The structure of ubiquitinated histone H2B

Histone ubiquitination: Role in genome integrity and chromatin organization

Maintenance of genome integrity is a precise but tedious and complex job for the cell. Several post-translational modifications (PTMs) play vital roles in maintaining the genome integrity. Although ubiquitination is one of the most crucial PTMs, which regulates the localization and stability of the nonhistone proteins in various cellular and developmental processes, ubiquitination of the histones is a pivotal epigenetic event critically regulating chromatin architecture. In addition to genome integrity, importance of ubiquitination of core histones (H2A, H2A, H3, and H4) and linker histone (H1) have been reported in several cellular processes. However, the complex interplay of histone ubiquitination and other PTMs, as well as the intricate chromatin architecture and dynamics, pose a significant challenge to unravel how histone ubiquitination safeguards genome stability. Therefore, further studies are needed to elucidate the interactions between histone ubiquitination and other PTMs, and their role in preserving genome integrity. Here, we review all types of histone ubiquitinations known till date in maintaining genomic integrity during transcription, replication, cell cycle, and DNA damage response processes. In addition, we have also discussed the role of histone ubiquitination in regulating other histone PTMs emphasizing methylation and acetylation as well as their potential implications in chromatin architecture. Further, we have also discussed the involvement of deubiquitination enzymes (DUBs) in controlling histone ubiquitination in modulating cellular processes.

Hypoxia-inducible factor 1 recruits FACT and RNF20/40 to mediate histone ubiquitination and transcriptional activation of target genes

Hypoxia-inducible factor 1 (HIF-1) is a transcriptional activator that mediates cellular adaptation to decreased oxygen availability. HIF-1 recruits chromatin-modifying enzymes leading to changes in histone acetylation, citrullination, and methylation at target genes. Here, we demonstrate that hypoxia-inducible gene expression in estrogen receptor (ER)-positive MCF7 and ER-negative SUM159 human breast cancer cells requires the histone H2A/H2B chaperone facilitates chromatin transcription (FACT) and the H2B ubiquitin ligase RING finger protein 20/40 (RNF20/40). Knockdown of FACT or RNF20/40 expression leads to decreased transcription initiation and elongation at HIF-1 target genes. Mechanistically, FACT and RNF20/40 are recruited to hypoxia response elements (HREs) by HIF-1 and stabilize binding of HIF-1 (and each other) at HREs. Hypoxia induces the monoubiquitination of histone H2B at lysine 120 at HIF-1 target genes in an HIF-1-dependent manner. Together, these findings delineate a cooperative molecular mechanism by which FACT and RNF20/40 stabilize multiprotein complex formation at HREs and mediate histone ubiquitination to facilitate HIF-1 transcriptional activity.

Deubiquitination module is critical for oxidative stress response and biofilm formation in Candida glabrata

Candidiasis is one of the most important fungal diseases and generally refers to diseases of the skin or mucosal tissues caused by Candida species. Candida glabrata is an opportunistic human fungal pathogen. Infection with C. glabrata has significantly increased due to innate antifungal drug tolerance and the ability to adhere to mucocutaneous surfaces. Spt-Ada-Gcn5 acetyltransferase complex contains two different post-translational modifications, histone acetylation (HAT) module and deubiquitination (DUB) module, which are decisive in gene regulation and highly conserved in eukaryotes. Previous research in our laboratory found that the HAT module ADA2 could regulate C. glabrata oxidative stress tolerance, drug tolerance, cell wall integrity, and virulence. However, the roles of the DUB module that is comprised of UBP8, SGF11, SGF73, and SUS1 genes in those phenotypes are not yet understood. In this study, we found that DUB module genes UBP8, SGF11, and SUS1, but not SGF73 positively regulate histone H2B DUB. Furthermore, ubp8, sgf11, and sus1 mutants exhibited decreased biofilm formation and sensitivity to cell wall-perturbing agent sodium dodecyl sulfate and antifungal drug amphotericin B. In addition, the sgf73 mutant showed increased biofilm formation but was susceptible to oxidative stresses, antifungal drugs, and cell wall perturbing agents. The ubp8, sgf11, and sus1 mutants showed marginal hypovirulence, whereas the sgf73 mutant exhibited virulence similar to the wild type in a murine systemic infection model. In conclusion, the C. glabrata DUB module plays distinct roles in H2B ubiquitination, oxidative stress response, biofilm formation, cell wall integrity, and drug tolerance, but exhibits minor roles in virulence.

The diverse roles of histone 2B monoubiquitination in the life of plants

Covalent modification of histones is an important tool for gene transcriptional control in eukaryotes, which coordinates growth, development, and adaptation to environmental changes. In recent years, an important role for monoubiquitination of histone 2B (H2B) has emerged in plants, where it is associated with transcriptional activation. In this review, we discuss the dynamics of the H2B monoubiquitination system in plants and its role in regulating developmental processes including flowering, circadian rhythm, photomorphogenesis, and the response to abiotic and biotic stress including drought, salinity, and fungal, bacterial, and viral pathogens. Furthermore, we highlight the crosstalk between H2B monoubiquitination and other histone modifications which fine-tunes transcription and ensures developmental plasticity. Finally, we put into perspective how this versatile regulatory mechanism can be developed as a useful tool for crop improvement.

Verticillium dahliae VdBre1 is required for cotton infection by modulating lipid metabolism and secondary metabolites

The soil-borne ascomycete Verticillium dahliae causes wilt disease in more than two hundred dicotyledonous plants including the economically important crop cotton, and results in a severe reduction in cotton fiber yield and quality. During infection, V. dahliae secretes numerous secondary metabolites, which act as toxic factors to promote the infection process. However, the mechanism underlying how V. dahliae secondary metabolites regulate cotton infection remains largely unexplored. In this study, we report that VdBre1, an ubiquitin ligase (E3) enzyme to modify H2B, regulates radial growth and conidia production of V. dahliae. The VdBre1 deletion strains show nonpathogenic symptoms on cotton, and microscopic inspection and penetration assay indicated that penetration ability of the ∆VdBre1 strain was dramatically reduced. RNA-seq revealed that a total of 1643 differentially expressed genes between the ∆VdBre1 strain and the wild type strain V592, among which genes related to lipid metabolism were significantly overrepresented. Remarkably, the volume of lipid droplets in the ∆VdBre1 conidia was shown to be smaller than that of wild-type strains. Further metabolomics analysis revealed that the pathways of lipid metabolism and secondary metabolites, such as steroid biosynthesis and metabolism of terpenoids and polyketides, have dramatically changed in the ∆VdBre1 metabolome. Taken together, these results indicate that VdBre1 plays crucial roles in cotton infection and pathogenecity, by globally regulating lipid metabolism and secondary metabolism of V. dahliae.

