Abstract
Ubiquitination has traditionally been viewed in the context of polyubiquitination that is essential for marking proteins for degradation via the proteasome. Recent discoveries have shed light on key cellular roles for monoubiquitination, including as a post-translational modification (PTM) of histones such as histone H2B. Monoubiquitination plays a significant role as one of the largest histone PTMs, alongside smaller, better-studied modifications such as methylation, acetylation and phosphorylation. Monoubiquitination of histone H2B at lysine 120 (H2Bub1) has been shown to have key roles in transcription, the DNA damage response and stem cell differentiation. The H2Bub1 enzymatic cascade involves E3 RING finger ubiquitin ligases, with the main E3 generally accepted to be the RNF20–RNF40 complex, and deubiquitinases including ubiquitin-specific protease 7 (USP7), USP22 and USP44. H2Bub1 has been shown to physically disrupt chromatin strands, fostering a more open chromatin structure accessible to transcription factors and DNA repair proteins. It also acts as a recruiting signal, actively attracting proteins with roles in transcription and DNA damage. H2Bub1 also appears to play central roles in histone cross-talk, influencing methylation events on histone H3, including H3K4 and H3K79. Most significantly, global levels of H2Bub1 are low to absent in advanced cancers including breast, colorectal, lung and parathyroid, marking H2Bub1 and the enzymes that regulate it as key molecules of interest as possible new therapeutic targets for the treatment of cancer. This review offers an overview of current knowledge regarding H2Bub1 and highlights links between dysregulation of H2Bub1-associated enzymes, stem cells and malignancy.
Introduction
Reversible post-translational modifications (PTMs) in core histones constituting the nucleosome influence the nature of the chromatin landscape. Histone PTMs occur at specific amino acids on histone tails and include acetylation, ADP ribosylation, deamination, methylation, phosphorylation, proline isomerisation, monoubiquitination and sumoylation (Kouzarides 2007, Dawson et al. 2012). Modified histones participate in key cellular processes, dictating the accessibility of chromatin to elements that drive gene transcription and proteins that function in DNA damage signalling. Along with DNA methylation, histone PTMs are major components of the epigenome and may become dysregulated during tumourigenesis.
Although less well studied than many other PTMs, histone monoubiquitination, i.e. addition of a single 8.5 kDa (76 amino acids) ubiquitin molecule to specific lysine residues on histone tails, offers new opportunities for targeting of the epigenome for the treatment of malignancy. Histones are the most abundantly monoubiquitinated conjugates in the nucleus of mammalian cells, including sites of monoubiquitination at lysines on histones H2A and H2B (Clague et al. 2008). In contrast to polyubiquitination that marks a protein for proteasomal degradation, monoubiquitination of histones is associated with the transcriptional control of gene expression and the DNA damage response. Furthermore, cleavage of this single ubiquitin from histones H2A and H2B has been reported to be associated with chromatin condensation prior to packaging of DNA into metaphase chromosomes (Mueller et al. 1985).
Lysine 120 (K120) at which monoubiquitination of histone H2B occurs (H2Bub1) is the only site of histone monoubiquitination shown to result in physical disruption of chromatin strands, leading to open and accessible fibre conformations (Minsky et al. 2008, Fierz et al. 2011). K120 of histone H2B is physically placed at the interface of adjacent nucleosomes and, when monoubiquitinated, probably interferes with nucleosome stacking and thus chromatin structure (Fierz et al. 2011). Notably, substitution of ubiquitin at K120 of histone H2B with the bulkier modification of small ubiquitin-like modifier (SUMO) does not functionally replace ubiquitin; therefore, epigenetic reprogramming via PTMs at this site cannot be solely explained by steric effects (Chandrasekharan et al. 2009, Fierz et al. 2011). Consistent with this, H2Bub1 has been shown to act as a recruiting signal for proteins functioning in histone cross-talk, transcription and DNA damage (Shema-Yaacoby et al. 2013). Although lysine 125 on histone H2B can be monoubiquitinated in vitro when K120 is artificially mutated, it has no known functional role in vivo (Minsky & Oren 2004). Lysine 34 on histone H2B can also be monoubiquitinated and is involved in histone cross-talk; however, it appears to utilise different ubiquitination machinery compared with H2Bub1 and its role in the regulation of chromatin structure, if any, remains to be elucidated (Wu et al. 2011). Monoubiquitination of histone H2A at lysine 119 does not influence fibre compaction, probably due to its location in the nucleosome (Jason et al. 2001). It is interesting then that monoubiquitination of histone H2A is generally associated with silencing gene expression (Osley et al. 2006, Weake & Workman 2008), whereas, for the most part, H2Bub1 is associated with increased levels of gene transcription (Minsky et al. 2008).
H2Bub1, therefore, appears to play a unique role, fittingly described as a ‘master switch’ for gene regulation (Kim et al. 2005), with important roles in transcriptional elongation (Pavri et al. 2006, Minsky et al. 2008, Johnsen 2012), maintenance of replication-dependent histone mRNA 3′-end processing (Pirngruber et al. 2009) and the DNA damage response (Minsky et al. 2008, Kari et al. 2011, Moyal et al. 2011). H2Bub1 also has roles in the maintenance of stem cell multipotency (Karpiuk et al. 2012), regulation of DNA replication (Trujillo & Osley 2012) and maintenance of centromeric chromatin, revealing significant roles in genome stability (Sadeghi et al. 2014). Recently, H2Bub1 has been shown to be lost in advanced cancers (Prenzel et al. 2011, Hahn et al. 2012, Urasaki et al. 2012). This review draws together discoveries related to H2Bub1, including those in the area of H2Bub1-associated ubiquitin ligases and deubiquitinases (DUBs) that may offer new opportunities for the design of epigenomic-based cancer therapeutics.
H2Bub1 and associated machinery in primary tumours
Cancer is frequently described as a disease of aberrant gene expression. Identification of H2Bub1 as a key transcriptional regulator raised the likelihood that it may be altered in cancer development and the possibility that H2Bub1 itself may have tumour-suppressive roles (Espinosa 2008). Loss of global H2Bub1 detected by immunohistochemical staining has been reported for a number of cancers, including breast (Prenzel et al. 2011), colorectal (Urasaki et al. 2012), lung (Urasaki et al. 2012) and parathyroid (Hahn et al. 2012). In the case of parathyroid cancer, a mechanistic explanation for the loss of H2Bub1 is provided by the frequent occurrence of mutations in the tumour suppressor CDC73, leading to the disruption of the RNA polymerase II-associated factor 1 (PAF1) transcriptional complex that is important for the regulation of H2Bub1 (Hahn et al. 2012). CDC73 (also known as parafibromin) is a member of the human PAF1 transcriptional complex that forms a larger complex with the RING finger E3 ubiquitin ligases RNF20–RNF40 that are responsible for the monoubiquitination of histone H2B (Rozenblatt-Rosen et al. 2005, Yart et al. 2005, Hahn et al. 2012). Notably, CDC73 was shown to be WT in benign parathyroid tumours where H2Bub1 levels were maintained (Hahn et al. 2012). Furthermore, in breast cancer, basal levels of H2Bub1 were found to be unchanged when comparing normal mammary epithelium with benign breast tumours; however, H2Bub1 levels in malignant and metastatic breast cancer cells were found to be significantly reduced (Prenzel et al. 2011). The mechanism of H2Bub1 loss in malignant and metastatic breast cancer, lung cancer and colorectal cancer cells remains to be elucidated.
Emerging evidence also indicates that RNF20 itself functions as a tumour suppressor. Hypermethylation of the RNF20 promoter in primary breast cancer cells has been reported (Shema et al. 2008, 2011), and RNF20 transcript levels are lower in metastatic prostate cancer cells relative to benign disease cells (Varambally et al. 2005). RNF20 levels are also lower in the testicular germ cell cancer seminoma relative to normal testis (Chernikova et al. 2012). A single mutation has been reported in RNF20 in colorectal cancer cells (Barber et al. 2008). A recent study of CpG island methylator phenotype 1 (CIMP1)-associated colorectal tumours has shown an enrichment of mutations in genes encoding proteins associated with chromatin remodelling, including a low frequency of mutations in RNF20 and RNF40 (Tahara et al. 2014). The effect of hypermethylation, or mutations, on RNF20 protein levels was not investigated in these studies; however, the implication is that these events probably lead to less active RNF20 capable of functioning to monoubiquitinate histone H2B.
Differential levels of expression and/or mutations have been reported in other H2Bub1-associated E3 ubiquitin ligases and DUBs in primary tumours, including BRCA1 mutation in breast and ovarian cancers (Network 2011, 2012, Alsop et al. 2012), ubiquitin-specific protease 36 (USP36) overexpression in ovarian tumours (Li et al. 2008), USP22 overexpression in multiple aggressive cancer types (Glinsky et al. 2005), and specifically, elevated USP22 protein levels in breast cancer progression and patient prognosis (Zhang et al. 2011a). A key mechanism of action of at least some of these changes is probably through dysregulation of H2Bub1.
H2Bub1-associated transcription
H2Bub1 preferentially associates with the transcribed regions of highly expressed genes. In a model of p53 overexpression, H2Bub1 was found throughout most of the transcribed region of the p53 target gene CDKN1A (encoding p21), but not in the upstream or downstream regions (Minsky et al. 2008). This region-specific increase in H2Bub1 was shown to correlate with the recruitment of RNA polymerase II (Pol II) before the increase in CDKN1A mRNA levels and to decrease again upon dissociation of RNA Pol II (Minsky et al. 2008). The human PAF1 transcriptional complex associates with RNA Pol II on the chromatin of actively transcribed genes, where it participates in transcriptional elongation, recruitment and activation of histone modification enzymes, and recruitment of 3′-end processing factors required to terminate transcription (Jaehning 2010; Fig. 1).
H2Bub1 and associated factors in transcriptional elongation. (A) Nucleosomes function in condensed chromatin to maintain the repression of transcription of target genes (red). The presence of H2Bub1-associated deubiquitinases (DUBs) and consequential absence of H2Bub1 contribute to a closed chromatin configuration. (B) In response to stimuli, pathways that require gene expression are activated. Cyclin-dependent kinase 9 (CDK9) phosphorylates the E2 UBE2A and Ser2 in the carboxy-terminal domain (CTD) of RNA polymerase II (Pol II), creating a binding domain for WAC and the associated RNF20–RNF40 heterodimeric complex that functions as the E3 to monoubiquitinate histone H2B at lysine 120 (ubiquitin represented by a red circle on H2B histone tails). The PAF1 complex (comprising PAF1, CDC73, CTR9, LEO1, SKI8 and RTF1) associates with RNA Pol II at the level of the chromatin and interacts with the RNF20–RNF40 complex to promote transcriptional elongation. Ubiquitin is cleaved by H2Bub1-associated DUBs to return to a closed chromatin structure. (C) H2Bub1 results in the recruitment of the chromatin remodelling factor FACT to facilitate the removal of the H2B–H2A dimer from the nucleosome resulting in the opening up of chromatin and removal of the physical block to RNA Pol II allowing transcriptional elongation to proceed (green arrow) resulting in gene expression.
