The highly conserved N-terminal domains of histones H3 and H4 are required for normal cell cycle progression

Localization of Drosophila CENP-A to non-centromeric sites depends on the NuRD complex

Centromere function requires the presence of the histone H3 variant CENP-A in most eukaryotes. The precise localization and protein amount of CENP-A are crucial for correct chromosome segregation, and misregulation can lead to aneuploidy. To characterize the loading of CENP-A to non-centromeric chromatin, we utilized different truncation- and localization-deficient CENP-A mutant constructs in Drosophila melanogaster cultured cells, and show that the N-terminus of Drosophila melanogaster CENP-A is required for nuclear localization and protein stability, and that CENP-A associated proteins, rather than CENP-A itself, determine its localization. Co-expression of mutant CENP-A with its loading factor CAL1 leads to exclusive centromere loading of CENP-A whereas co-expression with the histone-binding protein RbAp48 leads to exclusive non-centromeric CENP-A incorporation. Mass spectrometry analysis of non-centromeric CENP-A interacting partners identified the RbAp48-containing NuRD chromatin remodeling complex. Further analysis confirmed that NuRD is required for ectopic CENP-A incorporation, and RbAp48 and MTA1-like subunits of NuRD together with the N-terminal tail of CENP-A mediate the interaction. In summary, our data show that Drosophila CENP-A has no intrinsic specificity for centromeric chromatin and utilizes separate loading mechanisms for its incorporation into centromeric and ectopic sites. This suggests that the specific association and availability of CENP-A interacting factors are the major determinants of CENP-A loading specificity.

The origin of chromosomal histones in a 30S ribosomal protein

Histones are genes that regulate chromatin structure. They are present in both eukaryotes and archaea, and form nucleosomes with DNA, but their exact evolutionary origins have hitherto remained a mystery. A longstanding hypothesis is that they have precursors in ribosomal proteins with whom they share much in common in terms of size and chemistry. By examining the proteome of the Asgard archaeon, Lokiarchaeum, the most conserved of all the histones, H4, is found to plausibly be homologous with one of its 30S ribosomal proteins, RPS6. This is based on both sequence identity and statistical analysis. The N-terminal tail, containing key sites involved in post-translational modifications, is notably present in the precursor gene. Although other archaeal groups possess similar homologs, these are not as close to H4 as the one found in Lokiarchaeum. The other core histones, H2A, H2B and H3, appear to have also evolved from the same ribosomal protein. Parts of H4 are also similar to another ribosomal protein, namely RPS15, suggesting that the ancestral precursor could have resembled both. Eukaryotic histones, in addition, appear to have an independent origin to that of their archaeal counterparts that evolved from similar, but still different, 30S subunit proteins, some of which are much more like histones in terms of their physical structure. The nucleosome may, therefore, be not only of archaeal but also of ribosomal origin.

The amino-terminal tails of histones H2A and H3 coordinate efficient base excision repair, DNA damage signaling and postreplication repair in Saccharomyces cerevisiae

Histone amino-terminal tails (N-tails) are required for cellular resistance to DNA damaging agents; therefore, we examined the role of histone N-tails in regulating DNA damage response pathways in Saccharomyces cerevisiae. Combinatorial deletions reveal that the H2A and H3 N-tails are important for the removal of MMS-induced DNA lesions due to their role in regulating the basal and MMS-induced expression of DNA glycosylase Mag1. Furthermore, overexpression of Mag1 in a mutant lacking the H2A and H3 N-tails rescues base excision repair (BER) activity but not MMS sensitivity. We further show that the H3 N-tail functions in the Rad9/Rad53 DNA damage signaling pathway, but this function does not appear to be the primary cause of MMS sensitivity of the double tailless mutants. Instead, epistasis analyses demonstrate that the tailless H2A/H3 phenotypes are in the RAD18 epistasis group, which regulates postreplication repair. We observed increased levels of ubiquitylated PCNA and significantly lower mutation frequency in the tailless H2A/H3 mutant, indicating a defect in postreplication repair. In summary, our data identify novel roles of the histone H2A and H3 N-tails in (i) regulating the expression of a critical BER enzyme (Mag1), (ii) supporting efficient DNA damage signaling and (iii) facilitating postreplication repair.

