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: 41.46). 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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    • "The level of H2A ubiquitination varies at different stages of the cell cycle (4,5,9–18). H2A ubiquitination is correlated with cell cycle progression, and abnormality in either of the E3 ligases or deubiquitinases of H2A leads to a decreased rate of cell growth (2,16,17,19). However, the detailed mechanism linking regulators of H2A ubiquitination and cell cycle is still incompletely understood. "
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    ABSTRACT: Histone H2A ubiquitination plays critical roles in transcriptional repression and deoxyribonucleic acid (DNA) damage response. More attention has been focused on ubiquitin E3 ligases of H2A, however, less is known about the negative regulators of H2A ubiquitination. Here we identified HSCARG as a new negative regulatory protein for H2A ubiquitination and found a possible link between regulator of H2A ubiquitination and cell cycle. Mechanistically, HSCARG interacts with polycomb repressive complex 1 (PRC1) and deubiquitinase USP7 and inhibits PRC1 ubiquitination in a USP7-dependent manner. As ubiquitination of PRC1 is critical for its E3 ligase activity toward H2A, HSCARG and USP7 are further shown to decrease the level of H2A ubiquitination. Moreover, we demonstrated that HSCARG is involved in DNA damage response through affecting the level of H2A ubiquitination and localization of RAP80 at lesion points. Knockout of HSCARG results in persistent activation of checkpoint signaling and leads to cell cycle arrest. This study unravels a novel mechanism for the regulation of H2A ubiquitination and elucidates how regulators of H2A ubiquitination affect cell cycle.
    Nucleic Acids Research 04/2014; 42(9). DOI:10.1093/nar/gku230 · 9.11 Impact Factor
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    • "DUBs regulate their substrates not only by determining their proteolytic fate. For example, as it was also shown in plants, histone H2A or histone H2B ubiquitylation status is controlled by multiple DUBs (Joo et al., 2007; Sridhar et al., 2007; Zhu et al., 2007; Nakagawa et al., 2008; Schmitz et al., 2009). The ubiquitylation status of histones affects their methylation status and thus controls gene expression in the corresponding chromatin region. "
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    ABSTRACT: Ubiquitylation is a reversible post-translational modification that is involved in various cellular pathways and that thereby regulates various aspects of plant biology. For a long time, functional studies of ubiquitylation have focused on the function of ubiquitylating enzymes, especially the E3 ligases, rather than deubiquitylating enzymes (DUBs) or ubiquitin isopeptidases, enzymes that hydrolyze ubiquitin chains. One reason may be the smaller number of DUBs in comparison to E3 ligases, implying the broader substrate specificities of DUBs and the difficulties to identify the direct targets. However, recent studies have revealed that DUBs also actively participate in controlling cellular events and thus play pivotal roles in plant development and growth. DUBs are also essential for processing ubiquitin precursors and are important for recycling ubiquitin molecules from target proteins prior to their degradation and thereby maintaining the free ubiquitin pool in the cell. Here, we will discuss the five different DUB families (USP/UBP, UCH, JAMM, OTU, and MJD) and their known biochemical and physiological roles in plants.
    Frontiers in Plant Science 02/2014; 5:56. DOI:10.3389/fpls.2014.00056 · 3.95 Impact Factor
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    • "Since RING2 occupancy was unchanged at promoters that showed reduced H2AK119 ubiquitination (Figure 7) in cells expressing the L3MBTL2 K675/700R mutant, we also analysed for the presence of deubiquitinases. Several mammalian H2A deubiquitinating enzymes (DUBs) have been reported including 2A-DUB/Mysm1 (33), USP16/Ubp-M (34) and the dimeric polycomb repressive deubiquitinase (PR-DUB) complex composed of the catalytic subunit BAP1 and its binding partner ASXL1 (35). We failed to detect 2A-DUB/Mysm1, USP16/Ubp-M and BAP1, which could be due to poor antibody performance. "
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    ABSTRACT: Lethal(3) malignant brain tumour like 2 (L3MBTL2) is an integral component of the polycomb repressive complex 1.6 (PRC1.6) and has been implicated in transcriptional repression and chromatin compaction. Here, we show that L3MBTL2 is modified by SUMO2/3 at lysine residues 675 and 700 close to the C-terminus. SUMOylation of L3MBTL2 neither affected its repressive activity in reporter gene assays nor it’s binding to histone tails in vitro. In order to analyse whether SUMOylation affects binding of L3MBTL2 to chromatin, we performed ChIP-Seq analysis with chromatin of wild-type HEK293 cells and with chromatin of HEK293 cells stably expressing either FLAG-tagged SUMOylation-competent or SUMOylation-defective L3MBTL2. Wild-type FLAG-L3MBTL2 and the SUMOylation-defective FLAG-L3MBTL2 K675/700R mutant essentially occupied the same sites as endogenous L3MBTL2 suggesting that SUMOylation of L3MBTL2 does not affect chromatin binding. However, a subset of L3MBTL2-target genes, particularly those with low L3MBTL2 occupancy including pro-inflammatory genes, was de-repressed in cells expressing the FLAG-L3MBTL2 K675/700R mutant. Finally, we provide evidence that SUMOylation of L3MBTL2 facilitates repression of these PRC1.6-target genes by balancing the local H2Aub1 levels established by the ubiquitinating enzyme RING2 and the de-ubiquitinating PR–DUB complex.
    Nucleic Acids Research 12/2013; 42(5). DOI:10.1093/nar/gkt1317 · 9.11 Impact Factor
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