Histone H2B ubiquitination and beyond

Department of Biochemistry and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA.
Epigenetics: official journal of the DNA Methylation Society (Impact Factor: 5.11). 08/2010; 5(6):460-8. DOI: 10.4161/epi.5.6.12314
Source: PubMed

ABSTRACT Regulation of Set1-COMPASS-mediated H3K4 methylation and Dot1-mediated H3K79 methylation by H2BK123 ubiquitination (H2Bub1) is an evolutionarily conserved trans-histone crosstalk mechanism. How H2Bub1 impacts chromatin structure and affects Set1-COMPASS/Dot1 functions has not been fully defined. Ubiquitin was proposed to bind proteins to physically bridge H2Bub1 with Set1-COMPASS/Dot1. Alternatively, the bulky ubiquitin was thought to be a "wedge" that loosens the nucleosome for factor access. Contrary to the latter possibility, recent discoveries provide evidence for nucleosome stabilization by H2Bub1 via preventing the constant H2A-H2B eviction. Recent data has also uncovered a "docking-site" on H2B for Set1-COMPASS. Collectively, these findings invoke a model, where ubiquitin acts as a "glue" to bind the nucleosome together for supporting Set1-COMPASS/Dot1 functions. This review provides an overview of these novel findings. Additionally, how H2Bub1 and its deubiquitination might alter the chromatin dynamics during transcription is discussed. Possible models for nucleosome stabilization by ubiquitin are also provided.

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Available from: Mahesh B Chandrasekharan, Aug 14, 2015
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    • "In particular, all the ESCRT-I subunits are involved in transcriptional regulation (Figs 1, 2, 4) and some of these components (Vps23 and Mvb12) contain the domain for binding to ubiquitylated proteins. Thus, we examined whether the ESCRT-I complex interacts with or modulates the ubiquitylation of histone H2B, a modification closely associated with the activation of transcription through the methylation of histone H3 at lysine residues 4 and 79 (Chandrasekharan et al. 2010; Song and Ahn 2010; Sun and Allis 2002). To examine histone ubiquitylation, we used a yeast strain containing the Flag-tagged HTB1 gene and the hemagglutinin (HA)-tagged UBI4 gene as WT. "
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    ABSTRACT: Endosomal sorting complex required for transport (ESCRT) is involved in membrane protein degradation through the recognition and sorting of ubiquitylated cargo proteins into the multivesicular body before fusion with the lysosome/vacuole. However, recent studies have challenged this canonical cellular function of ESCRT and have implicated a role for this machinery in multiple intracellular pathways. Here, we provide evidence that ESCRT complexes contribute to the regulation of transcription elongation in Saccharomyces cerevisiae. Most strains deficient in each subunit of ESCRT-0, -I, -II, and -III showed significant sensitivity to 6-azauracil or mycophenolic acid, a phenotype associated with transcription elongation defects. Moreover, these deletion strains significantly reduced transcription activation through Gcn4, a regulator of the general amino acid control. The transcription factor Rim101, which is proteolytically activated through the multimerized component Vps32/Snf7 of ESCRT-III and its collaborative proteins, was not associated with transcription elongation or Gcn4 activation. In addition, we observed that ESCRT complexes were crosslinked at the 3′ region of the coding sequence in the actively transcribed gene. In summary, these results suggest that ESCRT complexes promote genes transcription during the late stages of elongation and are required for transcription activation through Gcn4.
    Genes & genomics 06/2014; 36(3). DOI:10.1007/s13258-013-0171-8 · 0.57 Impact Factor
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    • "However, the precise functions of Lys 112 ubiquitination have yet to be fully defined. A previous report had shown ubiquitination of histone H2BK123 enhanced its binding activity and stabilized nucleosome (Chandrasekharan et al., 2010). It is implicated that methylation of HMGB1 at Lys112 reduces its DNA-binding ability through the substitution of Lys112 ubiquitination. "
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    ABSTRACT: Background:The high mobility group box 1 (HMGB1) protein is a widespread nuclear protein present in most cell types. It typically locates in the nucleus and functions as a nuclear cofactor in transcription regulation. However, HMGB1 can also localize in the cytoplasm and be released into extracellular matrix, where it plays critical roles in carcinogenesis and inflammation. However, it remains elusive whether HMGB1 is relocated to cytoplasm in clear cell renal cell carcinoma (ccRCC). Methods: Nuclear and cytoplasmic proteins were extracted by different protocols from 20 ccRCC samples and corresponding adjacent renal tissues. Western blotting and immunohistochemistry were used to identify the expression of HMGB1 in ccRCC. To elucidate the potential mechanism of HMGB1 cytoplasmic translocation, HMGB1 proteins were enriched by immunoprecipitation and analyzed by mass spectrometry (MS). Results: The HMGB1 protein was overexpressed and partially localized in cytoplasm in ccRCC samples (12/20, 60%, p<0.05). Immunohistochemistry results indicated that ccRCC of high nuclear grade possess more HMGB1 relocation than those with low grade (p<0.05). Methylation of HMGB1 at lysine 112 in ccRCC was detected by MS. Bioinformatics analysis showed that post-translational modification might affect the binding ability to DNA and mediate its translocation. Conclusion: Relocation of HMGB1 to cytoplasm was confirmed in ccRCC. Methylation of HMGB1 at lysine 112 might the redistribution of this cofactor protein.
    Asian Pacific journal of cancer prevention: APJCP 10/2013; 14(10):5789-95. DOI:10.7314/APJCP.2013.14.10.5789 · 2.51 Impact Factor
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    • "These data are consistent with previous experiments showing that uH2B stabilizes nucleosomes in vivo (Chandrasekharan et al. 2009). These results suggest that USP49 bound at exons regulates local uH2B levels, thereby affecting nucleosome stability, a fundamental chromatin characteristic thought to play profound roles in transcription elongation and cotranscriptional splicing (Chandrasekharan et al. 2010; Dujardin et al. 2013). "
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    ABSTRACT: Post-translational histone modifications play important roles in regulating chromatin structure and function. Histone H2B ubiquitination and deubiquitination have been implicated in transcriptional regulation, but the function of H2B deubiquitination is not well defined, particularly in higher eukaryotes. Here we report the purification of ubiquitin-specific peptidase 49 (USP49) as a histone H2B-specific deubiquitinase and demonstrate that H2B deubiquitination by USP49 is required for efficient cotranscriptional splicing of a large set of exons. USP49 forms a complex with RuvB-like1 (RVB1) and SUG1 and specifically deubiquitinates histone H2B in vitro and in vivo. USP49 knockdown results in small changes in gene expression but affects the abundance of >9000 isoforms. Exons down-regulated in USP49 knockdown cells show both elevated levels of alternative splicing and a general decrease in splicing efficiency. Importantly, USP49 is relatively enriched at this set of exons. USP49 knockdown increased H2B ubiquitination (uH2B) levels at these exons as well as upstream 3' and downstream 5' intronic splicing elements. Change in H2B ubiquitination level, as modulated by USP49, regulates U1A and U2B association with chromatin and binding to nascent pre-mRNA. Although H3 levels are relatively stable after USP49 depletion, H2B levels at these exons are dramatically increased, suggesting that uH2B may enhance nucleosome stability. Therefore, this study identifies USP49 as a histone H2B-specific deubiquitinase and uncovers a critical role for H2B deubiquitination in cotranscriptional pre-mRNA processing events.
    Genes & development 07/2013; 27. DOI:10.1101/gad.211037.112 · 12.64 Impact Factor
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