Citation: Endocrine-Related Cancer 22, 1; 10.1530/ERC-14-0185
The PAF1 complex is composed of LEO1, CTR9, SKI8, RTF1, CDC73 and PAF1 (Jaehning 2010). It is the interaction between this complex and the main H2Bub1 E3 ubiquitin ligase RING finger complex RNF20–RNF40 that is thought to be responsible for the increase in H2Bub1 in actively transcribed genes (Kim et al. 2009). Whether it is individual PAF1 complex members or the intact complex itself that is important for H2Bub1 is not entirely clear; however, the PAF1 subunit itself, CTR9 and CDC73 have all been shown to be important for H2Bub1 (Zhu et al. 2005, Kim et al. 2009, Pirngruber et al. 2009, Hahn et al. 2012). Furthermore, RNF20, presumably through H2Bub1, interferes with binding of the transcription elongation factor TFIIS to the PAF1 complex, thus affecting the ability to relieve the stalled RNA Pol II and hindering transcriptional elongation (Shema et al. 2011). This may be a mechanism whereby RNF20 functions in a tumour-suppressive capacity to selectively repress pro-oncogenic genes that are preferentially residing in compacted chromatin and therefore minimally transcribed under normal conditions.
It has also been reported that the RNF20–RNF40 complex associates with WW domain-containing adaptor with coiled-coil (WAC) and so perhaps indirectly with the PAF1 complex, although the PAF1 complex is required for recruiting the WAC-associated RNF20–RNF40 complex to actively transcribed chromatin (Zhang & Yu 2011). Cyclin-dependent kinase 9 (CDK9) is also involved in this process, required to phosphorylate serine 2 (Ser2) in the carboxy-terminal domain of RNA Pol II, creating a binding domain for WAC at the chromatin level (Pirngruber et al. 2009; Fig. 1B).
A number of mechanisms have been proposed to explain the role of H2Bub1 in transcriptional elongation. One compelling model proposes that the histone chaperone FACT is recruited to chromatin at sites containing H2Bub1, resulting in the removal of a histone H2A–H2B dimer from the core nucleosome (Fig. 1C). Disruption of this nucleosomal barrier would then facilitate RNA Pol II to traverse through, enabling transcription (Pavri et al. 2006). Furthermore, H2Bub1 and FACT co-operate to influence chromatin dynamics required for DNA repair following the induction of double-strand breaks (DSBs) by affecting the recruitment of DNA repair proteins such as RAD51 (Kari et al. 2011).
In contrast, it has been reported that H2Bub1 enhances nucleosome stability (Chandrasekharan et al. 2009); however, a more recent study has suggested that the effect of H2Bub1 on nucleosome stability is modest (Fierz et al. 2012). Furthermore, in co-operation with the histone chaperone Spt16, H2Bub1 has been indicated to be important for nucleosome reassembly during RNA Pol II-mediated transcriptional elongation in yeast (Fleming et al. 2008). To add to the complexity, H2Bub1 has been reported to inhibit the assembly of transcriptional complexes at normally silent promoters, therefore associating H2Bub1 with transcriptional suppression, while also appearing integral for transcriptional elongation of transcribed regions (Batta et al. 2011). Perhaps keys to a deeper understanding of the roles of H2Bub1 in transcription, recently described as ‘enigmatic’ (Johnsen 2012), will be in appreciating the dynamic and reversible nature of this modification, as well as its genomic positioning, cellular type, level of cellular differentiation and function in disease-related or healthy cells.
H2Bub1 functions in DNA damage
Independently from its role in transcriptional elongation, H2Bub1 increases in cells after DNA damage at sites of DSBs. Following such damage, the protein kinase ataxia telangiectasia mutated (ATM) phosphorylates serine sites on both RNF20 and RNF40. This phosphorylated RNF20–RNF40 E3 ubiquitin ligase complex is then recruited to the sites of DSBs where it participates in the monoubiquitination of DNA damage-associated H2Bub1 (Moyal et al. 2011). RNF20 functions with NBS1 (a member of the mammalian MRE11–RAD50 DSB repair complex) at sites of DSBs to facilitate repair through SNF2H-mediated chromatin reorganisation (Nakamura et al. 2011). This process recruits factors required for both non-homologous end joining (XRCC4 and Ku80) and homologous recombination repair (HRR; RAD51, BRCA1 and BRCA2) (Moyal et al. 2011, Nakamura et al. 2011, Shiloh et al. 2011).
Although treatment of cells with DNA-damaging agents such as doxorubicin has been linked to a global loss of H2Bub1, specific areas of the genome, perhaps those encoding proteins that are key to mounting the DNA damage response, retain or increase H2Bub1 (Minsky et al. 2008). As has been mentioned previously, using a model of p53 overexpression, H2Bub1 was identified at the transcribed region of the p53 target CDKN1A, which correlated with the recruitment of RNA Pol II and increased levels of CDKN1A transcripts (Minsky et al. 2008).
Roles for H2Bub1 in histone cross-talk
Evidence indicates that H2Bub1 may be central to processes dependent upon chromatin dynamics such as transcription and DNA damage that are reliant on histone cross-talk. H2Bub1 can recruit methyltransferase complexes important for the methylation of lysines on histone H3, specifically H3K4 and H3K79 (Briggs et al. 2002, Ng et al. 2002, Sun & Allis 2002, Barski et al. 2007, Kim et al. 2009, Izzo & Schneider 2010, Wang et al. 2013a). A number of studies have suggested that H2Bub1 is a prerequisite for H3K4 di- and trimethylation (H3K4me2 and H3K4me3), as H2Bub1 recruits the histone methyltransferase complex COMPASS (complex of proteins associated with SET1) involved in the methylation of histone H3 (Wood et al. 2005, Kim et al. 2009, Smith & Shilatifard 2010). Methylated H3K4 then recruits the chromatin remodelling factor SNF2H (Kouskouti & Talianidis 2005), allowing recruitment of the DNA repair proteins RAD51 and BRCA1 (Nakamura et al. 2011). Still, other studies have shown that H2Bub1 may not be a prerequisite for H3K4 methylation (Shema et al. 2008, Moyal et al. 2011, Vethantham et al. 2012), including in primary tumours where H2Bub1 is lost, but H3K4me3 is retained (Hahn et al. 2012).
Similar to H3K4me2 and H3K4me3, H3K79me3 has also been identified in transcriptionally active genes. H2Bub1 has been shown to directly stimulate disrupter of telomere silencing 1-like (DOT1L) methyltransferase activity and consequently to facilitate H3K79 methylation in both yeast and human models (Ng et al. 2002, McGinty et al. 2008). DOT1L is the sole methyltransferase responsible for the methylation of H3K79 (Min et al. 2003). H3K79 methylation marks localise preferentially to the proximal regions of actively transcribed genes (Steger et al. 2008) and have in fact been found co-localised with H2Bub1 in actively transcribed regions (Jung et al. 2012). Although somewhat controversial, the recruitment of the DNA repair protein 53BP1 (TP53BP1) to sites of DSBs has been reported to be dependent upon H3K79 methylation (Huyen et al. 2004, Wakeman et al. 2012, Kim et al. 2014). Increased levels of methylation of both H3K4 and H3K79 have been shown to increase the expression of HOX genes in a manner dependent upon H2Bub1, indicating additional and important roles for H2Bub1 in the regulation of development (Zhu et al. 2005).
Less well studied than histone H3 methylation complexes, acetylation of K120 on histone H2B (H2BK120ac) is reported to precede H2Bub1 in a temporal fashion (Gatta et al. 2011). Earlier research has shown H2BK120ac to be present on the promoters of active genes (Wang et al. 2008). These studies suggest that H2BK120ac is an early mark of poised or active chromatin and, further, that this dual histone switch may keep nucleosomes ‘hot’ for rounds of induction and transcriptional elongation. Additional research is required to elucidate the physiological role(s) of H2BK120ac. K120 on histone H2B has also recently been shown to be methylated by the methyltransferase enhancer of zeste homolog 2, which is the catalytic unit of polycomb repressive complex 2 (Kogure et al. 2013). This modification would appear to act as a competitive inhibitor for H2Bub1 and may, at least in part, explain the loss of H2Bub1 observed in cancer cells. The control and role of H2Bub1 in histone cross-talk are clearly both complex and influential. It remains to be determined whether epigenomic-based therapeutics developed to treat malignancy, such as histone deacetylase inhibitors, functionally modify levels of H2Bub1 and consequently the expression of genes and other interactions in which H2Bub1 plays a role.
H2Bub1-associated ubiquitin ligation machinery
Ligation of ubiquitin to a protein requires an activating ATP-dependent ubiquitin enzyme (E1), a ubiquitin-conjugating enzyme (E2), and a ubiquitin-protein ligase (E3) that works in conjunction with E2 to covalently attach ubiquitin to a lysine residue of the target protein. Humans have just a few E1 enzymes, around 40 E2 enzymes and over 500 E3 ligases (Lipkowitz & Weissman 2011, Budhidarmo et al. 2012). It is perhaps not surprising then that E3s determine substrate recognition and are often members of multicomponent complexes (Braun & Madhani 2012). The most common type of E3 ligases are RING (really interesting new gene) domain proteins, HECT (homologous to E6-AP C terminus) domain E3s being less frequent (Jackson et al. 2000, Budhidarmo et al. 2012). Histone ubiquitination is a reversible modification, negatively regulated by DUBs (Fig. 2). There are ∼100 DUBs classified into six subfamilies, with the majority being cysteine proteases (Clague et al. 2013, Jacq et al. 2013). DUBs reported to deubiquitinate H2Bub1 belong to the USP subfamily. Recent studies have identified DUBs as having major roles in normal physiological processes and, when aberrantly active, roles in disease including cancer (Nijman et al. 2005, Singhal et al. 2008, Sowa et al. 2009, Clague et al. 2013, Jacq et al. 2013). Furthermore, as proteases, DUBs are realistic therapeutic targets for the treatment of malignancy (Colland 2010).