Bre1 and Ubp8 regulate H2B mono-ubiquitination and the reversible yeast-hyphae transition in Candida albicans

The reversible yeast-hyphae transition of the human fungal pathogen Candida albicans is tightly linked to its pathogenicity. In this study, we show that histone H2B mono-ubiquitination (H2Bub) at lysine 123 was maintained at a low level in the yeast state, whereas it increased significantly during yeast-to-hyphae transition and decreased when hyphae converted to yeast. The increased H2Bub level is correlated with activation of the hyphal program. H2B ubiquitination and deubiquitination are dynamically regulated by the E3 ligase Bre1 and the deubiquitinase Ubp8 during the reversible yeast-hyphae transition. The functions of Bre1 and Ubp8 in hypha-specific gene (HSG) regulation appears to be direct because both are recruited to the coding regions of HSGs during hyphal induction. The sequential recruitment of Bre1 and Ubp8 to HSGs coding regions is important for the initiation and maintenance of HSG expression. Additionally, Ubp8 contributes to the pathogenicity of C. albicans during early infection in a mouse model. Our study is the first to link H2B ubiquitination to the morphological plasticity and pathogenicity of the human fungal pathogen C. albicans and shed light on potential antifungal treatments.

Regulation of Histone Ubiquitination in Response to DNA Double Strand Breaks

Eukaryotic cells are constantly exposed to both endogenous and exogenous stressors that promote the induction of DNA damage. Of this damage, double strand breaks (DSBs) are the most lethal and must be efficiently repaired in order to maintain genomic integrity. Repair of DSBs occurs primarily through one of two major pathways: non-homologous end joining (NHEJ) or homologous recombination (HR). The choice between these pathways is in part regulated by histone post-translational modifications (PTMs) including ubiquitination. Ubiquitinated histones not only influence transcription and chromatin architecture at sites neighboring DSBs but serve as critical recruitment platforms for repair machinery as well. The reversal of these modifications by deubiquitinating enzymes (DUBs) is increasingly being recognized in a number of cellular processes including DSB repair. In this context, DUBs ensure proper levels of ubiquitin, regulate recruitment of downstream effectors, dictate repair pathway choice, and facilitate appropriate termination of the repair response. This review outlines the current understanding of histone ubiquitination in response to DSBs, followed by a comprehensive overview of the DUBs that catalyze the removal of these marks.

Analysis of the topology of ubiquitin chains

The small protein ubiquitin and its multiple polymers are encountered free in cells and as post-translational modifications on all proteins. Different polyubiquitin three dimensional structures are shown to correlate uniquely with different cellular functions as part of the diverse ubiquitin signaling. At the same time, this multiplicity of structures provides serious challenges to the analytical biochemist. Globally applicable strategies are presented here for the analyses of polyubiquitins and of ubiquitinated proteins, which take advantage of the speed, specificity and sensitivity of top-down tandem mass spectrometry. Particular attention is given to the supervised interpretation of fragmentation as revealed in the MS/MS spectra of these branched proteins. The strategy is compatible with any MS activation technology, is applicable to all polyubiquitin linkage and chain types, can be extended to ubiquitin-like proteins, and will be compatible with and enhanced by continuing advances in LC-MS/MS instrumentation and interpretation software.

The E3 ligase HOIL-1 catalyses ester bond formation between ubiquitin and components of the Myddosome in mammalian cells

The linear ubiquitin assembly complex (LUBAC) comprises 3 components: HOIP, HOIL-1, and Sharpin, of which HOIP and HOIL-1 are both members of the RBR subfamily of E3 ubiquitin ligases. HOIP catalyses the formation of Met1-linked ubiquitin oligomers (also called linear ubiquitin), but the function of the E3 ligase activity of HOIL-1 is unknown. Here, we report that HOIL-1 is an atypical E3 ligase that forms oxyester bonds between the C terminus of ubiquitin and serine and threonine residues in its substrates. Exploiting the sensitivity of HOIL-1-generated oxyester bonds to cleavage by hydroxylamine, and macrophages from knock-in mice expressing the E3 ligase-inactive HOIL-1[C458S] mutant, we identify IRAK1, IRAK2, and MyD88 as physiological substrates of the HOIL-1 E3 ligase during Toll-like receptor signaling. HOIL-1 is a monoubiquitylating E3 ubiquitin ligase that initiates the de novo synthesis of polyubiquitin chains that are attached to these proteins in macrophages. HOIL-1 also catalyses its own monoubiquitylation in cells and most probably the monoubiquitylation of Sharpin, in which ubiquitin is also attached by an oxyester bond. Our study establishes that oxyester-linked ubiquitylation is used as an intracellular signaling mechanism.

The Role of Ubiquitination in Regulating Embryonic Stem Cell Maintenance and Cancer Development

Ubiquitination regulates nearly every aspect of cellular events in eukaryotes. It modifies intracellular proteins with 76-amino acid polypeptide ubiquitin (Ub) and destines them for proteolysis or activity alteration. Ubiquitination is generally achieved by a tri-enzyme machinery involving ubiquitin activating enzymes (E1), ubiquitin conjugating enzymes (E2) and ubiquitin ligases (E3). E1 activates Ub and transfers it to the active cysteine site of E2 via a transesterification reaction. E3 coordinates with E2 to mediate isopeptide bond formation between Ub and substrate protein. The E1-E2-E3 cascade can create diverse types of Ub modifications, hence effecting distinct outcomes on the substrate proteins. Dysregulation of ubiquitination results in severe consequences and human diseases. There include cancers, developmental defects and immune disorders. In this review, we provide an overview of the ubiquitination machinery and discuss the recent progresses in the ubiquitination-mediated regulation of embryonic stem cell maintenance and cancer biology.

