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

Department of Biochemistry, Vanderbilt University School of Medicine, 613C Light Hall, Nashville, TN 37232, USA.
Molecular and Cellular Biology (Impact Factor: 4.78). 07/2010; 30(13):3216-32. DOI: 10.1128/MCB.01008-09
Source: PubMed


The trans-histone regulatory cross talk between H2BK123 ubiquitination (H2Bub1) and H3K4 and H3K79 methylation is not fully understood.
In this study, we report that the residues arginine 119 and threonine 122 in the H2B C-terminal helix are important for transcription
and cell growth and play a direct role in controlling H2Bub1 and H3K4 methylation. These residues modulate H2Bub1 levels by
controlling the chromatin binding and activities of the deubiquitinases. Furthermore, we find an uncoupling of the H2Bub1-mediated
coregulation of both H3K4 and -K79 methylation, as these H2B C-terminal helix residues are part of a distinct surface that
affects only Set1-COMPASS (complex proteins associated with Set1)-mediated H3K4 methylation without affecting the functions
of Dot1. Importantly, we also find that these residues interact with Spp1 and control the chromatin association, integrity,
and overall stability of Set1-COMPASS independent of H2Bub1. Therefore, we have uncovered a novel role for the H2B C-terminal
helix in the trans-histone cross talk as a binding surface for Set1-COMPASS. We provide further insight into the trans-histone cross talk and propose that H2Bub1 stabilizes the nucleosome by preventing H2A-H2B eviction and, thereby, retains
the “docking site” for Set1-COMPASS on chromatin to maintain its stable chromatin association, complex stability, and processive

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Available from: Mahesh B Chandrasekharan,
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    • "One possibility is that by modulating DNA-histone and/or histone-histone interactions , ubiquitin itself induces a conformational change(s) of the nucleosome that facilitates H3K4 methylation by the catalytic core. Earlier demonstrations of effects of H2B ubiquitylation on nucleosomal interactions and stability (Fierz et al., 2011; Chandrasekharan et al., 2010) and on H3 methylation by two different enzyme systems—H3K79 methylation by hDot1L (McGinty et al., 2008) and H3K4 methylation by ySet1C (this study)—lend support to this possibility. H2Bub may also bring about a conformational change of the ySet1C active site that involves the catalytic core, the n-SET domain, and Spp1 and, in turn, renders the active site accessible to H3K4 (Figure 7C). "
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    ABSTRACT: Past studies have documented a crosstalk between H2B ubiquitylation (H2Bub) and H3K4 methylation, but little (if any) direct evidence exists explaining the mechanism underlying H2Bub-dependent H3K4 methylation on chromatin templates. Here, we took advantage of an in vitro histone methyltransferase assay employing a reconstituted yeast Set1 complex (ySet1C) and a recombinant chromatin template containing fully ubiquitylated H2B to gain valuable insights. Combined with genetic analyses, we demonstrate that the n-SET domain within Set1, but not Swd2, is essential for H2Bub-dependent H3K4 methylation. Spp1, a homolog of human CFP1, is conditionally involved in this crosstalk. Our findings extend to the human Set1 complex, underscoring the conserved nature of this disease-relevant crosstalk pathway. As not all members of the H3K4 methyltransferase family contain n-SET domains, our studies draw attention to the n-SET domain as a predictor of an H2B ubiquitylation-sensing mechanism that leads to downstream H3K4 methylation.
    Molecular cell 02/2013; 49(6). DOI:10.1016/j.molcel.2013.01.034 · 14.02 Impact Factor
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    • "Next, we examined the histone methylation status at the locus of the DRAM promoter. The trimethyl-H3K4, a euchromatic marker [17]–[18], displayed a similar pattern with Diacetyl-H3 and Tetra-acetyl-H4 in Hep3B cell (Figure 4C), while the dimethyl-H3K9 was scored lowest in R6 region at basal level and was decreased along with prolonged serum starvation (Figure 4D). The dimethyl-H3K9 serves as a signal for chromatin silencing by recruiting the HP1 proteins (heterochromatin protein 1) and is mutually exclusive with H3-K9 acetylation [19]. "
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    ABSTRACT: DRAM is a lysosomal membrane protein and is critical for p53-mediated autophagy and apoptosis. DRAM has a potential tumor-suppressive function and is downregulated in many human cancers. However, the regulation of DRAM expression is poorly described so far. Here, we demonstrated that serum deprivation strongly induces DRAM expression in liver cancer cells and a core DNA sequence in the DRAM promoter is essential for its responsiveness to serum deprivation. We further observed that euchromatin markers for active transcriptions represented by diacetyl-H3, tetra-acetyl-H4 and the trimethyl-H3K4 at the core promoter region of DRAM gene are apparently increased in a time-dependent manner upon serum deprivation, and concomitantly the dimethyl-H3K9, a herterochromatin marker associated with silenced genes, was time-dependently decreased. Moreover, the chromatin remodeling factor Brg-1 is enriched at the core promoter region of the DRAM gene and is required for serum deprivation induced DRAM expression. These observations lay the ground for further investigation of the DRAM gene expression.
    PLoS ONE 12/2012; 7(12):e50502. DOI:10.1371/journal.pone.0050502 · 3.23 Impact Factor
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    • "A previous study reported that mutational alteration of H2B arginine 119 to alanine does not prevent H2BK123 mono-ubiquitination, but does affect the degree of H3K4 methylation (Chandrasekharan et al. 2010). As previously reported, changing H2BR119 to alanine (H2BR119A) reduces the chromatin association of Spp1 and therefore H3K4 tri-methylation, whereas changing H2B119 to aspartic acid (H2BR119D) results in loss of H3K4 di-and trimethylation to the same extent as eliminating H2BK123 mono-ubiquitination (Chandrasekharan et al. 2010). Our analysis of these histone H2B mutants revealed that strains expressing htb1-R119D displayed elevated plasmid loss rates similar to those of the htb1-K123R strain (Figure 6C). "
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    ABSTRACT: DNA replication is a highly regulated process that is initiated from replication origins, but the elements of chromatin structure that contribute to origin activity have not been fully elucidated. To identify histone post-translational modifications important for DNA replication, we initiated a genetic screen to identify interactions between genes encoding chromatin-modifying enzymes and those encoding proteins required for origin function in the budding yeast Saccharomyces cerevisiae. We found that enzymes required for histone H3K4 methylation, both the histone methyltransferase Set1 and the E3 ubiquitin ligase Bre1, are required for robust growth of several hypomorphic replication mutants, including cdc6-1. Consistent with a role for these enzymes in DNA replication, we found that both Set1 and Bre1 are required for efficient minichromosome maintenance. These phenotypes are recapitulated in yeast strains bearing mutations in the histone substrates (H3K4 and H2BK123). Set1 functions as part of the COMPASS complex to mono-, di-, and tri-methylate H3K4. By analyzing strains lacking specific COMPASS complex members or containing H2B mutations that differentially affect H3K4 methylation states, we determined that these replication defects were due to loss of H3K4 di-methylation. Furthermore, histone H3K4 di-methylation is enriched at chromosomal origins. These data suggest that H3K4 di-methylation is necessary and sufficient for normal origin function. We propose that histone H3K4 di-methylation functions in concert with other histone post-translational modifications to support robust genome duplication.
    Genetics 07/2012; 192(2):371-84. DOI:10.1534/genetics.112.142349 · 5.96 Impact Factor
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