Ubiquitin enzyme cascade associated with the monoubiquitination of histone H2B at lysine K120 (H2Bub1). An E1 ubiquitin (ub)-activating enzyme engages ATP to activate free ubiquitin, which is transferred to the active site of an E2 ubiquitin-conjugating enzyme, two of which have been reported to be associated with H2Bub1. E3 ubiquitin ligases work with E2 to transfer ubiquitin to the target protein. Four E3s, most of them appearing in RING finger complexes, have been identified in the H2Bub1 cascade; however, it is unclear how, or if, they function together for the monoubiquitination of histone H2B. Deubiquitinating (DUB) enzymes, of which nine have been reported to be associated with H2Bub1, cleave ubiquitin from its substrate.
Citation: Endocrine-Related Cancer 22, 1; 10.1530/ERC-14-0185
Terminology coined recently in the field of epigenomics describes histone modifications that are laid down by chromatin ‘writers’, removed by chromatin ‘erasers’, and used as signals to be interpreted and then acted upon by chromatin ‘readers’ such as molecules described above important for histone cross-talk (Dawson et al. 2012). Key writers and erasers of H2Bub1-associated ubiquitin machinery are discussed below.
‘Writing’ H2Bub1: as easy as E1, E2 and E3
E1 is the first enzyme in the ubiquitin pathway, activating free ubiquitin in an ATP-dependent fashion by formation of a thiol–ester bond between its active cysteine site and the carboxy-terminal glycine of ubiquitin. Activated ubiquitin is then transferred to the active site of an E2 ubiquitin-conjugating enzyme (Fang & Weissman 2004). The ubiquitin-conjugating enzyme 2A (UBE2A; yeast homolog RAD 6) is generally believed to be the chief E2 involved in H2Bub1 (Kim et al. 2009); however, another E2, UBE2E1, has also been reported to function in H2Bub1 (Zhu et al. 2005, Pavri et al. 2006). CDK9, in addition to phosphorylating Ser2 in the carboxy-terminal domain of RNA Pol II as mentioned previously, also phosphorylates UBE2A, increasing its activity (Shchebet et al. 2012, Zhang & Yu 2012). Interestingly, UBE2A also functions as the E2 for the monoubiquitination of proliferating cell nuclear antigen, a key protein activated in DNA repair (Zhang & Yu 2012). Multiple E3s are involved in H2Bub1, including MDM2 (Minsky & Oren 2004), BRCA1–BARD1 (Mallery et al. 2002, Thakar et al. 2010), BAF250B (Li et al. 2010) and the RING finger protein complex RNF20–RNF40, which is generally accepted as the main E3 for H2Bub1 (Zhu et al. 2005, Kim et al. 2009, Moyal et al. 2011, Fuchs & Oren 2014; Fig. 2).
The RING finger complex RNF20–RNF40
The RNF20 homolog BRE1 (also known as BRE1A) was discovered in the yeast Saccharomyces cerevisiae, where it was found to be the major E3 ligase involved in the monoubiquitination of yeast histone H2B at lysine 123 (Hwang et al. 2003). In humans, RNF20 forms a heterotetrameric complex with RNF40 (also known as BRE1B (Kim et al. 2009)), containing two copies of each polypeptide (Zhu et al. 2005). The RNF20–RNF40 complex is generally accepted to interact with an E2 conjugating enzyme as the main E3 enzyme to catalyse H2Bub1; however, whether this complex functions as a whole in humans to mediate H2Bub1 is not entirely clear (Moyal et al. 2011), as some studies have reported that RNF20 alone is the key functional unit (Kim et al. 2005). Down-regulation of either polypeptide leads to depletion of the other, as well as reduction of H2Bub1 (Moyal et al. 2011, Hahn et al. 2012). Conversely, overexpression of RNF20 results in elevated H2Bub1 levels (Kim et al. 2005).
RNF20 has been described as a putative tumour suppressor (Shema et al. 2008), possibly functioning through interaction with p53 and its presence at the promoter of p53 target genes such as MDM2 (Kim et al. 2005). H2Bub1 also increases at the coding regions of p53 target genes upon their activation (Minsky et al. 2008). Depletion of RNF20 has been reported to result in a decrease in p53 expression and an increase in cell migration and tumourigenesis (Shema et al. 2008). Down-regulation of RNF20 has also been shown to increase various growth promoting pro-oncogenic genes such as c-Myc and c-Fos (Shema et al. 2008). The selective suppression that RNF20 demonstrates against these oncogenes probably occurs by the prevention of recruitment of the elongation factor TFIIS (which interacts with the PAF1 complex to relieve the stalled RNA pol II) to chromatin so that the transcriptional block frequently seen in closed chromatin cannot be relieved, resulting in transcriptional repression (Shema et al. 2011). A tumour-suppressive role for RNF40 mediated through H2Bub1 has also been demonstrated in breast cancer cells (Prenzel et al. 2011).
A potential oncogenic role for RNF20 has also been reported in a number of studies; however, it is unclear whether this may be cancer type- or stage-specific (Liu et al. 2009, Wright et al. 2011, Blank et al. 2012, Wang et al. 2013a). Functionally, down-regulation of RNF20 was found to lead to the migration of MCF10A breast epithelial cells, as well as anchorage-independent growth of NIH-3T3 cells and increased tumourigenicity in nude mice (Shema et al. 2008). The role of RNF20 in transcriptional elongation and the DNA damage response has been discussed earlier in this review.
The BRCA1–BARD1 complex
Similar to RNF20 and RNF40, the tumour suppressor BRCA1 can function as a RING finger E3 ubiquitin ligase, forming a complex with BARD1 that stabilises the BRCA1 protein, facilitating the ubiquitination of histone H2B (Mallery et al. 2002, Thakar et al. 2010). Breast and/or ovarian cancer-associated mutations in the RING finger domain of BRCA1 abolish ubiquitin ligase activity in vitro, although it is unclear whether BRCA1 mutation influences the loss of H2Bub1 observed in primary breast tumours (Hashizume et al. 2001, Thakar et al. 2010, Prenzel et al. 2011). Loss of BRCA1 has been reported to correlate with the loss of ubiquitinated histone H2A (known to dimerise with H2B) at satellite DNA regions (Zhu et al. 2011).
The BRCA1–BARD1 complex has been shown to monoubiquitinate all nucleosome core histones – H2A/H2AX, H2B, H3 and H4, with the exception of the linker histone H1, including the H2AX variant that co-localises with BRCA1 following DNA damage (Mallery et al. 2002, Thakar et al. 2010). A recent study has demonstrated that the ubiquitination of histones H2B and H2A by the BRCA1–BARD1 complex has differing efficacies, whereby histone H2B is only modestly ubiquitinated in comparison with histone H2A, which may indicate a histone preference for monoubiquitination (Thakar et al. 2010). Links between BRCA1 and RNF20 at sites of DSBs following DNA damage have been discussed; however, it is not entirely clear how these E3 ligases may function together in vivo to enable H2Bub1.
Human double minute 2
Human double minute 2 (HDM2, human homolog of MDM2) is an E3 ubiquitin ligase that functions to maintain low levels of p53 by polyubiquitination, targeting p53 for degradation via the proteasome. In addition to regulating p53 levels, MDM2 is able to monoubiquitinate histones H2A and H2B (Minsky & Oren 2004). The ability of MDM2 to monoubiquitinate histones may not be in a global sense, but rather in a predominantly p53 target gene manner, given that overexpression of MDM2 increases histone monoubiquitination in the vicinity of a p53 consensus binding sequence within the p21 promoter (Minsky & Oren 2004). This discovery begins to provide some insight into why multiple E3s seem to have the apparently identical function of monoubiquitinating histone H2B, as we appreciate roles for gene-specific vs global H2Bub1 levels as a means of regulating the transcription of genes in response to cellular stress. It has also been proposed that the H2Bub1-associated role of MDM2 is limited to the monoubiquitination of free histone H2B rather than in the context of the nucleosome (Johnsen 2012).
The BAF250b-elongin C-cullin 2-Roc1 complex
The mammalian chromatin remodelling complex SWI/SNF-A subunit BAF250/ARID1 has also been reported to function as an E3 ubiquitin ligase in a complex with cullin 2, Roc1 and elongin C to target the monoubiquitination of H2Bub1 (Li et al. 2010). In this study, down-regulation of BAF250 was found to lead to a decrease in global H2Bub1. Interestingly, BAF250b has been implicated as a requirement for the maintenance of undifferentiated mouse embryonic stem cells (ESCs; Yan et al. 2008). The identification of a role for BAF250b in the maintenance of stem cell pluripotency indicates that H2Bub1 may also have a role in this system.
‘Erasing’ H2Bub1: DUBs
Empirical evidence indicates that the loss of H2Bub1 is associated with tumourigenesis; therefore, it is important to examine mechanisms by which ubiquitin is cleaved from histone H2B. Six DUBs from the USP subfamily have been reported to deubiquitinate mammalian H2Bub1 – USP3 (Nicassio et al. 2007), USP7 (van der Knaap et al. 2005), USP15 (Long et al. 2014), USP22 (Zhang et al. 2008), USP44 (Fuchs et al. 2012) and USP49 (Zhang et al. 2013) (Fig. 2). USP12 and USP46 regulate H2Bub1 in Xenopus development (Joo et al. 2011). The Drosophila homolog scrawny of a ninth human DUB, USP36, deubiquitinates H2Bub1 in Drosophila stem cells (Buszczak et al. 2009). It is likely that not all E3s or DUBs are functional in all tissue types and/or during tumour progression, with some requiring catalytic co-factors and/or assembly into large multicomponent complexes, e.g. USP7 and USP22 (Samara et al. 2010, Nicholson & Suresh Kumar 2011), to enable full catalytic activity. It is interesting to speculate, however, that the apparent redundancy among DUBs, with multiple DUBs appearing to serve the same purpose, speaks to the fundamental importance of these enzymes in maintaining cellular function. Conversely, many DUBs interact with multiple proteins, such as USP7 that displays both p53-dependent and -independent activity, including deubiquitination of histone H2B (Nicholson & Suresh Kumar 2011).
There is growing interest in therapeutic targeting of DUBs as these key regulators of the ubiquitin–proteasome system occur upstream of the proteasome itself and may offer greater specificity and less toxicity as cancer therapeutics compared with FDA-approved proteasome inhibitors such as Velcade (bortezomib) and Kyprolis (carfilzomib). PR-619 functions as a non-selective broad-range reversible DUB inhibitor (Altun et al. 2011), and numerous efforts are underway to identify specific DUB inhibitors, some of which are discussed below.