RNF20 controls astrocytic differentiation through epigenetic regulation of STAT3 in the developing brain

Astrocyte has crucial roles in the central nervous system and accumulating evidence has shown its core function for brain complexity, plasticity and cognition. However, the essential key factors in the precise regulation of astrocytic differentiation remain largely uncharacterized. Here, we identified that RNF20, an E3 ligase of H2BK120 in the mammalian system, regulates astrocyte production from neural precursor cells. RNF20 deficiency by shRNA knockdown or deletion in conditional knockout mice impairs the astrocytic differentiation. Overexpression of RNF20 promotes astrocytic differentiation and can rescue the astrocyte production deficiency caused by RNF20 disruption. Furthermore, we demonstrate that RNF20 functions cooperatively with acetyltransferase MOF to promote astrocytic generation. RNF20-mediated H2Bub1 cooperating with MOF-mediated H4K16ac activates the transcription of Stat3. Together, these data indicate RNF20 is a critical regulator of astrocytic production, which may contribute to the understanding of neurological disorders with glial dysgenesis.

Writers, Readers, and Erasers of Histone Ubiquitylation in DNA Double-Strand Break Repair

DNA double-strand breaks (DSBs) are highly cytotoxic DNA lesions, whose faulty repair may alter the content and organization of cellular genomes. To counteract this threat, numerous signaling and repair proteins are recruited hierarchically to the chromatin areas surrounding DSBs to facilitate accurate lesion repair and restoration of genome integrity. In vertebrate cells, ubiquitin-dependent modifications of histones adjacent to DSBs by RNF8, RNF168, and other ubiquitin ligases have a key role in promoting the assembly of repair protein complexes, serving as direct recruitment platforms for a range of genome caretaker proteins and their associated factors. These DNA damage-induced chromatin ubiquitylation marks provide an essential component of a histone code for DSB repair that is controlled by multifaceted regulatory circuits, underscoring its importance for genome stability maintenance. In this review, we provide a comprehensive account of how DSB-induced histone ubiquitylation is sensed, decoded and modulated by an elaborate array of repair factors and regulators. We discuss how these mechanisms impact DSB repair pathway choice and functionality for optimal protection of genome integrity, as well as cell and organismal fitness.

Preparing to read the ubiquitin code: characterization of ubiquitin trimers by top-down mass spectrometry

The profound effects of ubiquitination on the movement and processing of cellular proteins depend exquisitely on the structures of monoubiquitin and polyubiquitin modifications. Unconjugated polyubiquitins also have a variety of intracellular functions. Structures and functions are not well correlated yet, because the structures of polyubiquitins and polyubiquitin modifications of proteins are difficult to decipher. We are moving towards a robust strategy to provide that structural information. In this report electron transfer dissociation mass spectra of six synthetic ubiquitin trimers (multiply branched proteins with molecular masses exceeding 25,600 Da) are examined using an Orbitrap Fusion Lumos instrument to determine how top-down mass spectrometry can characterize the chain topology and linkage sites in a single, facile workflow. The efficacy of this method relies on the formation, detection, and interpretation of extensive fragmentation.

Preparing to read the ubiquitin code: a middle-out strategy for characterization of all lysine-linked diubiquitins

Multiple studies demonstrate that ubiquitination of proteins codes for regulation of cell differentiation, apoptosis, endocytosis and many other cellular functions. There is great interest in and considerable effort being given to defining the relationships between the structures of polyubiquitin modifications and the fates of the modified proteins. Does each ubiquitin modification achieve a specific effect, much like phosphorylation, or is ubiquitin like glycosylation, where there is heterogeneity and redundancy in the signal? The sensitive analytical tools needed to address such questions readily are not yet mature. To lay the foundation for mass spectrometry (MS)-based studies of the ubiquitin code, we have assembled seven isomeric diubiquitins with all-native sequences and isopeptide linkages. Using these compounds as standards enables the development and testing of a new MS-based strategy tailored specifically to characterize the number and sites of isopeptide linkages in polyubiquitin chains. Here, we report the use of Asp-selective acid cleavage, separation by reverse phase high-performance liquid chromatography and characterization by tandem MS to distinguish and characterize all seven isomeric lysine-linked ubiquitin dimers.

Regulation of chromatin structure via histone post-translational modification and the link to carcinogenesis

The loss of genome integrity contributes to the development of tumors. Although genome instability is associated with virtually all tumor types including both solid and liquid tumors, the aberrant molecular origins that drive this instability are poorly understood. It is now becoming clear that epigenetics and specific histone post-translational modifications (PTMs) have essential roles in maintaining genome stability under normal conditions. A strong relationship exists between aberrant histone PTMs, genome instability, and tumorigenesis. Changes in the genomic location of specific histone PTMs or alterations in the steady-state levels of the PTM are the consequence of imbalances in the enzymes and their activities catalyzing the addition of PTMs ("writers") or removal of PTMs ("erasers"). This review focuses on the misregulation of three specific types of histone PTMs: histone H3 phosphorylation at serines 10 and 28, H4 mono-methylation at lysine 20, and H2B ubiquitination at lysine 120. We discuss the normal regulation of these PTMs by the respective "writers" and "erasers" and the impact of their misregulation on genome stability.

