Histone H2B Ubiquitylation Is Not Required for Histone H3 Methylation at Lysine 4 in Tetrahymena

Abstract

Ubiquitylation of histone H2B and/or a component of the system that ubiquitylates H2B is required for methylation of histone H3 at lysine 4 (H3K4) in yeasts and probably in humans. In this study, the single ubiquitylation site was mapped to conserved lysine 115 of the C-terminal region of histone H2B in the single-cell model organism Tetrahymena thermophila. In strains lacking H2B ubiquitylation, H3K4 methylation was not detectably affected. As in other organisms, the E2 ubiquitinconjugating enzyme Ubc2 and the E3 ubiquitin ligase Bre1 were required for H2B ubiquitylation. However, neither enzyme was required for H3K4 methylation. These studies argue that, in T. thermophila, the histone ubiquitylation mechanism is not required for H3K4 methylation, demonstrating that different organisms can speak different languages in the "cross-talk" among post-translational modifications on different histones.In the nuclei of eukaryotic cells, DNA is highly compacted into chromatin, a nucleoprotein complex, whose major protein components are the histones. The basic unit of chromatin is the nucleosome core in which 146 base pairs of double-stranded DNA are wrapped in ϳ1.75 left-handed superhelical turns around an octamer containing two molecules of each of the four conserved core histones H2A, H2B, H3, and H4 (1, 2). A fifth, less conserved linker histone H1, associates with a variable length of linker DNA between nucleosome cores. Site-specific histone post-translational modifications, such as acetylation, methylation, phosphorylation, and ubiquitylation, are correlated with diverse chromatin functions, including DNA replication, DNA repair, chromatin assembly, gene transcription, and other chromatin-based processes (3, 4). It has been suggested that at least some distinct histone modifications act sequentially or in combination to form what has been variously referred to as a histone, epigenetic, or nucleosome "code" that is read by other proteins or protein complexes to alter chromatin structure and regulate distinct downstream events (5, 6). Deciphering this code, which is likely to have complex redundant, combinatorial, and multivalent features, is essential for understanding the in vivo function of the diverse post-translational modifications on histones.Ubiquitin is a 76-amino acid globular protein that is conserved in eukaryotes. Unlike proteins that are targeted by polyubiquitylation to the proteosome for degradation, histones are reversibly modified by covalent attachment of one ubiquitin or a short ubiquitin chain. The bulk of histone ubiquitylation occurs on chromatin by the addition of a single ubiquitin molecule via an isopeptide linkage to a specific lysine residue in the C-terminal tail of histones H2A and H2B (7,8). To a lesser extent, histones H1 (9), H3, and H4 (10, 11) also can be ubiquitylated in vivo. Ubiquitylation on different histones has distinct functions (12).A number of recent studies have focused on ubiquitylation of H2B. In the budding yeast Saccharomyces cerevisiae, H2B is monoubiquitylated at l...

SET1 and p300 Act Synergistically, through Coupled Histone Modifications, in Transcriptional Activation by p53

“…In an initial analysis of their HMT activities, these complexes exhibited clear H3K4 mono-, di-, and trimethylation activities on recombinant histone octamer substrates (Figure S2A) but very low activities on recombinant chromatin substrates (data not shown). In view of reports of enhanced H3K4 methylation of acetylated H3 peptides by an isolated MLL1 SET domain (Milne et al, 2002; Nightingale et al, 2007), as well as H3K4 methylation in the absence (Wang et al, 2009) or near absence (Vethantham et al, 2012) of H2B ubiquitylation in some physiological situations, we tested the ability of p300-mediated histone acetylation to increase the activity of SET1C on histone octamers with unmodified H2B but found no effects (data not shown).…”

Dynamic Loss of H2B Ubiquitylation without Corresponding Changes in H3K4 Trimethylation during Myogenic Differentiation

“…However, recent experiments, including our studies in muscle cells, suggest that our understanding is far from complete. For example, although a tight connection between H2Bub and trimethylation of H3K4 and H3K79 has been established in yeast, it is not an obligatory event in Tetrahymena thermophila (41). Interestingly, Tetrahymena does not possess Set1/ COMPASS type methylases and instead expresses a single methylase closely related to MLL (36,41), which could offer a possible explanation for the loss of H2Bub dependence.…”

“…For example, although a tight connection between H2Bub and trimethylation of H3K4 and H3K79 has been established in yeast, it is not an obligatory event in Tetrahymena thermophila (41). Interestingly, Tetrahymena does not possess Set1/ COMPASS type methylases and instead expresses a single methylase closely related to MLL (36,41), which could offer a possible explanation for the loss of H2Bub dependence. In mammalian systems, the presence of several different methylase complexes, some of which have H2Bub-independent functions, make the connection between H2B ubiquitylation and H3K4 methylation more complex.…”

The super elongation complex (SEC) and MLL in development and disease

“…4). Interestingly, it was reported recently that H3K4me3 levels were not affected by loss of H2B monoubiquitination in Tetrahymena (Z Wang et al 2009a). In support of Tetrahymena having only a MLL-type H3K4 methylase, loss of the ability to methylate H3K4 results in the loss of transcription of several hundred genes in Tetrahymena (Z Wang et al 2009a).…”

“…Interestingly, it was reported recently that H3K4me3 levels were not affected by loss of H2B monoubiquitination in Tetrahymena (Z Wang et al 2009a). In support of Tetrahymena having only a MLL-type H3K4 methylase, loss of the ability to methylate H3K4 results in the loss of transcription of several hundred genes in Tetrahymena (Z Wang et al 2009a). This differs from the situation in budding and fission yeast, where loss of H3K4 methylation by Set1/COMPASS has little effect on gene expression (Miller et al 2001;Tanny et al 2007).…”