Ubiquitin-specific protease 22
USP22 is arguably one of the most interesting and significant of all H2Bub1-associated DUBs described thus far. A large body of research has linked this enzyme to tumour progression and oncogenic activity, and USP22 is currently under investigation as a therapeutic target for cancer. Elevated expression has been shown to act as a key indicator of poor prognosis in a variety of different cancers including invasive breast cancer (Zhang et al. 2011a), colorectal carcinoma (Liu et al. 2011), oesophageal cancer (Li et al. 2012), papillary thyroid carcinoma (Wang et al. 2013b), gastric cancer (Yang et al. 2011), oral squamous cell carcinoma (Piao et al. 2012), salivary duct carcinoma (Piao et al. 2013), non-small cell lung carcinoma (Ning et al. 2012) and cervical cancer (Yang et al. 2014). In addition, inhibition of USP22 has been demonstrated to induce cell cycle arrest and inhibit proliferation in hepatocellular carcinoma (HCC; Ling et al. 2012) and bladder cancer (Lv et al. 2011). In a seminal study carried out by Glinsky et al. (2005), USP22 was identified as part of an 11-gene signature termed the ‘death-from-cancer’ signature that predicts rapid disease recurrence, distant metastatic sites and poor response to therapy across multiple solid tumours. This 11-gene signature appears to consist of genes with causal roles in human cancer as opposed to just markers of disease. It correlates with a stem cell-like expression profile and appears to be driven by the BMI1 oncogene, a member of the polycomb group of proteins that function in chromatin remodelling to lead to events such as HOX gene silencing. Polycomb/BMI1-driven pathways are active in both normal stem cells and some highly malignant cancers. Recent expansion of this study has confirmed that USP22 is a critical enzyme associated with end-stage disease and that its levels are especially elevated in drug-resistant tumours (Schrecengost et al. 2014).
USP22 is a subunit of the human SAGA transcriptional co-factor acetylation complex and, as a member of this complex, functions to deubiquitinate histone H2B (Zhang et al. 2008). Ubp8, the yeast homolog of USP22, is also necessary for SAGA-mediated deubiquitination of histone H2B (Henry et al. 2003). Given this and the association of expression of USP22 with stem cell-like features in many cancers, it is possible that the deubiquitination of histone H2B would result in reversion to a non-differentiated-like phenotype. Whether the key role of USP22 in late-stage cancers is H2Bub1-related or -independent remains to be elucidated.
USP22 has also been demonstrated to stabilise the histone deacetylase Sirt1, removing polyubiquitin chains that would otherwise lead to this protein's degradation via the proteasome (Lin et al. 2012). Sirt1 antagonises the transcriptional activity of p53 by decreasing p53 acetylation, and down-regulation of USP22 leads to the degradation of Sirt1 and increases p53-dependent apoptosis, again flagging strategies to inhibit USP22 as of possible value as a cancer therapeutic.
Ubiquitin-specific protease 7
The ubiquitin protease USP7/HAUSP (Herpes virus-associated USP) was originally isolated as an interactor of the herpes simplex virus type 1 immediate-early protein Vmw110 (ICP0) (Everett et al. 1998). USP7 has both p53-dependent and -independent activity, with additional substrates, as well as H2Bub1, including PTEN, FOXO4 and PRC1/INK4a (Nicholson & Suresh Kumar 2011). USP7 deubiquitinates the p53 E3 ligase MDM2, inhibiting MDM2 degradation resulting in the polyubiquitination of p53 that leads to its degradation via the proteasome (Li et al. 2002, 2004, Cummins et al. 2004). In this regard, USP7 acts as a cell cycle regulator through the degradation of p53, which promotes cell cycle progression and consequently cellular proliferation.
In vitro research demonstrated the reliance of USP7 on guanosine-5′-monophosphate synthetase (GMPS) for the deubiquitination of histone H2B (van der Knaap et al. 2005). GMPS is a metabolic enzyme required for the synthesis of guanine nucleotides, the levels of which are correlated with proliferating cells (Boritzki et al. 1981). Loss of either GMPS or USP7 results in increased levels of H2Bub1 (van der Knaap et al. 2010). USP7 also appears to have a role as an enhancer of polycomb-related silencing of homeotic genes in vivo, correlating with other observations of a role for H2Bub1 in the expression of HOX genes as discussed earlier (van der Knaap et al. 2005, Zhu et al. 2005). USP7 is further implicated to be part of the H2Bub1 ligation machinery as it forms a complex with the H2Bub1 E2 conjugating enzyme UBE2E1, attenuating its role (Sarkari et al. 2013).
Given the eminent druggability of DUBs, and the particular interest in USP7 given its influence on p53 levels, interest in developing small-molecule USP7 inhibitors as therapeutics for some cancers is emerging (Colland et al. 2009, Colland 2010, Chauhan et al. 2012, Reverdy et al. 2012). HBX 41 108, a cyano-indenopyrazine derivative that reversibly inhibits USP7 in a non-competitive fashion, has been shown to stabilise p53, with concomitant increase in the levels of the cell cycle inhibitor p21 and inhibition of cancer cell growth (Colland et al. 2009). Other USP7 inhibitors, HBX 19 818 and HBX 28 258, have been identified as possible irreversible inhibitors of USP7 (Reverdy et al. 2012). Furthermore, the USP7 inhibitor P5091 has been shown to be well tolerated by animals in human tumour xenograft models of multiple myeloma and to have a synergistic effect with drugs such as HDAC inhibitors that are used in combination with the proteasome inhibitor bortezomib (Chauhan et al. 2012). Whether these USP7 inhibition strategies based on p53 stabilisation will be efficacious in TP53-mutant tumours where mutations themselves function to stabilise the mutant protein (Muller & Vousden 2014) remains to be determined, and this may depend on the relative importance of other USP7 substrates such as H2Bub1 compared with p53 as drivers of tumourigenesis.
Ubiquitin-specific protease 44
USP44 has been identified as a novel H2Bub1 DUB playing an important role in stem cell differentiation. In a study examining increasing H2Bub1 levels identified during ESC differentiation, a concomitant down-regulation of USP44 was observed (Fuchs et al. 2012). USP44 has a number of roles similar to those of other proteins found in the H2Bub1 pathway. An Usp44-null mouse model was shown to have defects in mitotic checkpoint regulation and in chromosome lagging, leading to missegregation of chromosomes and aneuploidy and highlighting roles for USP44 in centrosome functioning and mitotic spindle formation (Zhang et al. 2012). In the same study, USP44 was also shown to be down-regulated in lung cancer cells and associated with a poor prognosis. The levels of USP44 have also been shown to be elevated in T-cell acute lymphoblastic leukaemia cells (Zhang et al. 2011b).
Additional H2Bub1-associated DUBs
In addition to the three DUBs described, USP3, USP15, USP46, USP12, USP49 and USP36 have all been reported to be involved in the deubiquitination of H2Bub1. Currently, limited research exists on these DUBs; however, based on the diverse roles of DUBs, it is important to understand all the DUBs involved in the moderation of H2Bub1. USP3 has been shown to associate with chromatin and to function as a DUB for both histones H2A and H2B (Nicassio et al. 2007, Sharma et al. 2014). USP3 was demonstrated to be required for timely progression through S phase and subsequent mitotic entry, and furthermore, its inhibition was found to lead to the accumulation of DNA breaks and activation of the ATM-regulated DNA damage response pathway (Nicassio et al. 2007). Nuclear USP15 associates with the RNF20–RNF40 complex, as well as directly with SART3, a component of splicing machinery also known as TIP110 or p110 (Long et al. 2014). Interestingly, the loss of USP15 has been reported to be associated with resistance to paclitaxel in ovarian cancer (Xu et al. 2009). The Drosophila homolog of USP36 (scrawny, scny) deubiquitinates H2Bub1 in Drosophila stem cells and functions in gene silencing, indicating that these cells use the loss of H2Bub1 to repress the expression of genes involved in differentiation such as Notch target genes (Buszczak et al. 2009). These findings are supported by an earlier paper that identified the importance of the Drosophila RNF20 homolog for the regulation of H3K4 methylation and transcription of Notch target genes (Bray et al. 2005). Furthermore, the levels of USP36 are elevated in ovarian cancer cells (Li et al. 2008).
USP12 and USP46 have been shown to have roles in Xenopus development as DUBs that can deubiquitinate both histones H2A and H2B (Joo et al. 2011). Both USP12 and USP46 interact with other proteins for their activation, including WD40 repeat-containing proteins and Usp1-associated factor 1 (UAF1; Kee et al. 2010). USP12 has also been implicated as a negative regulator of Notch signalling, an evolutionarily conserved pathway that has key roles in the determination of cell fate (Moretti et al. 2012).
Lastly, USP49 has recently been identified as a novel H2Bub1 DUB that functions to regulate exonic splicing. In order to behave as a H2Bub1 DUB, USP49 forms a complex with RuvB-like1 (RVB1), an ATPase with diverse cellular roles, including transcription and chromatin remodelling, and a suppressor for Gal1 (SUG1), a subunit of the 26S proteasome (Zhang et al. 2013).
In summary, there exist a large range of H2Bub1-related DUBs that predominately function to regulate development, DNA damage repair, cell cycle progression and stem cell differentiation, all of which are important pathways that affect tumourigenesis. The importance of H2Bub1 vs that of other DUB substrates in tumourigenesis remains to be determined. The discovery of DUB inhibitors is a relatively new field but rapidly gaining momentum, with the potential to identify new therapeutic strategies for the treatment of aggressive tumours.
Roles for H2Bub1 in controlling ‘stemness’?
As has been already described in this review, H2Bub1 plays important roles in a variety of cellular processes, including the regulation of histone cross-talk and interactions with various DUBs. Both histone cross-talk and DUBs have been demonstrated to have significant roles in stem cells where they can act to maintain an undifferentiated stem cell state through gene silencing (Buckley et al. 2012). Therefore, it is not surprising that a substantial body of evidence that links H2Bub1 to the regulation of stem cells exists. A significant number of studies have reported the role of histone PTMs in ESCs, including H3K4, H3K27 and H3K79, H3K4me and H3K79me known to cross-talk with H2Bub1 (Bibikova et al. 2008, Orkin & Hochedlinger 2011). Many enzymes associated with H2Bub1 ubiquitination or deubiquitination have been linked to stem cell differentiation as already mentioned, including BAF250b (Yan et al. 2008), USP36 (Buszczak et al. 2009), USP22 (Glinsky et al. 2005), RNF20 and USP44 (Fuchs et al. 2012).
Fuchs et al. (2012) demonstrated that H2Bub1 increased during induced differentiation of both human and mouse ESCs. This study was supported by Chen et al. (2012), who showed that H2Bub1 levels were very low in mouse stem cells, but increased dramatically after embryoid body and ESC differentiation. H3K4me3 levels were also found to be increased after embryoid body differentiation.