The arabidopsis histone methyltransferase SUVR4 binds ubiquitin via a domain with a four-helix bundle structure

In eukaryotes, different chromatin states facilitate or repress gene expression and restrict the activity of transposable elements. Post-translational modifications (PTMs) of amino acid residues on the N-terminal tails of histones are suggested to define such states. The histone lysine methyltransferase (HKMTase) SU(VAR)3-9 RELATED4 (SUVR4) of Arabidopsis thaliana functions as a repressor of transposon activity. Binding of ubiquitin by the WIYLD domain facilitates the addition of two methyl groups to monomethylated lysine 9 of histone H3. By using nuclear magnetic resonance (NMR) spectroscopy, we identified SUVR4 WIYLD (S4WIYLD) as a domain with a four-helix bundle structure, in contrast to three-helix bundles of other ubiquitin binding domains. NMR titration analyses showed that residues of helix α1 (Q38, L39, and D40) and helix α4 (N68, T70, A71, V73, D74, I76, S78, and E82) of S4WIYLD and residues between the first and second β-strands (T9 and G10) and on β-strands 3 (R42, G47, K48, and Q49) and 4 (H68, R72, and L73) undergo significant chemical shift changes when the two proteins interact. A model of the complex, generated using HADDOCK, suggests that the N-terminal and C-terminal parts of S4WIYLD constitute a surface that interacts with charged residues close to the hydrophobic patch of ubiquitin. The WIYLD domains of the closely related SUVR1 and SUVR2 Arabidopsis proteins also bind ubiquitin, indicating that this is a general feature of this domain. The question of whether SUVR proteins act as both readers of monoubiquitinated H2B and writers of histone PTMs is discussed.

RNF20 and USP44 regulate stem cell differentiation by modulating H2B monoubiquitylation

Embryonic stem cells (ESCs) maintain high genomic plasticity, which is essential for their capacity to enter diverse differentiation pathways. Posttranscriptional modifications of chromatin histones play a pivotal role in maintaining this plasticity. We now report that one such modification, monoubiquitylation of histone H2B on lysine 120 (H2Bub1), catalyzed by the E3 ligase RNF20, increases during ESC differentiation and is required for efficient execution of this process. This increase is particularly important for the transcriptional induction of relatively long genes during ESC differentiation. Furthermore, we identify the deubiquitinase USP44 as a negative regulator of H2B ubiquitylation, whose downregulation during ESC differentiation contributes to the increase in H2Bub1. Our findings suggest that optimal ESC differentiation requires dynamic changes in H2B ubiquitylation patterns, which must occur in a timely and well-coordinated manner.

Enzymatic assays for assessing histone deubiquitylation activity

While the post-translational modification of histones by the addition of ubiquitin was discovered decades ago, it has only recently been appreciated that the dynamic regulation of histone ubiquitylation patterns is an important mechanism for controlling a variety of biological processes. The processes include transcription, the recognition and repair of genomic damage and DNA replication, among others. Enzymes that catalyze the addition of ubiquitin to histones, such as the polycomb family, have been well-studied. In contrast, the enzymes that remove ubiquitin from histones are less well understood. The assay strategies described here provide a platform for the thorough in vitro and in vivo analysis of histone deubiquitylation. In some cases, these poorly characterized enzymes are likely to provide new opportunities for therapeutic targeting and a detailed understanding of their biochemical and biological activities is a prerequisite to these clinical advances.

Detection and characterization of ubiquitylated H2B in mammalian cells

Histone H2B ubiquitylation was shown to be associated with actively transcribed genes in mammalian cells and has been suggested to be involved in transcriptional regulation. Despite the limited applicability of genetic tools to analyze H2B ubiquitylation in mammals, several biochemical and immunological approaches have been successfully implemented to study this modification. Here we describe several techniques to detect ubiquitylated H2B in mammalian cells and to dissect its genomic localization.

Extensive and varied modifications in histone H2B of wild-type and histone deacetylase 1 mutant Neurospora crassa

DNA methylation is deficient in a histone deacetylase 1 (HDA1) mutant (hda-1) strain of Neurospora crassa with inactivated histone deacetylase 1. Difference two-dimensional (2D) gels identified the primary histone deacetylase 1 target as histone H2B. Acetylation was identified by LC-MS/MS at five different lysines in wild-type H2B and at 11 lysines in hda-1 H2B, suggesting Neurospora H2B is a complex combination of different acetylated species. Individual 2D gel spots were shifted by single lysine acetylations. FTICR MS-observed methylation ladders identify an ensemble of 20-25 or more modified forms for each 2D gel spot. Twelve different lysines or arginines were methylated in H2B from the wild type or hda-1; only two were in the N-terminal tail. Arginines were modified by monomethylation, dimethylation, or deimination. H2B from wild-type and hda-1 ensembles may thus differ by acetylation at multiple sites, and by additional modifications. Combined with asymmetry-generated diversity in H2B structural states in nucleosome core particles, the extensive modifications identified here can create substantial histone-generated structural diversity in nucleosome core particles.

Role of ubiquitination in meiotic recombination repair

Programmed and unprogrammed double-strand breaks (DSBs) often arise from such physiological requirements as meiotic recombination, and exogenous insults, such as ionizing radiation (IR). Due to deleterious impacts on genome stability, DSBs must be appropriately processed and repaired in a regulatory manner. Recent investigations have indicated that ubiquitination is a critical factor in DNA damage response and meiotic recombination repair. This review summarizes the effects of proteins and complexes associated with ubiquitination with regard to homologous recombination (HR)-dependent DSB repair.

Identification, analysis, and prediction of protein ubiquitination sites

Ubiquitination plays an important role in many cellular processes and is implicated in many diseases. Experimental identification of ubiquitination sites is challenging due to rapid turnover of ubiquitinated proteins and the large size of the ubiquitin modifier. We identified 141 new ubiquitination sites using a combination of liquid chromatography, mass spectrometry, and mutant yeast strains. Investigation of the sequence biases and structural preferences around known ubiquitination sites indicated that their properties were similar to those of intrinsically disordered protein regions. Using a combined set of new and previously known ubiquitination sites, we developed a random forest predictor of ubiquitination sites, UbPred. The class-balanced accuracy of UbPred reached 72%, with the area under the ROC curve at 80%. The application of UbPred showed that high confidence Rsp5 ubiquitin ligase substrates and proteins with very short half-lives were significantly enriched in the number of predicted ubiquitination sites. Proteome-wide prediction of ubiquitination sites in Saccharomyces cerevisiae indicated that highly ubiquitinated substrates were prevalent among transcription/enzyme regulators and proteins involved in cell cycle control. In the human proteome, cytoskeletal, cell cycle, regulatory, and cancer-associated proteins display higher extent of ubiquitination than proteins from other functional categories. We show that gain and loss of predicted ubiquitination sites may likely represent a molecular mechanism behind a number of disease-associatedmutations. UbPred is available at http://www.ubpred.org.

