Histone H2B C-Terminal Helix Mediates trans-Histone H3K4 Methylation Independent of H2B Ubiquitination

Posttranslational modifications of the four core histones (H2A, H2B, H3, and H4) play an important role in controlling nucleosome/chromatin structure for factor access (2, 22-23, 27). These covalent modifications include acetylation, phosphorylation, methylation, ubiquitination, sumoylation, and ADP-ribosylation. In histone methylation, each modified lysine exists as a monomethylated (me1), dimethylated (me2), or trimethylated (me3) form, adding yet another level of variation. Histone modifications are regulated during replication, transcription, recombination, and repair (7, 23, 37, 51). In turn, several modifications serve as “marks” for a cellular process and are recognized by proteins with specific interaction domains (2, 41). Additionally, these modifications regulate the establishment of other modifications within the same histone (in cis) (20) or on different histones at a distant site(s) (in trans) (10, 25), a phenomenon termed “histone cross talk.” One well-studied example of a trans-histone cross talk is the regulation of H3K4 and H3K79 methylation by H2BK123 monoubiquitination (H2Bub1) (35, 45, 53). The primary components involved in this evolutionarily conserved, transcription-coupled, and regulatory cross talk are as follows. Rad6/Bre1 are the E2/E3 ubiquitin-conjugating/ligating enzymes, which add a single ubiquitin to K123 at the H2B C-terminal region. Dot1, a distributive, nonprocessive, and non-SET domain methyltransferase (12), catalyzes H3K79 methylation (3, 34). Set1-COMPASS (complex proteins associated with Set1), a multiprotein complex consisting of the methyltransferase (Set1) and seven regulatory subunits (Swd1, Swd2, Swd3, Bre2, Sdc1, Spp1, and Shg1), catalyzes processive H3K4 methylation. While Swd1 and Swd3 are essential for complex integrity, Bre2 and Sdc1 are needed for maintaining normal levels of all forms of H3K4 methylation, and Spp1 is important only for H3K4me3 (6, 31, 43). Regulation of the cross talk is seen from the diverse and drastic changes in H3K4 and -K79 methylation levels in the absence of H2Bub1 (5, 44). Initial models proposed to explain this cross talk suggested that H2Bub1 acts as a “wedge” to nonspecifically unfold chromatin for Set1 and Dot1 to gain access to their substrates or, alternatively, that it functions as a “bridge” to directly recruit them (16, 49). In a previous study, we discovered that H2Bub1 does not “open up” the chromatin; instead, it stabilizes the nucleosome by preventing H2A-H2B eviction (4). Further, we proposed nucleosome stabilization as a likely mechanism by which H2Bub1 promotes stable and prolonged association of the methyltransferases with chromatin and their substrates to catalyze high levels of H3K4 and -K79 methylation. Two studies with conflicting conclusions have implicated Swd2, a Set1-COMPASS subunit, as the key link between H2Bub1 and H3K4 methylation. Whereas one study showed that H2Bub1 regulates the integrity of Set1-COMPASS by affecting Swd2 levels (26), the other revealed that the H2Bub1-dependent ubiquitination of Swd2 and the subsequent recruitment of Spp1 are important for H3K4 methylation (52). Therefore, regulation of Set1-COMPASS functions is still not fully understood. Additionally, Swd2 has also been implicated in the regulation of H3K79 methylation by recruiting Dot1 (26). Recently, the basic patch in the H4 N terminus was shown to play a role in the trans-histone pathway by controlling the chromatin binding and functions of Dot1 (9). However, binding sites for Set1-COMPASS on chromatin are not known. In this study, we report that the residues R119 and T122 in the H2B C-terminal helix play a direct role in controlling both H2Bub1 and H3K4 methylation levels. Importantly, we find that these residues interact with Spp1 and modulate the chromatin association, integrity, and overall stability of Set1-COMPASS independent of H2Bub1. Collectively, our study uncovers a novel role for the H2B C-terminal helix in the trans-histone cross talk by serving as a “docking” surface for Set1-COMPASS, without affecting the functions of Dot1, and therefore reveals an uncoupling of the H2Bub1-mediated coregulation of H3K4 and -K79 methylation.