In addition, it was shown that USP44 was present in ESCs where it acted to suppress H2Bub1 levels and thereby to maintain the stem cell phenotype, with concomitant decrease upon differentiation, contributing to the increase observed in H2Bub1. H2Bub1, but not monoubiquitinated histone H2A, levels were also shown to increase significantly during the differentiation of human mesenchymal stem cells into osteoblast or adipocyte lineages, with reliance on CDK9, WAC and RNF40 levels (Karpiuk et al. 2012). This study concluded that H2Bub1 is a requirement for the differentiation of multipotent stem cells, flagging key roles for H2Bub1 in the control of stem cell differentiation (Fig. 3). These discoveries, firmly demonstrating the importance of H2Bub1 in stem cell differentiation, have the potential to inform studies of cancer stem cells.
The role of H2Bub1 in a stem cell vs a normal differentiated cell. (A) H2Bub1 is actively repressed in stem cells through the up-regulation of H2Bub1-associated DUBs (indicated by an upward pointing red arrow) resulting in closed chromatin and suppression of genes involved in differentiation. Loss of H2Bub1 (indicated by a red cross) inhibits histone cross-talk, preventing the recruitment of histone methyltransferase complexes containing SET1 or DOT1 (indicated by red crosses) required for the active chromatin marks of H3K4me and H3K79me. (B) H2Bub1 is expressed in the differentiated cell (depicted by a red circle), where there is lower expression of DUBs (indicated by a downward pointing red arrow). Histone cross-talk is facilitated by H2Bub1-related recruitment of methyltransferase complexes containing SET1 or DOT1, promoting H3K4me and H3K79me respectively (indicated by triplicate circles) at lineage-specific genes, resulting in open chromatin and active transcription of genes required for differentiation. The likelihood that H2Bub1 disrupts the nucleosomal unit is depicted.
Citation: Endocrine-Related Cancer 22, 1; 10.1530/ERC-14-0185
Conclusions
Study of H2Bub1 and its associated enzymatic machinery is rapidly gaining momentum, with specific relevance to our understanding of cancer and the regulation of stem cell differentiation. Control of H2Bub1 is undoubtedly complex, with numerous E3s and DUBs appearing to play similar roles in H2Bub1 enzymatic machinery and many having significant roles external to the mediation of H2Bub1. The rapidly advancing field of DUB inhibitors is developing new ways to manipulate H2Bub1 levels in vivo, offering potential opportunities for the future treatment of malignancy. Future studies will undoubtedly need to address H2Bub1 at both the global and gene-specific levels, both in vitro and in vivo, to continue to unravel the complex manner in which H2Bub1 influences gene expression, plays a role in the DNA damage response and influences the multipotent nature of stem cells.
Declaration of interest
The authors declare that there is no conflict of interest that could be perceived as prejudicing the impartiality of this review.
Funding
This work was supported by the Australian Research Council (ARC) (ARC Future Fellowship (FT100100489) to D J Marsh), Cancer Institute NSW (Career Development Fellowship (10/CDF/2-11) to D J Marsh), National Health and Medical Research Council (NHMRC) (NHMRC Senior Research Fellowship (APP1004799) to D J Marsh), Cancer Council NSW ((RG 13-10) to D J Marsh), Australian Postgraduate Award (to A J Cole), Northern Clinical School Top-Up Scholarship (to A J Cole) and Northern Translational Cancer Research Unit Scholar Award (to A J Cole).
Author contribution statement
A J Cole and D J Marsh conceived and wrote this review with input and discussion from R Clifton-Bligh. All authors critically reviewed the manuscript.
Acknowledgements
The authors thank Prof. Robert Baxter (Kolling Institute of Medical Research, University of Sydney) for helpful discussions.
References
Alsop K, Fereday S, Meldrum C, deFazio A, Emmanuel C, George J, Dobrovic A, Birrer MJ, Webb PM & Stewart C et al. 2012 BRCA mutation frequency and patterns of treatment response in BRCA mutation-positive women with ovarian cancer: a report from the Australian Ovarian Cancer Study Group. Journal of Clinical Oncology 30 2654–2663. (doi:10.1200/JCO.2011.39.8545).
Altun M, Kramer HB, Willems LI, McDermott JL, Leach CA, Goldenberg SJ, Kumar KG, Konietzny R, Fischer R & Kogan E et al. 2011 Activity-based chemical proteomics accelerates inhibitor development for deubiquitylating enzymes. Chemistry & Biology 18 1401–1412. (doi:10.1016/j.chembiol.2011.08.018).
Barber TD, McManus K, Yuen KW, Reis M, Parmigiani G, Shen D, Barrett I, Nouhi Y, Spencer F & Markowitz S et al. 2008 Chromatid cohesion defects may underlie chromosome instability in human colorectal cancers. PNAS 105 3443–3448. (doi:10.1073/pnas.0712384105).
Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I & Zhao K 2007 High-resolution profiling of histone methylations in the human genome. Cell 129 823–837. (doi:10.1016/j.cell.2007.05.009).
Batta K, Zhang Z, Yen K, Goffman DB & Pugh BF 2011 Genome-wide function of H2B ubiquitylation in promoter and genic regions. Genes and Development 25 2254–2265. (doi:10.1101/gad.177238.111).
Bibikova M, Laurent LC, Ren B, Loring JF & Fan JB 2008 Unraveling epigenetic regulation in embryonic stem cells. Cell Stem Cell 2 123–134. (doi:10.1016/j.stem.2008.01.005).
Blank M, Tang Y, Yamashita M, Burkett SS, Cheng SY & Zhang YE 2012 A tumor suppressor function of Smurf2 associated with controlling chromatin landscape and genome stability through RNF20. Nature Medicine 18 227–234. (doi:10.1038/nm.2596).
Boritzki TJ, Jackson RC, Morris HP & Weber G 1981 Guanosine-5′-phosphate synthetase and guanosine-5′-phosphate kinase in rat hepatomas and kidney tumors. Biochimica et Biophysica Acta 658 102–110. (doi:10.1016/0005-2744(81)90253-9).
Braun S & Madhani HD 2012 Shaping the landscape: mechanistic consequences of ubiquitin modification of chromatin. EMBO Reports 13 619–630. (doi:10.1038/embor.2012.78).
Bray S, Musisi H & Bienz M 2005 Bre1 is required for Notch signaling and histone modification. Developmental Cell 8 279–286. (doi:10.1016/j.devcel.2004.11.020).
Briggs SD, Xiao T, Sun ZW, Caldwell JA, Shabanowitz J, Hunt DF, Allis CD & Strahl BD 2002 Gene silencing: trans-histone regulatory pathway in chromatin. Nature 418 498. (doi:10.1038/nature00970).
Buckley SM, Aranda-Orgilles B, Strikoudis A, Apostolou E, Loizou E, Moran-Crusio K, Farnsworth CL, Koller AA, Dasgupta R & Silva JC et al. 2012 Regulation of pluripotency and cellular reprogramming by the ubiquitin–proteasome system. Cell Stem Cell 11 783–798. (doi:10.1016/j.stem.2012.09.011).
Budhidarmo R, Nakatani Y & Day CL 2012 RINGs hold the key to ubiquitin transfer. Trends in Biochemical Sciences 37 58–65. (doi:10.1016/j.tibs.2011.11.001).
Buszczak M, Paterno S & Spradling AC 2009 Drosophila stem cells share a common requirement for the histone H2B ubiquitin protease scrawny. Science 323 248–251. (doi:10.1126/science.1165678).
Chandrasekharan MB, Huang F & Sun ZW 2009 Ubiquitination of histone H2B regulates chromatin dynamics by enhancing nucleosome stability. PNAS 106 16686–16691. (doi:10.1073/pnas.0907862106).
Chauhan D, Tian Z, Nicholson B, Kumar KG, Zhou B, Carrasco R, McDermott JL, Leach CA, Fulcinniti M & Kodrasov MP et al. 2012 A small molecule inhibitor of ubiquitin-specific protease-7 induces apoptosis in multiple myeloma cells and overcomes bortezomib resistance. Cancer Cell 22 345–358. (doi:10.1016/j.ccr.2012.08.007).
Chen S, Li J, Wang DL & Sun FL 2012 Histone H2B lysine 120 monoubiquitination is required for embryonic stem cell differentiation. Cell Research 22 1402–1405. (doi:10.1038/cr.2012.114).
Chernikova SB, Razorenova OV, Higgins JP, Sishc BJ, Nicolau M, Dorth JA, Chernikova DA, Kwok S, Brooks JD & Bailey SM et al. 2012 Deficiency in mammalian histone H2B ubiquitin ligase Bre1 (Rnf20/Rnf40) leads to replication stress and chromosomal instability. Cancer Research 72 2111–2119. (doi:10.1158/0008-5472.CAN-11-2209).
Clague MJ, Coulson JM & Urbe S 2008 Deciphering histone 2A deubiquitination. Genome Biology 9 202. (doi:10.1186/gb-2008-9-1-202).
Clague MJ, Barsukov I, Coulson JM, Liu H, Rigden DJ & Urbe S 2013 Deubiquitylases from genes to organism. Physiological Reviews 93 1289–1315. (doi:10.1152/physrev.00002.2013).
Colland F 2010 The therapeutic potential of deubiquitinating enzyme inhibitors. Biochemical Society Transactions 38 137–143. (doi:10.1042/BST0380137).
Colland F, Formstecher E, Jacq X, Reverdy C, Planquette C, Conrath S, Trouplin V, Bianchi J, Aushev VN & Camonis J et al. 2009 Small-molecule inhibitor of USP7/HAUSP ubiquitin protease stabilizes and activates p53 in cells. Molecular Cancer Therapeutics 8 2286–2295. (doi:10.1158/1535-7163.MCT-09-0097).
Cummins JM, Rago C, Kohli M, Kinzler KW, Lengauer C & Vogelstein B 2004 Tumour suppression: disruption of HAUSP gene stabilizes p53. Nature 428 1 p following 486. (doi:10.1038/nature02501).
Dawson MA, Kouzarides T & Huntly BJ 2012 Targeting epigenetic readers in cancer. New England Journal of Medicine 367 647–657. (doi:10.1056/NEJMra1112635).
Espinosa JM 2008 Histone H2B ubiquitination: the cancer connection. Genes and Development 22 2743–2749. (doi:10.1101/gad.1732108).
Everett RD, Freemont P, Saitoh H, Dasso M, Orr A, Kathoria M & Parkinson J 1998 The disruption of ND10 during herpes simplex virus infection correlates with the Vmw110- and proteasome-dependent loss of several PML isoforms. Journal of Virology 72 6581–6591.
Fang S & Weissman AM 2004 A field guide to ubiquitylation. Cellular and Molecular Life Sciences 61 1546–1561. (doi:10.1007/s00018-004-4129-5).