Studying histone modifications and their genomic functions by employing chromatin immunoprecipitation and immunoblotting

Histones are one of the most abundant and highly conserved proteins in eukaryotes. Apart from serving as structural entities for orderly compaction of genomes, they play an instrumental role in the regulation of many important biological processes involving DNA such as transcription, DNA repair, and the cell cycle. Histone modifications have been implicated in maintaining the transcriptionally poised state of important genesin embryonic stem cells. Histone modifications are believed to be responsible for compartmentalization of chromatin into active and inactive domains. Hence, the tools and techniques required for studying these proteins are of utmost importance to biologists. This chapter provides a brief review of the posttranslational modifications of the N-terminal tails of histones and their biological roles, followed by step-by-step protocols for the most common techniques employed to study them. Here, we describe chromatin immunoprecipitation (ChIP) for studying the genomic functions of the most widely studied histone modifications, namely, histone H3 lysine 9 acetylation and histone H3 lysine 9 trimethylation that are typically associated with transcriptional activation and repression, respectively. Special emphasis has been given on the method of preparation of sonicated chromatin prior to immunoprecipitation since this single step affects the success of ChIP greatly and is often poorly described in published protocols. Protocol for histone isolation by acid-extraction and detection by Coomassie staining has also been described. We also describe the protocol for immunoblot analysis of histones using antibodies against key histone modifications. This chapter will serve as a useful resource in the study of histones and their posttranslational modifications.

The dynamic epigenetic program in male germ cells: Its role in spermatogenesis, testis cancer, and its response to the environment

Spermatogenesis is a truly remarkable process that requires exquisite control and synchronization of germ cell development. It is prone to frequent error, as paternal infertility contributes to 30-50% of all infertility cases; yet, in many cases, the mechanisms underlying its causes are unknown. Strikingly, aberrant epigenetic profiles, in the form of anomalous DNA and histone modifications, are characteristic of cancerous testis cells. Germ cell development is a critical period during which epigenetic patterns are established and maintained. The progression from diploid spermatogonia to haploid spermatozoa involves stage- and testis-specific gene expression, mitotic and meiotic division, and the histone-protamine transition. All are postulated to engender unique epigenetic controls. In support of this idea are the findings that mouse models with gene deletions for epigenetic modifiers have severely compromised fertility. Underscoring the importance of understanding how epigenetic marks are set and interpreted is evidence that abnormal epigenetic programming of gametes and embryos contributes to heritable instabilities in subsequent generations. Numerous studies have documented the existence of transgenerational consequences of maternal nutrition, or other environmental exposures, but it is only now recognized that there are sex-specific male-line transgenerational responses in humans and other species. Epigenetic events in the testis have just begun to be studied. New work on the function of specific histone modifications, chromatin modifiers, DNA methylation, and the impact of the environment on developing sperm suggests that the correct setting of the epigenome is required for male reproductive health and the prevention of paternal disease transmission.

Histone H2B ubiquitylation is not required for histone H3 methylation at lysine 4 in tetrahymena

Ubiquitylation of histone H2B and/or a component of the system that ubiquitylates H2B is required for methylation of histone H3 at lysine 4 (H3K4) in yeasts and probably in humans. In this study, the single ubiquitylation site was mapped to conserved lysine 115 of the C-terminal region of histone H2B in the single-cell model organism Tetrahymena thermophila. In strains lacking H2B ubiquitylation, H3K4 methylation was not detectably affected. As in other organisms, the E2 ubiquitin-conjugating enzyme Ubc2 and the E3 ubiquitin ligase Bre1 were required for H2B ubiquitylation. However, neither enzyme was required for H3K4 methylation. These studies argue that, in T. thermophila, the histone ubiquitylation mechanism is not required for H3K4 methylation, demonstrating that different organisms can speak different languages in the "cross-talk" among post-translational modifications on different histones.

Global histone analysis by mass spectrometry reveals a high content of acetylated lysine residues in the malaria parasite Plasmodium falciparum

Post-translational modifications (PTMs) of histone tails play a key role in epigenetic regulation of gene expression in a range of organisms from yeast to human; however, little is known about histone proteins from the parasite that causes malaria in humans, Plasmodium falciparum. We characterized P. falciparum histone PTMs using advanced mass spectrometry driven proteomics. Acid-extracted proteins were resolved in SDS-PAGE, in-gel trypsin digested, and analyzed by reversed-phase LC-MS/MS. Through the combination of Q-TOF and LTQ-FT mass spectrometry we obtained high mass accuracy of both precursor and fragment ions, which is a prerequisite for high-confidence identifications of multisite peptide modifications. We utilize MS/MS fragment marker ions to validate the identification of histone modifications and report the m/z 143 ion as a novel MS/MS marker ion for monomethylated lysine. We identified all known P. falciparum histones and mapped 44 different modifications, providing a comprehensive view of epigenetic marks in the parasite. Interestingly, the parasite exhibits a histone modification pattern that is distinct from its human host. A general preponderance for modifications associated with a transcriptionally permissive state was observed. Additionally, a novel differentiation in the modification pattern of the two histone H2B variants (H2B and H2Bv) was observed, suggesting divergent functions of the two H2B variants in the parasite. Taken together, our results provide a first comprehensive map of histone modifications in P. falciparum and highlight the utility of tandem MS for detailed analysis of peptides containing multiple PTMs.