Subnucleosomal structures and nucleosome asymmetry across a genome

Genes are packaged into nucleosomal arrays, each nucleosome typically having two copies of histones H2A, H2B, H3, and H4. Histones have distinct posttranslational modifications, variant isoforms, and dynamics. Whether each histone copy within a nucleosome has distinct properties, particularly in relation to the direction of transcription, is unknown. Here we use chromatin immunoprecipitation-exonuclease (ChIP-exo) to resolve the organization of individual histones on a genomic scale. We detect widespread subnucleosomal structures in dynamic chromatin, including what appear to be half-nucleosomes consisting of one copy of each histone. We also detect interactions of H3 tails with linker DNA between nucleosomes, which may be negatively regulated by methylation of H3K36. Histone variant H2A.Z is enriched on the promoter-distal half of the +1 nucleosome, whereas H2BK123 ubiquitylation and H3K9 acetylation are enriched on the promoter-proximal half in a transcription-linked manner. Subnucleosome asymmetries might serve as molecular beacons that guide transcription.

An unconventional antimicrobial protein histone from freshwater prawn Macrobrachium rosenbergii: analysis of immune properties

In this study, we have reported the first histone characterized at molecular level from freshwater prawn Macrobrachium rosenbergii (MrHis). A full length cDNA of MrHis (751 base pairs) was identified from an established M. rosenbergii cDNA library using GS-FLX technique. It encodes 137 amino acid residues with a calculated molecular mass of 15 kDa and an isoelectric point of 10.5. MrHis peptide contains a histone H2A signature between 21 and 27 amino acids. Homologous analysis showed that MrHis had a significant sequence identity (99%) with other known histone H2A groups especially from Penaeus monodon. Phylogenetic analysis of MrHis showed a strong relationship with other amino acid sequences from histone H2A arthropod groups. Further phylogenetic analysis showed that the MrHis belongs to histone H2A superfamily and H2A1A sub-family. Secondary structure of MrHis showed that the protein contains 50.36% α-helical region and 49.64% coils. The 3D model of MrHis was predicted by I-Tasser program and the model was evaluated for quality analysis including C-score analysis, Ramachandran plot analysis and RMSD analysis. The surface view analysis of MrHis showed the active domain at the N terminal. The antimicrobial property of MrHis protein was confirmed by the helical structure and the total hydrophobic surface along with its net charge. The MFE of the predicted RNA structure of MrHis is -128.62 kcal/mol, shows its mRNA stability. Schiffer-Edmundson helical wheel analysis of the N-terminal of MrHis showed a perfect amphipathic nature of the peptide. Significantly (P < 0.05) highest gene expression was noticed in the hemocyte and is induced with viral (WSBV and MrNV) and bacteria (A eromonas hydrophila and Vibrio harveyi) infections. The coding sequence of recombinant MrHis protein was expressed in a pMAL vector and purified to study the antimicrobial properties. The recombinant product showed antimicrobial activity against both Gram negative and Gram positive bacteria. In this study, the recombinant MrHis protein displayed antimicrobial activity in its entirety. Hence, it is possible to suggest that the activity may be due to the direct defense role of histone or its N-terminal antimicrobial property. However, this remains to be verified by detailed investigations.

