Histone ubiquitination: triggering gene activity

Hit and run: transient deubiquitylase activity in a chromatin-remodeling complex

In this issue of Molecular Cell, Conaway and colleagues (Yao et al., 2008) provide a glimpse into an interesting mechanism to control a deubiquitylating enzyme via interaction of two complexes-the 19S proteasome regulatory particle and an ATP-dependent nucleosome remodeling complex.

Nuclear microenvironments and cancer

Nucleic acids and regulatory proteins are architecturally organized in nuclear microenvironments. The compartmentalization of regulatory machinery for gene expression, replication and repair, is obligatory for fidelity of biological control. Perturbations in the organization, assembly and integration of regulatory machinery have been functionally linked to the onset and progression of tumorigenesis. The combined application of cellular, molecular, biochemical and in vivo genetic approaches, together with structural biology, genomics, proteomics and bioinformatics, will likely lead to new approaches in cancer diagnostics and therapy.

Histone H2B monoubiquitination in the chromatin of FLOWERING LOCUS C regulates flowering time in Arabidopsis

Ubiquitination is one of many known histone modifications that regulate gene expression. Here, we examine the Arabidopsis thaliana homologs of the yeast E2 and E3 enzymes responsible for H2B monoubiquitination (H2Bub1). Arabidopsis has two E3 homologs (HISTONE MONOUBIQUITINATION1 [HUB1] and HUB2) and three E2 homologs (UBIQUITIN CARRIER PROTEIN [UBC1] to UBC3). hub1 and hub2 mutants show the loss of H2Bub1 and early flowering. By contrast, single ubc1, ubc2, or ubc3 mutants show no flowering defect; only ubc1 ubc2 double mutants, and not double mutants with ubc3, show early flowering and H2Bub1 defects. This suggests that ubc1 and ubc2 are redundant, but ubc3 is not involved in flowering time regulation. Protein interaction analysis showed that HUB1 and HUB2 interact with each other and with UBC1 and UBC2, as well as self-associating. The expression of FLOWERING LOCUS C (FLC) and its homologs was repressed in hub1, hub2, and ubc1 ubc2 mutant plants. Association of H2Bub1 with the chromatin of FLC clade genes depended on UBC1,2 and HUB1,2, as did the dynamics of methylated histones H3K4me3 and H3K36me2. The monoubiquitination of H2B via UBC1,2 and HUB1,2 represents a novel form of histone modification that is involved in flowering time regulation.

Quantitative analysis of global ubiquitination in HeLa cells by mass spectrometry

Ubiquitination regulates a host of cellular processes by labeling proteins for degradation, but also by functioning as a regulatory, nonproteolytic posttranslational modification. Proteome-wide strategies to monitor changes in ubiquitination profiles are important to obtain insight into the various cellular functions of ubiquitination. Here we describe generation of stable cell lines expressing a tandem hexahistidine-biotin tag (HB-tag) fused to ubiquitin for two-step purification of the ubiquitinated proteome under fully denaturing conditions. Using this approach we identified 669 ubiquitinated proteins from HeLa cells, including 44 precise ubiquitin attachment sites on substrates and all seven possible ubiquitin chain-linkage types. To probe the dynamics of ubiquitination in response to perturbation of the ubiquitin/proteasome pathway, we combined ubiquitin profiling with quantitative mass spectrometry using the stable isotope labeling with amino acids in cell culture (SILAC) strategy. We compared untreated cells and cells treated with the proteasome inhibitor MG132 to identify ubiquitinated proteins that are targeted to the proteasome for degradation. A number of proteasome substrates were identified. In addition, the quantitative approach allowed us to compare proteasome targeting by different ubiquitin chain topologies in vivo. The tools and strategies described here can be applied to detect changes in ubiquitination dynamics in response to various changes in growth conditions and cellular stress and will contribute to our understanding of the ubiquitin/proteasome system.

Just the FACTs: histone H2B ubiquitylation and nucleosome dynamics

In this issue of Molecular Cell, Fleming et al. (2008) show that histone H2B ubiquitylation and FACT function interdependently to facilitate nucleosome reassembly during transcription elongation, thereby demonstrating that histone posttranslational modifications can provide important but transient transcriptional signaling cues.

Protein modifications in transcription elongation

Posttranslational modifications (PTMs) of proteins play essential roles in regulating signaling, protein-protein modifications and subcellular localization. In this review, we focus on posttranslational modification of histones and RNA polymerase II (RNAPII) and their roles in gene transcription. A survey of the basic features of PTMs is provided followed by a more detailed account of how PTMs on histones and RNAPII regulate transcription in the model organism Saccharomyces cerevisiae. We emphasize the interconnections between histone and RNAPII PTMs and speculate upon the larger role PTMs have in regulating protein function in the cell.

The role of histone H2A and H2B post-translational modifications in transcription: a genomic perspective

In eukaryotic cells, the genome is packaged with histones H2A, H2B, H3, and H4 to form nucleosomes. Each of the histone proteins is extensively post-translationally modified, particularly in the flexible N-terminal histone tail domains. Curiously, while post-translational modifications in histone H3 and H4 have been extensively studied, relatively little is known about post-translational modifications in the N-terminal domains of histone H2A and H2B. In this review, we will summarize current knowledge of post-translational modifications in the N-terminal domains of histone H2A and H2B, and the histone variant H2AZ. We will examine the distribution of these modifications in genomic chromatin, and the function of these modifications in transcription.

Zinc-finger UBPs: regulators of deubiquitylation

Deubiquitylating enzymes have key regulatory roles in multiple cellular processes by mediating ubiquitin removal and processing. The ubiquitin-specific processing proteases (USPs) represent the largest subclass of deubiquitylases. Recently, several USPs that recognize the monoubiquitylated histones H2A and/or H2B have been identified. Among these enzymes, three USPs contain a zinc-finger ubiquitin-specific protease (ZnF-UBP) domain, indicating that this domain plays a crucial part in regulating their activity. To address the putative function of this domain, we systematically analysed and aligned yeast and human ZnF-UBP-containing proteins. By complementing our analysis with structural and functional data, we present a classification of the different ZnF-UBP-containing proteins and a model for their regulation.