Alterations of histone modifications by cobalt compounds

In the present study, we examined the effects of CoCl(2) on multiple histone modifications at the global level. We found that in both human lung carcinoma A549 cells and human bronchial epithelial Beas-2B cells, exposure to CoCl(2) (>/=200 muM) for 24 h increased H3K4me3, H3K9me2, H3K9me3, H3K27me3, H3K36me3, uH2A and uH2B but decreased acetylation at histone H4 (AcH4). Further investigation demonstrated that in A549 cells, the increase in H3K4me3 and H3K27me3 by cobalt ions exposure was probably through enhancing histone methylation processes, as methionine-deficient medium blocked the induction of H3K4me3 and H3K27me3 by cobalt ions, whereas cobalt ions increased H3K9me3 and H3K36me3 by directly inhibiting JMJD2A demethylase activity in vitro, which was probably due to the competition of cobalt ions with iron for binding to the active site of JMJD2A. Furthermore, in vitro ubiquitination and deubiquitination assays revealed that the cobalt-induced histone H2A and H2B ubiquitination is the result of inhibition of deubiquitinating enzyme activity. Microarray data showed that exposed to 200 microM of CoCl(2) for 24 h, A549 cells not only increased but also decreased expression of hundreds of genes involved in different cellular functions, including tumorigenesis. This study is the first to demonstrate that cobalt ions altered epigenetic homeostasis in cells. It also sheds light on the possible mechanisms involved in cobalt-induced alteration of histone modifications, which may lead to altered programs of gene expression and carcinogenesis since cobalt at higher concentrations is a known carcinogen.

The many faces of ubiquitinated histone H2A: insights from the DUBs

Monoubiquitination of H2A is a major histone modification in mammalian cells. Understanding how monoubiquitinated H2A (uH2A) regulates DNA-based processes in the context of chromatin is a challenging question. Work in the past years linked uH2A to transcriptional repression by the Polycomb group proteins of developmental regulators. Recently, a number of mammalian deubiquitinating enzymes (DUBs) that catalyze the removal of ubiquitin from H2A have been discovered. These studies provide convincing evidence that H2A deubiquitination is connected with gene activation. In addition, uH2A regulatory enzymes have crucial roles in the cellular response to DNA damage and in cell cycle progression. In this review we will discuss new insights into uH2A biology, with emphasis on the H2A DUBs.

Histone H2A monoubiquitination represses transcription by inhibiting RNA polymerase II transcriptional elongation

Solving the biological roles of covalent histone modifications, including monoubiquitination of histone H2A, and the molecular mechanisms by which these modifications regulate specific transcriptional programs remains a central question for all eukaryotes. Here we report that the N-CoR/HDAC1/3 complex specifically recruits a specific histone H2A ubiquitin ligase, 2A-HUB/hRUL138, to a subset of regulated gene promoters. 2A-HUB catalyzes monoubiquitination of H2A at lysine 119, functioning as a combinatoric component of the repression machinery required for specific gene regulation programs. Thus, 2A-HUB mediates a selective repression of a specific set of chemokine genes in macrophages, critically modulating migratory responses to TLR activation. H2A monoubiquitination acts to prevent FACT recruitment at the transcriptional promoter region, blocking RNA polymerase II release at the early stage of elongation. We suggest that distinct H2A ubiquitinases, each recruited based on interactions with different corepressor complexes, contribute to distinct transcriptional repression programs.

The putative cancer stem cell marker USP22 is a subunit of the human SAGA complex required for activated transcription and cell-cycle progression

Polycomb genes encode critical regulators of both normal stem cells and cancer stem cells. A gene signature that includes Polycomb genes and additional genes coregulated with Polycomb genes was recently identified. The expression of this signature has been reported to identify tumors with the cancer stem cell phenotypes of aggressive growth, metastasis, and therapy resistance. Most members of this 11 gene signature encode proteins with well-defined roles in human cancer. However, the function of the signature member USP22 remains unknown. We report that USP22 is a previously uncharacterized subunit of the human SAGA transcriptional cofactor complex. Within SAGA, USP22 deubiquitylates histone H2B. Furthermore, USP22 is recruited to specific genes by activators such as the Myc oncoprotein, where it is required for transcription. In support of a functional role within the Polycomb/cancer stem cell signature, USP22 is required for appropriate progression through the cell cycle.

A histone H2A deubiquitinase complex coordinating histone acetylation and H1 dissociation in transcriptional regulation

Deciphering the epigenetic "code" remains a central issue in transcriptional regulation. Here, we report the identification of a JAMM/MPN(+) domain-containing histone H2A deubiquitinase (2A-DUB, or KIAA1915/MYSM1) specific for monoubiquitinated H2A (uH2A) that has permitted delineation of a strategy for specific regulatory pathways of gene activation. 2A-DUB regulates transcription by coordinating histone acetylation and deubiquitination, and destabilizing the association of linker histone H1 with nucleosomes. 2A-DUB interacts with p/CAF in a coregulatory protein complex, with its deubiquitinase activity modulated by the status of acetylation of nucleosomal histones. Consistent with this mechanistic role, 2A-DUB participates in transcriptional regulation events in androgen receptor-dependent gene activation, and the levels of uH2A are dramatically decreased in prostate tumors, serving as a cancer-related mark. We suggest that H2A ubiquitination represents a widely used mechanism for many regulatory transcriptional programs and predict that various H2A ubiquitin ligases/deubiquitinases will be identified for specific cohorts of regulated transcription units.

Characterization of post-translational modifications of histone H2B-variants isolated from Arabidopsis thaliana

Eukaryotic DNA is structurally packed into chromatin by the basic histone proteins H2A, H2B, H3, and H4. There is increasing evidence that incorporation and post-translational modifications of histone variants have a fundamental role in gene regulation. While modifications of H3 and H4 histones are now well-established, considerably less is known about H2B modifications. Here, we present the first detailed characterization of H2B-variants isolated from the model plant Arabidopsis thaliana. We combined reversed-phase chromatography with tandem mass spectrometry to identify post-translational modifications of the H2B-variants HTB1, HTB2, HTB4, HTB9, and HTB11, isolated from total chromatin and euchromatin-enriched fractions. The HTB9-variant has acetylation sites at lysines 6, 11, 27, 32, 38, and 39, while Lys-145 can be ubiquitinated. Analogous modifications and an additional methylation of Lys-3 were identified for HTB11. HTB2 shows similar acetylation and ubiquitination sites and an additional methylation at Lys-11. Furthermore, the N-terminal alanine residues of HTB9 and HTB11 were found to be mono-, di-, or trimethylated or unmodified. No methylation of arginine residues was detected. The data suggest that most of these modification sites are only partially occupied. Our study significantly expands the map of covalent Arabidopsis histone modifications and is the first step to unraveling the histone code in higher plants.