Fierz B, Chatterjee C, McGinty RK, Bar-Dagan M, Raleigh DP & Muir TW 2011 Histone H2B ubiquitylation disrupts local and higher-order chromatin compaction. Nature Chemical Biology 7 113–119. (doi:10.1038/nchembio.501).
Fierz B, Kilic S, Hieb AR, Luger K & Muir TW 2012 Stability of nucleosomes containing homogenously ubiquitylated H2A and H2B prepared using semisynthesis. Journal of the American Chemical Society 134 19548–19551. (doi:10.1021/ja308908p).
Fleming AB, Kao CF, Hillyer C, Pikaart M & Osley MA 2008 H2B ubiquitylation plays a role in nucleosome dynamics during transcription elongation. Molecular Cell 31 57–66. (doi:10.1016/j.molcel.2008.04.025).
Fuchs G & Oren M 2014 Writing and reading H2B monoubiquitylation. Biochimica et Biophysica Acta 1839 694–701. (doi:10.1016/j.bbagrm.2014.01.002).
Fuchs G, Shema E, Vesterman R, Kotler E, Wolchinsky Z, Wilder S, Golomb L, Pribluda A, Zhang F & Haj-Yahya M et al. 2012 RNF20 and USP44 regulate stem cell differentiation by modulating H2B monoubiquitylation. Molecular Cell 46 662–673. (doi:10.1016/j.molcel.2012.05.023).
Gatta R, Dolfini D, Zambelli F, Imbriano C, Pavesi G & Mantovani R 2011 An acetylation-mono-ubiquitination switch on lysine 120 of H2B. Epigenetics 6 630–637. (doi:10.4161/epi.6.5.15623).
Glinsky GV, Berezovska O & Glinskii AB 2005 Microarray analysis identifies a death-from-cancer signature predicting therapy failure in patients with multiple types of cancer. Journal of Clinical Investigation 115 1503–1521. (doi:10.1172/JCI23412).
Hahn MA, Dickson KA, Jackson S, Clarkson A, Gill AJ & Marsh DJ 2012 The tumor suppressor CDC73 interacts with the ring finger proteins RNF20 and RNF40 and is required for the maintenance of histone 2B monoubiquitination. Human Molecular Genetics 21 559–568. (doi:10.1093/hmg/ddr490).
Hashizume R, Fukuda M, Maeda I, Nishikawa H, Oyake D, Yabuki Y, Ogata H & Ohta T 2001 The RING heterodimer BRCA1–BARD1 is a ubiquitin ligase inactivated by a breast cancer-derived mutation. Journal of Biological Chemistry 276 14537–14540. (doi:10.1074/jbc.C000881200).
Henry KW, Wyce A, Lo WS, Duggan LJ, Emre NC, Kao CF, Pillus L, Shilatifard A, Osley MA & Berger SL 2003 Transcriptional activation via sequential histone H2B ubiquitylation and deubiquitylation, mediated by SAGA-associated Ubp8. Genes and Development 17 2648–2663. (doi:10.1101/gad.1144003).
Huyen Y, Zgheib O, Ditullio RA Jr, Gorgoulis VG, Zacharatos P, Petty TJ, Sheston EA, Mellert HS, Stavridi ES & Halazonetis TD 2004 Methylated lysine 79 of histone H3 targets 53BP1 to DNA double-strand breaks. Nature 432 406–411. (doi:10.1038/nature03114).
Hwang WW, Venkatasubrahmanyam S, Ianculescu AG, Tong A, Boone C & Madhani HD 2003 A conserved RING finger protein required for histone H2B monoubiquitination and cell size control. Molecular Cell 11 261–266. (doi:10.1016/S1097-2765(02)00826-2).
Izzo A & Schneider R 2010 Chatting histone modifications in mammals. Briefings in Functional Genomics 9 429–443. (doi:10.1093/bfgp/elq024).
Jackson PK, Eldridge AG, Freed E, Furstenthal L, Hsu JY, Kaiser BK & Reimann JD 2000 The lore of the RINGs: substrate recognition and catalysis by ubiquitin ligases. Trends in Cell Biology 10 429–439. (doi:10.1016/S0962-8924(00)01834-1).
Jacq X, Kemp M, Martin NM & Jackson SP 2013 Deubiquitylating enzymes and DNA damage response pathways. Cell Biochemistry and Biophysics 67 25–43. (doi:10.1007/s12013-013-9635-3).
Jaehning JA 2010 The Paf1 complex: platform or player in RNA polymerase II transcription? Biochimica et Biophysica Acta 1799 379–388. (doi:10.1016/j.bbagrm.2010.01.001).
Jason LJ, Moore SC, Ausio J & Lindsey G 2001 Magnesium-dependent association and folding of oligonucleosomes reconstituted with ubiquitinated H2A. Journal of Biological Chemistry 276 14597–14601. (doi:10.1074/jbc.M011153200).
Johnsen SA 2012 The enigmatic role of H2Bub1 in cancer. FEBS Letters 586 1592–1601. (doi:10.1016/j.febslet.2012.04.002).
Joo HY, Jones A, Yang C, Zhai L, Smith AD IV, Zhang Z, Chandrasekharan MB, Sun ZW, Renfrow MB & Wang Y et al. 2011 Regulation of histone H2A and H2B deubiquitination and Xenopus development by USP12 and USP46. Journal of Biological Chemistry 286 7190–7201. (doi:10.1074/jbc.M110.158311).
Jung I, Kim SK, Kim M, Han YM, Kim YS, Kim D & Lee D 2012 H2B monoubiquitylation is a 5′-enriched active transcription mark and correlates with exon–intron structure in human cells. Genome Research 22 1026–1035. (doi:10.1101/gr.120634.111).
Kari V, Shchebet A, Neumann H & Johnsen SA 2011 The H2B ubiquitin ligase RNF40 cooperates with SUPT16H to induce dynamic changes in chromatin structure during DNA double-strand break repair. Cell Cycle 10 3495–3504. (doi:10.4161/cc.10.20.17769).
Karpiuk O, Najafova Z, Kramer F, Hennion M, Galonska C, Konig A, Snaidero N, Vogel T, Shchebet A & Begus-Nahrmann Y et al. 2012 The histone H2B monoubiquitination regulatory pathway is required for differentiation of multipotent stem cells. Molecular Cell 46 705–713. (doi:10.1016/j.molcel.2012.05.022).
Kee Y, Yang K, Cohn MA, Haas W, Gygi SP & D'Andrea AD 2010 WDR20 regulates activity of the USP12 × UAF1 deubiquitinating enzyme complex. Journal of Biological Chemistry 285 11252–11257. (doi:10.1074/jbc.M109.095141).
Kim J, Hake SB & Roeder RG 2005 The human homolog of yeast BRE1 functions as a transcriptional coactivator through direct activator interactions. Molecular Cell 20 759–770. (doi:10.1016/j.molcel.2005.11.012).
Kim J, Guermah M, McGinty RK, Lee JS, Tang Z, Milne TA, Shilatifard A, Muir TW & Roeder RG 2009 RAD6-mediated transcription-coupled H2B ubiquitylation directly stimulates H3K4 methylation in human cells. Cell 137 459–471. (doi:10.1016/j.cell.2009.02.027).
Kim W, Choi M & Kim JE 2014 The histone methyltransferase Dot1/DOT1L as a critical regulator of the cell cycle. Cell Cycle 13 726–738. (doi:10.4161/cc.28104).
van der Knaap JA, Kumar BR, Moshkin YM, Langenberg K, Krijgsveld J, Heck AJ, Karch F & Verrijzer CP 2005 GMP synthetase stimulates histone H2B deubiquitylation by the epigenetic silencer USP7. Molecular Cell 17 695–707. (doi:10.1016/j.molcel.2005.02.013).
van der Knaap JA, Kozhevnikova E, Langenberg K, Moshkin YM & Verrijzer CP 2010 Biosynthetic enzyme GMP synthetase cooperates with ubiquitin-specific protease 7 in transcriptional regulation of ecdysteroid target genes. Molecular and Cellular Biology 30 736–744. (doi:10.1128/MCB.01121-09).
Kogure M, Takawa M, Saloura V, Sone K, Piao L, Ueda K, Ibrahim R, Tsunoda T, Sugiyama M & Atomi Y et al. 2013 The oncogenic polycomb histone methyltransferase EZH2 methylates lysine 120 on histone H2B and competes ubiquitination. Neoplasia 15 1251–1261.
Kouskouti A & Talianidis I 2005 Histone modifications defining active genes persist after transcriptional and mitotic inactivation. EMBO Journal 24 347–357. (doi:10.1038/sj.emboj.7600516).
Kouzarides T 2007 Chromatin modifications and their function. Cell 128 693–705. (doi:10.1016/j.cell.2007.02.005).
Li M, Chen D, Shiloh A, Luo J, Nikolaev AY, Qin J & Gu W 2002 Deubiquitination of p53 by HAUSP is an important pathway for p53 stabilization. Nature 416 648–653. (doi:10.1038/nature737).
Li M, Brooks CL, Kon N & Gu W 2004 A dynamic role of HAUSP in the p53–Mdm2 pathway. Molecular Cell 13 879–886. (doi:10.1016/S1097-2765(04)00157-1).
Li J, Olson LM, Zhang Z, Li L, Bidder M, Nguyen L, Pfeifer J & Rader JS 2008 Differential display identifies overexpression of the USP36 gene, encoding a deubiquitinating enzyme, in ovarian cancer. International Journal of Medical Sciences 5 133–142. (doi:10.7150/ijms.5.133).
Li XS, Trojer P, Matsumura T, Treisman JE & Tanese N 2010 Mammalian SWI/SNF – a subunit BAF250/ARID1 is an E3 ubiquitin ligase that targets histone H2B. Molecular and Cellular Biology 30 1673–1688. (doi:10.1128/MCB.00540-09).
Li J, Wang Z & Li Y 2012 USP22 nuclear expression is significantly associated with progression and unfavorable clinical outcome in human esophageal squamous cell carcinoma. Journal of Cancer Research and Clinical Oncology 138 1291–1297. (doi:10.1007/s00432-012-1191-5).
Lin Z, Yang H, Kong Q, Li J, Lee SM, Gao B, Dong H, Wei J, Song J & Zhang DD et al. 2012 USP22 antagonizes p53 transcriptional activation by deubiquitinating Sirt1 to suppress cell apoptosis and is required for mouse embryonic development. Molecular Cell 46 484–494. (doi:10.1016/j.molcel.2012.03.024).
Ling SB, Sun DG, Tang B, Guo C, Zhang Y, Liang R & Wang LM 2012 Knock-down of USP22 by small interfering RNA interference inhibits HepG2 cell proliferation and induces cell cycle arrest. Cellular and Molecular Biology 58 (Suppl) OL1803–OL1808.