Protein arginine methylation in Saccharomyces cerevisiae

Recent research has implicated arginine methylation as a major regulator of cellular processes, including transcription, translation, nucleocytoplasmic transport, signalling, DNA repair, RNA processing and splicing. Arginine methylation is evolutionarily conserved, and it is now thought that it may rival other post-translational modifications such as phosphorylation in terms of its occurrence in the proteome. In addition, multiple recent examples demonstrate an exciting new theme: the interplay between methylation and other post-translational modifications such as phosphorylation. In this review, we summarize our current understanding of arginine methylation and the recent advances made, with a focus on the lower eukaryote Saccharomyces cerevisiae. We cover the types of methylated proteins, their responsible methyltransferases, where and how the effects of arginine methylation are seen in the cell, and, finally, discuss the conservation of the biological function of methylarginines between S. cerevisiae and mammals.

The adjustable nucleosome: an epigenetic signaling module

This review examines the proposition that the nucleosome, in addition to its role as a DNA packaging device, is a signaling module through which changing environmental and metabolic conditions can influence genomic functions. The role of enzyme-catalyzed post-translational modifications of the core histones is critically assessed, leading to the conclusion that they play varied, often crucial and sometimes causative roles in this signaling process.

Histone chaperones link histone nuclear import and chromatin assembly

Histone chaperones are proteins that shield histones from nonspecific interactions until they are assembled into chromatin. After their synthesis in the cytoplasm, histones are bound by different histone chaperones, subjected to a series of posttranslational modifications and imported into the nucleus. These evolutionarily conserved modifications, including acetylation and methylation, can occur in the cytoplasm, but their role in regulating import is not well understood. As part of histone import complexes, histone chaperones may serve to protect the histones during transport, or they may be using histones to promote their own nuclear localization. In addition, there is evidence that histone chaperones can play an active role in the import of histones. Histone chaperones have also been shown to regulate the localization of important chromatin modifying enzymes. This review is focused on the role histone chaperones play in the early biogenesis of histones, the distinct cytoplasmic subcomplexes in which histone chaperones have been found in both yeast and mammalian cells and the importins/karyopherins and nuclear localization signals that mediate the nuclear import of histones. We also address the role that histone chaperone localization plays in human disease. This article is part of a Special Issue entitled: Histone chaperones and chromatin assembly.

Replication-coupled chromatin assembly of newly synthesized histones: distinct functions for the histone tail domains

The maintenance of the genome during replication requires the assembly of nucleosomes with newly synthesized histones. Achieving the deposition of newly synthesized histones in chromatin implies their transport from the cytoplasm to the nucleus at the replication sites. Several lines of evidence have revealed critical functions of the histone tail domains in these conserved cellular processes. In this review, we discuss the role of the amino termini of the nucleosome building blocks, H2A/H2B and H3/H4, in different model systems. The experimental data showed that H2A/H2B tails and H3/H4 tails display distinct functions in nuclear import and chromatin assembly. Furthermore, we describe recent studies exploiting the unique properties of the slime mold, Physarum polycephalum , that have advanced understanding of the function of the highly conserved replication-dependent diacetylation of H4.

Activator-independent transcription of Snf1-dependent genes in mutants lacking histone tails

Transcriptional regulation of Snf1-dependent genes occurs in part by histone-acetylation-dependent binding of the transcription factor Adr1. Analysis of previously published microarray data indicated unscheduled transcription of a large number of Snf1- and Adr1-dependent genes when either the histone H3 or H4 tail was deleted. Quantitative real-time PCR confirmed that the tails were important to preserve stringent transcriptional repression of Snf1-dependent genes when glucose was present. The absence of the tails allowed Adr1 and RNA Polymerase II to bind promoters in normally inhibitory conditions. The promoters escaped glucose repression to a limited extent and the weak constitutive ADH2 transcription induced by deletion of the histone tails was transcription factor- and Snf1-independent. These effects were apparently due to a permissive chromatin structure that allowed transcription in the absence of repression mediated by the histone tails. Deleting REG1, and thus activating Snf1 in the H3 tail mutant enhanced transcription in repressing conditions, indicating that Snf1 and the H3 tail influence transcription independently. Deleting REG1 in the histone H4 tail mutant appeared to be lethal, even in the absence of Snf1, suggesting that Reg1 and the H4 tail have redundant functions that are important for cell viability.