Epigenetics--an epicenter of gene regulation: histones and histone-modifying enzymes

The treatment of cancer through the development of new therapies is one of the most important challenges of our time. The decoding of the human genome has yielded important insights into the molecular basis of physical disorders, and in most cases a connection between failures in specific genes and the resulting clinical symptoms can be made. The modulation of epigenetic mechanisms enables, by definition, the alteration of cellular phenotype without altering the genotype. The information content of a single gene can be crucial or harmful, but the prerequisite for a cellular effect is active gene transcription. To this end, epigenetic mechanisms play a very important role, and the transcription of a given gene is directly influenced by the modification pattern of the surrounding histone proteins as well as the methylation pattern of the DNA. These processes are effected by different enzymes which can be directly influenced through the development of specific modulators. Of course, all genetic information is written as a four-character code in DNA. However, epigenetics describes the art of reading between the lines.

Ni(II) affects ubiquitination of core histones H2B and H2A

The molecular mechanisms of nickel-induced malignant cell transformation include effects altering the structure and covalent modifications of core histones. Previously, we found that exposure of cells to Ni(II) resulted in truncation of histones H2A and H2B and thus elimination of some modification sites. Here, we investigated the effect of Ni(II) on one such modification, ubiquitination, of histones H2B and H2A in nuclei of cultured 1HAEo- and HPL1D human lung cells. After 1-5 days of exposure, Ni(II) up to 0.25 mM stimulated mono-ubiquitination of both histones, while at higher concentrations a suppression was found. Di-ubiquitination of H2A was not affected except for a drop after 5 days at 0.5 mM Ni(II). The decrease in mono-ubiquitination coincided with the appearance of truncated H2B that lacks the K120 ubiquitination site. However, prevention of truncation did not avert the decrease of H2B ubiquitination, indicating mechanistic independence of these effects. The changes in H2B ubiquitination did not fully coincide with concurrent changes in the nuclear levels of the ubiquitin-conjugating enzymes Rad6 and UbcH6. Overall, our results suggest that dysregulation of H2B ubiquitination is a part of Ni(II) adverse effects on gene expression and DNA repair which may assist in cell transformation.

Histone Ubiquitylation and the Regulation of Transcription

The small (76 amino acids) and highly conserved ubiquitin protein plays key roles in the physiology of eukaryotic cells. Protein ubiquitylation has emerged as one of the most important intracellular signaling mechanisms, and in 2004 the Nobel Prize was awarded to Aaron Ciechanower, Avram Hersko, and Irwin Rose for their pioneering studies of the enzymology of ubiquitin attachment. One of the most common features of protein ubiquitylation is the attachment of polyubiquitin chains (four or more ubiquitin moieties attached to each other), which is a widely used mechanism to target proteins for degradation via the 26S proteosome. However, it is noteworthy that the first ubiquitylated protein to be identified was histone H2A, to which a single ubiquitin moiety is most commonly attached. Following this discovery, other histones (H2B, H3, H1, H2A.Z, macroH2A), as well as many nonhistone proteins, have been found to be monoubiquitylated. The role of monoubiquitylation is still elusive because a single ubiquitin moiety is not sufficient to target proteins for turnover, and has been hypothesized to control the assembly or disassembly of multiprotein complexes by providing a protein-binding site. Indeed, a number of ubiquitin-binding domains have now been identified in both polyubiquitylated and monoubiquitylated proteins. Despite the early discovery of ubiquitylated histones, it has only been in the last five or so years that we have begun to understand how histone ubiquitylation is regulated and what roles it plays in the cell. This review will discuss current research on the factors that regulate the attachment and removal of ubiquitin from histones, describe the relationship of histone ubiquitylation to histone methylation, and focus on the roles of ubiquitylated histones in gene expression.

The human homolog of yeast BRE1 functions as a transcriptional coactivator through direct activator interactions

Diverse histone modifications such as acetylation, methylation, and phosphorylation play important roles in transcriptional regulation throughout eukaryotes, and recent studies in yeast also have implicated H2B ubiquitylation in the transcription of specific genes. Here, we report the identification of a functional human homolog, hBRE1, of the yeast BRE1 E3 ubiquitin ligase. hBRE1 specifically increases the global level of H2B ubiquitylation at lysine 120 and enhances activator-dependent transcription. Moreover, reduction of hBRE1 by RNAi decreases endogenous H2B ubiquitylation, activator-dependent transcription, and interestingly, H3-K4 and -K79 methylation. Of special significance, we show that hBRE1 directly interacts with p53 and that it is recruited to the mdm2 promoter in a p53-dependent manner. These studies suggest that hBRE1 is an H2B-specific E3 ubiquitin ligase and that it functions, through direct activator interactions, as a transcriptional coactivator. Importantly, they thus provide a paradigm for BRE1 recruitment and function in both yeast and higher eukaryotes.

Monoubiquitination of human histone H2B: the factors involved and their roles in HOX gene regulation

In yeast, histone H2B monoubiquitination is a cotranscriptional event regulating histone H3 methylation at lysines 4 and 79. However, mammalian H2B monoubiquitination remains poorly understood. We report that in humans, the 600 kDa RNF20/40 complex is the E3 ligase and UbcH6 is the ubiquitin E2-conjugating enzyme for H2B-Lys120 monoubiquitination. RNF20 and RNF40 are both homologs of Bre1, the E3 ligase in the yeast case. UbcH6 physically interacts with RNF20/40 and with the hPAF complex. Formation of a trimeric complex with hPAF stimulates H2B monoubiquitination activity in vitro. Accordingly, UbcH6, RNF20/40, and the hPAF complex are recruited to transcriptionally active genes in vivo. RNF20 overexpression leads to elevated H2B monoubiquitination, subsequently higher levels of methylation at H3 lysines 4 and 79, and stimulation of HOX gene expression. In contrast, RNAi against the RNF20/40 complex or hPAF complex reduces H2B monoubiquitination, lowers methylation levels at H3 lysines 4 and 79, and represses HOX gene expression.