Lipkowitz S & Weissman AM 2011 RINGs of good and evil: RING finger ubiquitin ligases at the crossroads of tumour suppression and oncogenesis. Nature Reviews. Cancer 11 629–643. (doi:10.1038/nrc3120).
Liu Z, Oh SM, Okada M, Liu X, Cheng D, Peng J, Brat DJ, Sun SY, Zhou W & Gu W et al. 2009 Human BRE1 is an E3 ubiquitin ligase for Ebp1 tumor suppressor. Molecular Biology of the Cell 20 757–768. (doi:10.1091/mbc.E08-09-0983).
Liu YL, Yang YM, Xu H & Dong XS 2011 Aberrant expression of USP22 is associated with liver metastasis and poor prognosis of colorectal cancer. Journal of Surgical Oncology 103 283–289. (doi:10.1002/jso.21802).
Long L, Thelen JP, Furgason M, Haj-Yahya M, Brik A, Cheng D, Peng J & Yao T 2014 The U4/U6 recycling factor SART3 has histone chaperone activity and associates with USP15 to regulate H2B deubiquitination. Journal of Biological Chemistry 289 8916–8930. (doi:10.1074/jbc.M114.551754).
Lv L, Xiao XY, Gu ZH, Zeng FQ, Huang LQ & Jiang GS 2011 Silencing USP22 by asymmetric structure of interfering RNA inhibits proliferation and induces cell cycle arrest in bladder cancer cells. Molecular and Cellular Biochemistry 346 11–21. (doi:10.1007/s11010-010-0585-4).
Mallery DL, Vandenberg CJ & Hiom K 2002 Activation of the E3 ligase function of the BRCA1/BARD1 complex by polyubiquitin chains. EMBO Journal 21 6755–6762. (doi:10.1093/emboj/cdf691).
McGinty RK, Kim J, Chatterjee C, Roeder RG & Muir TW 2008 Chemically ubiquitylated histone H2B stimulates hDot1L-mediated intranucleosomal methylation. Nature 453 812–816. (doi:10.1038/nature06906).
Min J, Feng Q, Li Z, Zhang Y & Xu RM 2003 Structure of the catalytic domain of human DOT1L, a non-SET domain nucleosomal histone methyltransferase. Cell 112 711–723. (doi:10.1016/S0092-8674(03)00114-4).
Minsky N & Oren M 2004 The RING domain of Mdm2 mediates histone ubiquitylation and transcriptional repression. Molecular Cell 16 631–639. (doi:10.1016/j.molcel.2004.10.016).
Minsky N, Shema E, Field Y, Schuster M, Segal E & Oren M 2008 Monoubiquitinated H2B is associated with the transcribed region of highly expressed genes in human cells. Nature Cell Biology 10 483–488. (doi:10.1038/ncb1712).
Moretti J, Chastagner P, Liang CC, Cohn MA, Israel A & Brou C 2012 The ubiquitin-specific protease 12 (USP12) is a negative regulator of notch signaling acting on notch receptor trafficking toward degradation. Journal of Biological Chemistry 287 29429–29441. (doi:10.1074/jbc.M112.366807).
Moyal L, Lerenthal Y, Gana-Weisz M, Mass G, So S, Wang SY, Eppink B, Chung YM, Shalev G & Shema E et al. 2011 Requirement of ATM-dependent monoubiquitylation of histone H2B for timely repair of DNA double-strand breaks. Molecular Cell 41 529–542. (doi:10.1016/j.molcel.2011.02.015).
Mueller RD, Yasuda H, Hatch CL, Bonner WM & Bradbury EM 1985 Identification of ubiquitinated histones 2A and 2B in Physarum polycephalum. Disappearance of these proteins at metaphase and reappearance at anaphase. Journal of Biological Chemistry 260 5147–5153.
Muller PA & Vousden KH 2014 Mutant p53 in cancer: new functions and therapeutic opportunities. Cancer Cell 25 304–317. (doi:10.1016/j.ccr.2014.01.021).
Nakamura K, Kato A, Kobayashi J, Yanagihara H, Sakamoto S, Oliveira DV, Shimada M, Tauchi H, Suzuki H & Tashiro S et al. 2011 Regulation of homologous recombination by RNF20-dependent H2B ubiquitination. Molecular Cell 41 515–528. (doi:10.1016/j.molcel.2011.02.002).
Network CGA Integrated genomic analyses of ovarian carcinoma Nature 474 2011 609–615. (doi:10.1038/nature10166).
Network CGA Comprehensive molecular portraits of human breast tumours Nature 490 2012 61–70. (doi:10.1038/nature11412).
Ng HH, Xu RM, Zhang Y & Struhl K 2002 Ubiquitination of histone H2B by Rad6 is required for efficient Dot1-mediated methylation of histone H3 lysine 79. Journal of Biological Chemistry 277 34655–34657. (doi:10.1074/jbc.C200433200).
Nicassio F, Corrado N, Vissers JH, Areces LB, Bergink S, Marteijn JA, Geverts B, Houtsmuller AB, Vermeulen W & Di Fiore PP et al. 2007 Human USP3 is a chromatin modifier required for S phase progression and genome stability. Current Biology 17 1972–1977. (doi:10.1016/j.cub.2007.10.034).
Nicholson B & Suresh Kumar KG 2011 The multifaceted roles of USP7: new therapeutic opportunities. Cell Biochemistry and Biophysics 60 61–68. (doi:10.1007/s12013-011-9185-5).
Nijman SM, Luna-Vargas MP, Velds A, Brummelkamp TR, Dirac AM, Sixma TK & Bernards R 2005 A genomic and functional inventory of deubiquitinating enzymes. Cell 123 773–786. (doi:10.1016/j.cell.2005.11.007).
Ning J, Zhang J, Liu W, Lang Y, Xue Y & Xu S 2012 Overexpression of ubiquitin-specific protease 22 predicts poor survival in patients with early-stage non-small cell lung cancer. European Journal of Histochemistry 56 e46. (doi:10.4081/ejh.2012.e46).
Orkin SH & Hochedlinger K 2011 Chromatin connections to pluripotency and cellular reprogramming. Cell 145 835–850. (doi:10.1016/j.cell.2011.05.019).
Osley MA, Fleming AB & Kao CF 2006 Histone ubiquitylation and the regulation of transcription. Results and Problems in Cell Differentiation 41 47–75.
Pavri R, Zhu B, Li G, Trojer P, Mandal S, Shilatifard A & Reinberg D 2006 Histone H2B monoubiquitination functions cooperatively with FACT to regulate elongation by RNA polymerase II. Cell 125 703–717. (doi:10.1016/j.cell.2006.04.029).
Piao S, Liu Y, Hu J, Guo F, Ma J, Sun Y & Zhang B 2012 USP22 is useful as a novel molecular marker for predicting disease progression and patient prognosis of oral squamous cell carcinoma. PLoS ONE 7 e42540. (doi:10.1371/journal.pone.0042540).
Piao S, Ma J, Wang W, Liu Y, Zhang M, Chen H, Guo F, Zhang B & Guo F 2013 Increased expression of USP22 is associated with disease progression and patient prognosis of salivary duct carcinoma. Oral Oncology 49 796–801. (doi:10.1016/j.oraloncology.2013.03.454).
Pirngruber J, Shchebet A, Schreiber L, Shema E, Minsky N, Chapman RD, Eick D, Aylon Y, Oren M & Johnsen SA 2009 CDK9 directs H2B monoubiquitination and controls replication-dependent histone mRNA 3′-end processing. EMBO Reports 10 894–900. (doi:10.1038/embor.2009.108).
Prenzel T, Begus-Nahrmann Y, Kramer F, Hennion M, Hsu C, Gorsler T, Hintermair C, Eick D, Kremmer E & Simons M et al. 2011 Estrogen-dependent gene transcription in human breast cancer cells relies upon proteasome-dependent monoubiquitination of histone H2B. Cancer Research 71 5739–5753. (doi:10.1158/0008-5472.CAN-11-1896).
Reverdy C, Conrath S, Lopez R, Planquette C, Atmanene C, Collura V, Harpon J, Battaglia V, Vivat V & Sippl W et al. 2012 Discovery of specific inhibitors of human USP7/HAUSP deubiquitinating enzyme. Chemistry & Biology 19 467–477. (doi:10.1016/j.chembiol.2012.02.007).
Rozenblatt-Rosen O, Hughes CM, Nannepaga SJ, Shanmugam KS, Copeland TD, Guszczynski T, Resau JH & Meyerson M 2005 The parafibromin tumor suppressor protein is part of a human Paf1 complex. Molecular and Cellular Biology 25 612–620. (doi:10.1128/MCB.25.2.612-620.2005).
Sadeghi L, Siggens L, Svensson JP & Ekwall K 2014 Centromeric histone H2B monoubiquitination promotes noncoding transcription and chromatin integrity. Nature Structural & Molecular Biology 21 236–243. (doi:10.1038/nsmb.2776).
Samara NL, Datta AB, Berndsen CE, Zhang X, Yao T, Cohen RE & Wolberger C 2010 Structural insights into the assembly and function of the SAGA deubiquitinating module. Science 328 1025–1029. (doi:10.1126/science.1190049).
Sarkari F, Wheaton K, La Delfa A, Mohamed M, Shaikh F, Khatun R, Arrowsmith CH, Frappier L, Saridakis V & Sheng Y 2013 Ubiquitin-specific protease 7 is a regulator of ubiquitin-conjugating enzyme UbE2E1. Journal of Biological Chemistry 288 16975–16985. (doi:10.1074/jbc.M113.469262).
Schrecengost RS, Dean JL, Goodwin JF, Schiewer MJ, Urban MW, Stanek TJ, Sussman RT, Hicks JL, Birbe RC & Draganova-Tacheva RA et al. 2014 USP22 regulates oncogenic signaling pathways to drive lethal cancer progression. Cancer Research 74 272–286. (doi:10.1158/0008-5472.CAN-13-1954).
Sharma N, Zhu Q, Wani G, He J, Wang QE & Wani AA 2014 USP3 counteracts RNF168 via deubiquitinating H2A and γH2AX at lysine 13 and 15. Cell Cycle 13 106–114. (doi:10.4161/cc.26814).
Shchebet A, Karpiuk O, Kremmer E, Eick D & Johnsen SA 2012 Phosphorylation by cyclin-dependent kinase-9 controls ubiquitin-conjugating enzyme-2A function. Cell Cycle 11 2122–2127. (doi:10.4161/cc.20548).
Shema E, Tirosh I, Aylon Y, Huang J, Ye C, Moskovits N, Raver-Shapira N, Minsky N, Pirngruber J & Tarcic G et al. 2008 The histone H2B-specific ubiquitin ligase RNF20/hBRE1 acts as a putative tumor suppressor through selective regulation of gene expression. Genes and Development 22 2664–2676. (doi:10.1101/gad.1703008).