H4 replication-dependent diacetylation and Hat1 promote S-phase chromatin assembly in vivo

This study examined the function of H3 and H4 tail domains in replication-dependent chromatin assembly. Results show distinct functions of H3 and H4 tails in nuclear import and chromatin assembly. Further investigations show that H4 diacetylation is essential but not sufficient for nuclear import, as preventing Hat1 binding impedes histone transport in nuclei.

While specific posttranslational modification patterns within the H3 and H4 tail domains are associated with the S-phase, their actual functions in replication-dependent chromatin assembly have not yet been defined. Here we used incorporation of trace amounts of recombinant proteins into naturally synchronous macroplasmodia of Physarum polycephalum to examine the function of H3 and H4 tail domains in replication-coupled chromatin assembly. We found that the H3/H4 complex lacking the H4 tail domain was not efficiently recovered in nuclei, whereas depletion of the H3 tail domain did not impede nuclear import but chromatin assembly failed. Furthermore, our results revealed that the proper pattern of acetylation on the H4 tail domain is required for nuclear import and chromatin assembly. This is most likely due to binding of Hat1, as coimmunoprecipitation experiments showed Hat1 associated with predeposition histones in the cytoplasm and with replicating chromatin. These results suggest that the type B histone acetyltransferase assists in shuttling the H3/H4 complex from cytoplasm to the replication forks.

How eukaryotic genes are transcribed

Regulation of eukaryotic gene expression is far more complex than one might have imagined 30 years ago. However, progress towards understanding gene regulatory mechanisms has been rapid and comprehensive, which has made the integration of detailed observations into broadly connected concepts a challenge. This review attempts to integrate the following concepts: (1) a well-defined organization of nucleosomes and modification states at most genes; (2) regulatory networks of sequence-specific transcription factors; (3) chromatin remodeling coupled to promoter assembly of the general transcription factors and RNA polymerase II; and (4) phosphorylation states of RNA polymerase II coupled to chromatin modification states during transcription. The wealth of new insights arising from the tools of biochemistry, genomics, cell biology, and genetics is providing a remarkable view into the mechanics of gene regulation.

What controls nucleosome positions?

The DNA of eukaryotic genomes is wrapped in nucleosomes, which strongly distort and occlude the DNA from access to most DNA-binding proteins. An understanding of the mechanisms that control nucleosome positioning along the DNA is thus essential to understanding the binding and action of proteins that carry out essential genetic functions. New genome-wide data on in vivo and in vitro nucleosome positioning greatly advance our understanding of several factors that can influence nucleosome positioning, including DNA sequence preferences, DNA methylation, histone variants and post-translational modifications, higher order chromatin structure, and the actions of transcription factors, chromatin remodelers and other DNA-binding proteins. We discuss how these factors function and ways in which they might be integrated into a unified framework that accounts for both the preservation of nucleosome positioning and the dynamic nucleosome repositioning that occur across biological conditions, cell types, developmental processes and disease.

RSC regulates nucleosome positioning at Pol II genes and density at Pol III genes

Nucleosomes can restrict the access of transcription factors to chromatin. RSC is a SWI/SNF-family chromatin-remodeling complex from yeast that repositions and ejects nucleosomes in vitro. Here, we examined these activities and their importance in vivo. We utilized array-based methods to examine nucleosome occupancy and positioning at more than 200 locations in the genome following the controlled destruction of the catalytic subunit of RSC, Sth1. Loss of RSC function caused pronounced and general reductions in new transcription from Pol I, II, and III genes. At Pol III genes, Sth1 loss conferred a general reduction in RNA Pol III occupancy and a gain in nucleosome density. Notably at the one Pol III gene examined, histone restoration was partly replication-dependent. In contrast, at Pol II promoters we observed primarily single nucleosome changes, including movement. Importantly, alterations near the transcription start site were more common at RSC-occupied promoters than at non-occupied promoters. Thus, RSC action affects both nucleosome density and positioning in vivo, but applies these remodeling modes differently at Pol II and Pol III genes.