Histone H2A Ubiquitination Does Not Preclude Histone H1 Binding, but It Facilitates Its Association with the Nucleosome

Histone H2A ubiquitination is a bulky posttranslational modification that occurs at the vicinity of the binding site for linker histones in the nucleosome. Therefore, we took several experimental approaches to investigate the role of ubiquitinated H2A (uH2A) in the binding of linker histones. Our results showed that uH2A was present in situ in histone H1-containing nucleosomes. Notably in vitro experiments using nucleosomes reconstituted onto 167-bp random sequence and 208-bp (5 S rRNA gene) DNA fragments showed that ubiquitination of H2A did not prevent binding of histone H1 but it rather enhanced the binding of this histone to the nucleosome. We also showed that ubiquitination of H2A did not affect the positioning of the histone octamer in the nucleosome in either the absence or the presence of linker histones.

The RING domain of Mdm2 mediates histone ubiquitylation and transcriptional repression

Histone modifications play a pivotal role in regulating transcription and other chromatin-associated processes. In yeast, histone H2B monoubiquitylation affects gene silencing. However, mammalian histone ubiquitylation remains poorly understood. We report that the Mdm2 oncoprotein, a RING domain E3 ubiquitin ligase known to ubiquitylate the p53 tumor suppressor protein, can interact directly with histones and promote in vitro monoubiquitylation of histones H2A and H2B. Moreover, Mdm2 induces H2B monoubiquitylation in vivo. Endogenous Mdm2 is tethered in vivo, presumably via p53, to chromatin comprising the p53-responsive p21(waf1) promoter, and Mdm2 overexpression enhances protein ubiquitylation in the vicinity of a p53 binding site within that promoter. Moreover, when recruited to a promoter in the absence of p53, Mdm2 can repress transcription dependently on its RING domain, suggesting that its E3 activity contributes to repression. Histone ubiquitylation may thus constitute a novel mechanism of transcriptional repression by Mdm2, possibly underlying some of its oncogenic activities.

Lessons from the genome sequence of Neurospora crassa: tracing the path from genomic blueprint to multicellular organism

We present an analysis of over 1,100 of the approximately 10,000 predicted proteins encoded by the genome sequence of the filamentous fungus Neurospora crassa. Seven major areas of Neurospora genomics and biology are covered. First, the basic features of the genome, including the automated assembly, gene calls, and global gene analyses are summarized. The second section covers components of the centromere and kinetochore complexes, chromatin assembly and modification, and transcription and translation initiation factors. The third area discusses genome defense mechanisms, including repeat induced point mutation, quelling and meiotic silencing, and DNA repair and recombination. In the fourth section, topics relevant to metabolism and transport include extracellular digestion; membrane transporters; aspects of carbon, sulfur, nitrogen, and lipid metabolism; the mitochondrion and energy metabolism; the proteasome; and protein glycosylation, secretion, and endocytosis. Environmental sensing is the focus of the fifth section with a treatment of two-component systems; GTP-binding proteins; mitogen-activated protein, p21-activated, and germinal center kinases; calcium signaling; protein phosphatases; photobiology; circadian rhythms; and heat shock and stress responses. The sixth area of analysis is growth and development; it encompasses cell wall synthesis, proteins important for hyphal polarity, cytoskeletal components, the cyclin/cyclin-dependent kinase machinery, macroconidiation, meiosis, and the sexual cycle. The seventh section covers topics relevant to animal and plant pathogenesis and human disease. The results demonstrate that a large proportion of Neurospora genes do not have homologues in the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe. The group of unshared genes includes potential new targets for antifungals as well as loci implicated in human and plant physiology and disease.

H2B ubiquitylation: the end is in sight

Historically, the first eukaryotic protein found to be modified by ubiquitin was H2A, originally isolated from HeLa cells in 1975 by Harrison Busch and coworkers as a histone-like, nonhistone chromosomal protein called A24. Ubiquitylated histones have subsequently been found in many eukaryotic species, and to date, the core histones H2A, H2B, H3, the linker histone H1, and the histone variant H2A.Z are known to carry this modification. Although first on the scene, it was only recently that studies on histone ubiquitylation have enjoyed a renaissance. Part of the reason for the relatively slow pace of research on this fascinating histone modification was the absence of a good genetic system with which to study its cellular roles. This changed in 2000, when histone H2B was found to be ubiquitylated in the budding yeast S. cerevisiae, an organism with a low histone gene copy number and highly tractable genetics. Another factor was the almost exclusive focus of research on the role of polyubiquitylation in protein turnover. Because histones are generally monoubiquitylated, a form of the modification that is not associated with protein degradation, the significance of this minimalist ubiquitin conjugation was not heavily pursued. But perhaps the key reason for the renewed interest in histone ubiquitylation was the unexpected discovery of the past year that ubiquitylated H2B plays an important role in the trans-histone methylation of histone H3, a modification with close ties to the regulation of gene expression. This review will highlight some of the recent findings on the regulation and cellular roles of H2B ubiquitylation in yeast.

A haploid affair: core histone transitions during spermatogenesis

The process of meiosis reduces a diploid cell to four haploid gametes and is accompanied by extensive recombination. Thus, the dynamics of chromatin during meiosis are significantly different than in mitotic cells. As spermatogenesis progresses, there is a widespread reorganization of the haploid genome followed by extensive DNA compaction. It has become increasingly clear that the dynamic composition of chromatin plays a critical role in the activities of enzymes and processes that act upon it. Therefore, an analysis of the role of histone variants and modifications in these processes may shed light upon the mechanisms involved and the control of chromatin structure in general. Histone variants such as histone H3.3, H2AX, and macroH2A appear to play key roles in the various stages of spermiogenesis, in addition to the specifically modulated acetylation of histone H4 (acH4), ubiquitination of histones H2A and H2B (uH2A, uH2B), and phosphorylation of histone H3 (H3p). This review will examine recent discoveries concerning the role of histone modifications and variants during meiosis and spermatogenesis.