Shema E, Kim J, Roeder RG & Oren M 2011 RNF20 inhibits TFIIS-facilitated transcriptional elongation to suppress pro-oncogenic gene expression. Molecular Cell 42 477–488. (doi:10.1016/j.molcel.2011.03.011).
Shema-Yaacoby E, Nikolov M, Haj-Yahya M, Siman P, Allemand E, Yamaguchi Y, Muchardt C, Urlaub H, Brik A & Oren M et al. 2013 Systematic identification of proteins binding to chromatin-embedded ubiquitylated H2B reveals recruitment of SWI/SNF to regulate transcription. Cell Reports 4 601–608. (doi:10.1016/j.celrep.2013.07.014).
Shiloh Y, Shema E, Moyal L & Oren M 2011 RNF20–RNF40: a ubiquitin-driven link between gene expression and the DNA damage response. FEBS Letters 585 2795–2802. (doi:10.1016/j.febslet.2011.07.034).
Singhal S, Taylor MC & Baker RT 2008 Deubiquitylating enzymes and disease. BMC Biochemistry 9 (Suppl 1) S3. (doi:10.1186/1471-2091-9-S1-S3).
Smith E & Shilatifard A 2010 The chromatin signaling pathway: diverse mechanisms of recruitment of histone-modifying enzymes and varied biological outcomes. Molecular Cell 40 689–701. (doi:10.1016/j.molcel.2010.11.031).
Sowa ME, Bennett EJ, Gygi SP & Harper JW 2009 Defining the human deubiquitinating enzyme interaction landscape. Cell 138 389–403. (doi:10.1016/j.cell.2009.04.042).
Steger DJ, Lefterova MI, Ying L, Stonestrom AJ, Schupp M, Zhuo D, Vakoc AL, Kim JE, Chen J & Lazar MA et al. 2008 DOT1L/KMT4 recruitment and H3K79 methylation are ubiquitously coupled with gene transcription in mammalian cells. Molecular and Cellular Biology 28 2825–2839. (doi:10.1128/MCB.02076-07).
Sun ZW & Allis CD 2002 Ubiquitination of histone H2B regulates H3 methylation and gene silencing in yeast. Nature 418 104–108. (doi:10.1038/nature00883).
Tahara T, Yamamoto E, Madireddi P, Suzuki H, Maruyama R, Chung W, Garriga J, Jelinek J, Yamano HO & Sugai T et al. 2014 Colorectal carcinomas with CpG island methylator phenotype 1 frequently contain mutations in chromatin regulators. Gastroenterology 146 530–538.e5. (doi:10.1053/j.gastro.2013.10.060).
Thakar A, Parvin JD & Zlatanova J 2010 BRCA1/BARD1 E3 ubiquitin ligase can modify histones H2A and H2B in the nucleosome particle. Journal of Biomolecular Structure & Dynamics 27 399–406. (doi:10.1080/07391102.2010.10507326).
Trujillo KM & Osley MA 2012 A role for H2B ubiquitylation in DNA replication. Molecular Cell 48 734–746. (doi:10.1016/j.molcel.2012.09.019).
Urasaki Y, Heath L & Xu CW 2012 Coupling of glucose deprivation with impaired histone H2B monoubiquitination in tumors. PLoS ONE 7 e36775. (doi:10.1371/journal.pone.0036775).
Varambally S, Yu J, Laxman B, Rhodes DR, Mehra R, Tomlins SA, Shah RB, Chandran U, Monzon FA & Becich MJ et al. 2005 Integrative genomic and proteomic analysis of prostate cancer reveals signatures of metastatic progression. Cancer Cell 8 393–406. (doi:10.1016/j.ccr.2005.10.001).
Vethantham V, Yang Y, Bowman C, Asp P, Lee JH, Skalnik DG & Dynlacht BD 2012 Dynamic loss of H2B ubiquitylation without corresponding changes in H3K4 trimethylation during myogenic differentiation. Molecular and Cellular Biology 32 1044–1055. (doi:10.1128/MCB.06026-11).
Wakeman TP, Wang Q, Feng J & Wang XF 2012 Bat3 facilitates H3K79 dimethylation by DOT1L and promotes DNA damage-induced 53BP1 foci at G1/G2 cell-cycle phases. EMBO Journal 31 2169–2181. (doi:10.1038/emboj.2012.50).
Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S, Cui K, Roh TY, Peng W & Zhang MQ et al. 2008 Combinatorial patterns of histone acetylations and methylations in the human genome. Nature Genetics 40 897–903. (doi:10.1038/ng.154).
Wang E, Kawaoka S, Yu M, Shi J, Ni T, Yang W, Zhu J, Roeder RG & Vakoc CR 2013a Histone H2B ubiquitin ligase RNF20 is required for MLL-rearranged leukemia. PNAS 110 3901–3906. (doi:10.1073/pnas.1301045110).
Wang H, Li YP, Chen JH, Yuan SF, Wang L, Zhang JL, Yao Q, Li NL, Bian JF & Fan J et al. 2013b Prognostic significance of USP22 as an oncogene in papillary thyroid carcinoma. Tumour Biology 34 1635–1639. (doi:10.1007/s13277-013-0696-0).
Weake VM & Workman JL 2008 Histone ubiquitination: triggering gene activity. Molecular Cell 29 653–663. (doi:10.1016/j.molcel.2008.02.014).
Wood A, Schneider J & Shilatifard A 2005 Cross-talking histones: implications for the regulation of gene expression and DNA repair. Biochemistry and Cell Biology 83 460–467. (doi:10.1139/o05-116).
Wright DE, Wang CY & Kao CF 2011 Flickin' the ubiquitin switch: the role of H2B ubiquitylation in development. Epigenetics 6 1165–1175. (doi:10.4161/epi.6.10.17745).
Wu L, Zee BM, Wang Y, Garcia BA & Dou Y 2011 The RING finger protein MSL2 in the MOF complex is an E3 ubiquitin ligase for H2B K34 and is involved in crosstalk with H3 K4 and K79 methylation. Molecular Cell 43 132–144. (doi:10.1016/j.molcel.2011.05.015).
Xu M, Takanashi M, Oikawa K, Tanaka M, Nishi H, Isaka K, Kudo M & Kuroda M 2009 USP15 plays an essential role for caspase-3 activation during paclitaxel-induced apoptosis. Biochemical and Biophysical Research Communications 388 366–371. (doi:10.1016/j.bbrc.2009.08.015).
Yan Z, Wang Z, Sharova L, Sharov AA, Ling C, Piao Y, Aiba K, Matoba R, Wang W & Ko MS 2008 BAF250B-associated SWI/SNF chromatin-remodeling complex is required to maintain undifferentiated mouse embryonic stem cells. Stem Cells 26 1155–1165. (doi:10.1634/stemcells.2007-0846).
Yang DD, Cui BB, Sun LY, Zheng HQ, Huang Q, Tong JX & Zhang QF 2011 The co-expression of USP22 and BMI-1 may promote cancer progression and predict therapy failure in gastric carcinoma. Cell Biochemistry and Biophysics 61 703–710. (doi:10.1007/s12013-011-9229-x).
Yang M, Liu YD, Wang YY, Liu TB, Ge TT & Lou G 2014 Ubiquitin-specific protease 22: a novel molecular biomarker in cervical cancer prognosis and therapeutics. Tumour Biology 35 929–934. (doi:10.1007/s13277-013-1121-4).
Yart A, Gstaiger M, Wirbelauer C, Pecnik M, Anastasiou D, Hess D & Krek W 2005 The HRPT2 tumor suppressor gene product parafibromin associates with human PAF1 and RNA polymerase II. Molecular and Cellular Biology 25 5052–5060. (doi:10.1128/MCB.25.12.5052-5060.2005).
Zhang F & Yu X 2011 WAC, a functional partner of RNF20/40, regulates histone H2B ubiquitination and gene transcription. Molecular Cell 41 384–397. (doi:10.1016/j.molcel.2011.01.024).
Zhang H & Yu DS 2012 One stone, two birds: CDK9-directed activation of UBE2A regulates monoubiquitination of both H2B and PCNA. Cell Cycle 11 2418. (doi:10.4161/cc.21068).
Zhang XY, Varthi M, Sykes SM, Phillips C, Warzecha C, Zhu W, Wyce A, Thorne AW, Berger SL & McMahon SB 2008 The putative cancer stem cell marker USP22 is a subunit of the human SAGA complex required for activated transcription and cell-cycle progression. Molecular Cell 29 102–111. (doi:10.1016/j.molcel.2007.12.015).
Zhang Y, Yao L, Zhang X, Ji H, Wang L, Sun S & Pang D 2011a Elevated expression of USP22 in correlation with poor prognosis in patients with invasive breast cancer. Journal of Cancer Research and Clinical Oncology 137 1245–1253. (doi:10.1007/s00432-011-0998-9).
Zhang Y, van Deursen J & Galardy PJ 2011b Overexpression of ubiquitin specific protease 44 (USP44) induces chromosomal instability and is frequently observed in human T-cell leukemia. PLoS ONE 6 e23389. (doi:10.1371/journal.pone.0023389).
Zhang Y, Foreman O, Wigle DA, Kosari F, Vasmatzis G, Salisbury JL, van Deursen J & Galardy PJ 2012 USP44 regulates centrosome positioning to prevent aneuploidy and suppress tumorigenesis. Journal of Clinical Investigation 122 4362–4374. (doi:10.1172/JCI63084).
Zhang Z, Jones A, Joo HY, Zhou D, Cao Y, Chen S, Erdjument-Bromage H, Renfrow M, He H & Tempst P et al. 2013 USP49 deubiquitinates histone H2B and regulates cotranscriptional pre-mRNA splicing. Genes and Development 27 1581–1595. (doi:10.1101/gad.211037.112).
Zhu B, Zheng Y, Pham AD, Mandal SS, Erdjument-Bromage H, Tempst P & Reinberg D 2005 Monoubiquitination of human histone H2B: the factors involved and their roles in HOX gene regulation. Molecular Cell 20 601–611. (doi:10.1016/j.molcel.2005.09.025).
Zhu Q, Pao GM, Huynh AM, Suh H, Tonnu N, Nederlof PM, Gage FH & Verma IM 2011 BRCA1 tumour suppression occurs via heterochromatin-mediated silencing. Nature 477 179–184. (doi:10.1038/nature10371).
This paper forms part of a thematic review section on Ubiquitination and Cancer. The guest editor for this section was Deborah Marsh, The University of Sydney, Sydney, Australia. She was not involved in the handling of this paper, on which she is listed as an author.
