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Regulation of cell cycle progression and gene expression by H2A deubiquitination

Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Kaul Human Genetics Building 402A, 720 South 20th Street, Birmingham, Alabama 35294, USA.
Nature (Impact Factor: 42.35). 11/2007; 449(7165):1068-72. DOI: 10.1038/nature06256
Source: PubMed

ABSTRACT Post-translational histone modifications have important regulatory roles in chromatin structure and function. One example of such modifications is histone ubiquitination, which occurs predominately on histone H2A and H2B. Although the recent identification of the ubiquitin ligase for histone H2A has revealed important roles for H2A ubiquitination in Hox gene silencing as well as in X-chromosome inactivation, the enzyme(s) involved in H2A deubiquitination and the function of H2A deubiquitination are not known. Here we report the identification and functional characterization of the major deubiquitinase for histone H2A, Ubp-M (also called USP16). Ubp-M prefers nucleosomal substrates in vitro, and specifically deubiquitinates histone H2A but not H2B in vitro and in vivo. Notably, knockdown of Ubp-M in HeLa cells results in slow cell growth rates owing to defects in the mitotic phase of the cell cycle. Further studies reveal that H2A deubiquitination by Ubp-M is a prerequisite for subsequent phosphorylation of Ser 10 of H3 and chromosome segregation when cells enter mitosis. Furthermore, we demonstrate that Ubp-M regulates Hox gene expression through H2A deubiquitination and that blocking the function of Ubp-M results in defective posterior development in Xenopus laevis. This study identifies the major deubiquitinase for histone H2A and demonstrates that H2A deubiquitination is critically involved in cell cycle progression and gene expression.

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Available from: Hediye Erdjument-Bromage, Apr 29, 2015
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    • "USP49 and USP49 C262A mutants were transfected into cells with Effectene following the manufacturer's instructions. A Western blot assay with anti-uH2A and anti-uH2B antibodies on transfected cells was performed as described (Joo et al. 2007). "
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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.
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    • "Modification with Ub can be reversed by Ub proteases called de-ubiquitinating enzymes (DUBs) and some DUB activities can modulate DNA damage signalling and repair by editing Ub-conjugates: BRCC36 specifically hydrolyses Ub- K63 polymers and regulates 53BP1 accumulation; overexpression of the H2A DUB, USP3, abolishes RAP80 and 53BP1 localisation; and USP16 is required for local transcriptional restoration after recovery from a DSB (Joo et al, 2007; Doil et al, 2009; Shao et al, 2009; Shanbhag et al, 2010). Given the complexity and degree of involvement of poly-Ub in DNA repair it is highly likely that further DUB activities form part of the DSB response. "
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    ABSTRACT: The regulation of Ubiquitin (Ub) conjugates generated by the complex network of proteins that promote the mammalian DNA double-strand break (DSB) response is not fully understood. We show here that the Ub protease POH1/rpn11/PSMD14 resident in the 19S proteasome regulatory particle is required for processing poly-Ub formed in the DSB response. Proteasome activity is required to restrict tudor domain-dependent 53BP1 accumulation at sites of DNA damage. This occurs both through antagonism of RNF8/RNF168-mediated lysine 63-linked poly-Ub and through the promotion of JMJD2A retention on chromatin. Consistent with this role POH1 acts in opposition to RNF8/RNF168 to modulate end-joining DNA repair. Additionally, POH1 acts independently of 53BP1 in homologous recombination repair to promote RAD51 loading. Accordingly, POH1-deficient cells are sensitive to DNA damaging agents. These data demonstrate that proteasomal POH1 is a key de-ubiquitinating enzyme that regulates ubiquitin conjugates generated in response to damage and that several aspects of the DSB response are regulated by the proteasome.
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    • "USP44, a direct target of Oct4 (Boyer et al., 2005), was indeed already reported to be downregulated during ESC differentiation (Jung et al., 2010). Interestingly, USP44 shares substantial homology with the histone DUBs ubp8, USP22, USP16 and USP3 (Henry et al., 2003; Joo et al., 2007; Nicassio et al., 2007; Zhang et al., 2008). Moreover, USP44 is localized to the nucleus (Stegmeier et al., 2007; Suresh et al., 2010) and associates with chromatin (Fig. 4B). "
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