79 and that acetylation of the BAH domain is required for the binding specificity of Sir3 for nucleosomes unmethylated at H3K79.Gene silencing in Saccharomyces cerevisiae at telomeres and the silent mating type loci is mediated by Sir proteins, which are recruited to DNA elements called silencers by sequencespecific DNA binding proteins (16,20,61). Upon the recruitment of Sir2 and Sir4 to silencers, Sir3 can bind, and the silent chromatin structure can subsequently spread in cis by interactions with neighboring nucleosomes (42). Silent chromatin in yeast is characterized by the absence of histone modifications, suggesting that the Sir complex preferentially binds to unmodified histones (16, 61). The NAD-dependent histone deacetylase activity of Sir2 is required for the spread and formation of a repressive Sir2-Sir3-Sir4 (Sir2/3/4) chromatin structure (35,42,74), and the binding of Sir3 to histone peptides in vitro has been shown to be negatively affected by the methylation and acetylation of the tails of histone H3 and H4 (8, 42, 63). Binding of Sir3 to histone tails is mediated by the C terminus of Sir3 (20). However, full-length Sir3 can bind to nucleosomes which lack histone tails, suggesting that Sir3 also interacts with other features of the nucleosome (23).In addition to modifications on the histone tails, silencing is positively affected by the methylation of lysine 79 of histone H3 (H3K79), a residue on the nucleosome core (15,39,47,49,76). The responsible methyltransferase Dot1 methylates ϳ90% of histone H3 and does so predominantly in euchromatin (39,47,49,76). In the absence of Dot1, binding of Sir2 and Sir3 at silent chromatin is reduced, and Sir3 becomes redistributed (47,49,62,76). We previously proposed that the methylated H3K79 (H3K79me) in euchromatin prevents nonspecific binding of Sir proteins to euchromatin...

BackgroundMethylation of histone H3 lysine 79 (H3K79) by Dot1 is highly conserved among species and has been associated with both gene repression and activation. To eliminate indirect effects and examine the direct consequences of Dot1 binding and H3K79 methylation, we investigated the effects of targeting Dot1 to different positions in the yeast genome.ResultsTargeting Dot1 did not activate transcription at a euchromatic locus. However, chromatin-bound Dot1 derepressed heterochromatin-mediated gene silencing over a considerable distance. Unexpectedly, Dot1-mediated derepression was established by both a H3K79 methylation-dependent and a methylation-independent mechanism; the latter required the histone acetyltransferase Gcn5. By monitoring the localization of a fluorescently tagged telomere in living cells, we found that the targeting of Dot1, but not its methylation activity, led to the release of a telomere from the repressive environment at the nuclear periphery. This probably contributes to the activity-independent derepression effect of Dot1.ConclusionsTargeting of Dot1 promoted gene expression by antagonizing gene repression through both histone methylation and chromatin relocalization. Our findings show that binding of Dot1 to chromatin can positively affect local gene expression by chromatin rearrangements over a considerable distance.

In the eukaryotic cell nucleus, the DNA is packaged in a structure called chromatin. The fundamental building block of chromatin is the nucleosome, which is composed of DNA wrapped around an octamer of four distinct histone proteins. Post-translational modifications (PTMs) of histone proteins can affect chromatin structure and function and thereby play critical roles in regulating gene expression. Most histone PTMs are found in unstructured histone tails that protrude from the nucleosome core. As a consequence, (synthetic) peptide truncations of these tails provide convenient substrates for the analysis of histone binding proteins and modifying enzymes. Modifications located on residues that reside in the nucleosome core are more difficult to study because short peptides do not recapitulate this defined structured state well. Methylation of histone H3 on Lys79 (H3K79), mediated by the Dot1 enzyme, is an example of such a core PTM. This modification, which is highly conserved, is linked to human leukemia, and pharmacological modulation of Dot1 activity could be a strategy to treat leukemia. Here we review the available and emerging genetic, biochemical, and chemical methods that together are starting to reveal the function and regulation of this and other histone modifications on the nucleosome core.

SummaryDot1 is a highly conserved methyltransferase that modifies histone H3 on the nucleosome core surface. In contrast to yeast, flies, and humans where a single Dot1 enzyme is responsible for all methylation of H3 lysine 79 (H3K79), African trypanosomes express two DOT1 proteins that methylate histone H3K76 (corresponding to H3K79 in other organisms) in a cell-cycle-regulated manner. Whereas DOT1A is essential for normal cell cycle progression, DOT1B is involved in differentiation and control of antigenic variation of this protozoan parasite. Analysis of DOT1A and DOT1B in trypanosomes or in vitro, to understand how H3K76 methylation is controlled during the cell cycle, is complicated by the lack of genetic tools and biochemical assays. To eliminate these problems, we developed a heterologous expression system in yeast. Whereas Trypanosoma brucei DOT1A predominantly dimethylated H3K79, DOT1B trimethylated H3K79 even in the absence of dimethylation by DOT1A. Furthermore, DOT1A activity was selectively reduced by eliminating ubiquitylation of H2B. The tail of histone H4 was not required for activity of DOT1A or DOT1B. These findings in yeast provide new insights into possible mechanisms of regulation of H3K76 methylation in Trypanosoma brucei.

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