Histone proteomics and the epigenetic regulation of nucleosome mobility

Chromatin structure plays a vital role in the transmission of heritable gene expression patterns. The recent application of mass spectrometry to histone biology provides several striking insights into chromatin regulation. The continuing identification of new histone post-translational modifications is revolutionizing the ways in which we think about how access to genomic DNA is controlled. While post-translational modifications of the flexible histone tails continue to be an active area of investigation, the recent discovery of multiple modifications in the structured globular domains of histones provides new insights into how the nucleosome works. Recent experiments underscore the importance of a subgroup of these modifications: those that regulate histone-DNA interactions on the lateral surface of the nucleosome. This information highlights an emerging new paradigm in chromatin control, that of the epigenetic regulation of nucleosome mobility.

Orchestration of chromatin-based processes: mind the TRRAP

Chromatin modifications at core histones including acetylation, methylation, phosphorylation and ubiquitination play an important role in diverse biological processes. Acetylation of specific lysine residues within the N terminus tails of core histones is arguably the most studied histone modification; however, its precise roles in different cellular processes and how it is disrupted in human diseases remain poorly understood. In the last decade, a number of histone acetyltransferases (HATs) enzymes responsible for histone acetylation, has been identified and functional studies have begun to unravel their biological functions. The activity of many HATs is dependent on HAT complexes, the multiprotein assemblies that contain one HAT catalytic subunit, adapter proteins, several other molecules of unknown function and a large protein called TRansformation/tRanscription domain-Associated Protein (TRRAP). As a common component of many HAT complexes, TRRAP appears to be responsible for the recruitment of these complexes to chromatin during transcription, replication and DNA repair. Recent studies have shed new light on the role of TRRAP in HAT complexes as well as mechanisms by which it mediates diverse cellular processes. Thus, TRRAP appears to be responsible for a concerted and context-dependent recruitment of HATs and coordination of distinct chromatin-based processes, suggesting that its deregulation may contribute to diseases. In this review, we summarize recent developments in our understanding of the function of TRRAP and TRRAP-containing HAT complexes in normal cellular processes and speculate on the mechanism underlying abnormal events that may lead to human diseases such as cancer.

2. Chromatin assembly with H3 histones: full throttle down multiple pathways

The typical eukaryotic genome packages roughly 6 feet of DNA into a nucleus about 5 mum in diameter, yet this compaction blocks access to the DNA. At the first level of compaction, DNA is wrapped around octamers of core histone proteins to form arrays of nucleosomes. Nucleosomes are sufficient to block access to DNA, and cells must therefore manipulate nucleosomes in the course of activating the genome. Dramatic progress has been made in understanding the mechanisms by which nucleosomes are manipulated. In addition to the major core histones, most eukaryotic genomes also encode additional variant histones, which have some structural similarity. These are targeted to specific loci by coupling specialized nucleosome assembly pathways to DNA replication, transcription, or to developmental processes. We review evidence that nucleosome assembly pathways are interlinked with histone-modification systems, and may thereby perpetuate epigenetic chromatin states.

Three-dimensional structure of the bacterial multidrug transporter EmrE shows it is an asymmetric homodimer

The small multidrug resistance family of transporters is widespread in bacteria and is responsible for bacterial resistance to toxic aromatic cations by proton-linked efflux. We have determined the three-dimensional (3D) structure of the Escherichia coli multidrug transporter EmrE by electron cryomicroscopy of 2D crystals, including data to 7.0 A resolution. The structure of EmrE consists of a bundle of eight transmembrane alpha-helices with one substrate molecule bound near the centre. The substrate binding chamber is formed from six helices and is accessible both from the aqueous phase and laterally from the lipid bilayer. The most remarkable feature of the structure of EmrE is that it is an asymmetric homodimer. The possible arrangement of the two polypeptides in the EmrE dimer is discussed based on the 3D density map.

Centromere Silencing and Function in Fission Yeast Is Governed by the Amino Terminus of Histone H3

BACKGROUND

Centromeric domains often consist of repetitive elements that are assembled in specialized chromatin, characterized by hypoacetylation of histones H3 and H4 and methylation of lysine 9 of histone H3 (K9-MeH3). Perturbation of this underacetylated state by transient treatment with histone deacetylase inhibitors leads to defective centromere function, correlating with delocalization of the heterochromatin protein Swi6/HP1. Likewise, deletion of the K9-MeH3 methyltransferase Clr4/Suvar39 causes defective chromosome segregation. Here, we create fission yeast strains retaining one histone H3 and H4 gene; the creation of these strains allows mutation of specific N-terminal tail residues and their role in centromeric silencing and chromosome stability to be investigated.

RESULTS

Reduction of H3/H4 gene dosage to one-third does not affect cell viability or heterochromatin formation. Mutation of lysines 9 or 14 or serine 10 within the amino terminus of histone H3 impairs centromere function, leading to defective chromosome segregation and Swi6 delocalization. Surprisingly, silent centromeric chromatin does not require the conserved lysine 8 and 16 residues of histone H4.

CONCLUSIONS

To date, mutation of conserved N-terminal residues in endogenous histone genes has only been performed in budding yeast, which lacks the Clr4/Suvar39 histone methyltransferase and Swi6/HP1. We demonstrate the importance of conserved residues within the histone H3 N terminus for the maintenance of centromeric heterochromatin in fission yeast. In sharp contrast, mutation of two conserved lysines within the histone H4 tail has no impact on the integrity of centromeric heterochromatin. Our data highlight the striking divergence between the histone tail requirements for the fission yeast and budding yeast silencing pathways.

Site-specific loss of acetylation upon phosphorylation of histone H3

Post-translational modification of histones is a central aspect of gene regulation. Emerging data indicate that modification at one site can influence modification of a second site. As one example, histone H3 phosphorylation at serine 10 (Ser(10)) facilitates acetylation of lysine 14 (Lys(14)) by Gcn5 in vitro (, ). In vivo, phosphorylation of H3 precedes acetylation at certain promoters. Whether H3 phosphorylation globally affects acetylation, or whether it affects all acetylation sites in H3 equally, is not known. We have taken a genetic approach to this question by mutating Ser(10) in H3 to fix either a negative or a neutral charge at this position, followed by analysis of the acetylation states of the mutant histones using site-specific antibodies. Surprisingly, we find that conversion of Ser(10) to glutamate (S10E) or aspartate (S10D) causes almost complete loss of H3 acetylation at lysine 9 (Lys(9)) in vivo. Acetylation of Lys(9) is also significantly reduced in cells bearing mutations in the Glc7 phosphatase that increase H3 phosphorylation levels. Mutation of Ser(10) in H3 and the concomitant loss of Lys(9) acetylation has minimal effects on expression of a Gcn5-dependent reporter gene. However, synergistic growth defects are observed upon loss of GCN5 in cells bearing H3 Ser(10) mutations that are reminiscent of delays in G(2)/M progression caused by combined loss of GCN5 and acetylation site mutations. Together these results demonstrate that H3 phosphorylation directly causes site-specific and opposite changes in acetylation levels of two residues within this histone, Lys(9) and Lys(14), and they highlight the importance of these histone modifications to normal cell functions.

Chromatin assembly. Cooperation between histone chaperones and ATP-dependent nucleosome remodeling machines

Chromatin is a highly dynamic structure that plays an essential role in regulating all nuclear processes that utilize the DNA template including DNA repair, replication, transcription and recombination. Thus, the mechanisms by which chromatin structures are assembled and modified are questions of broad interest. This minireview will focus on two groups of proteins: (a) histone chaperones and (b) ATP-dependent chromatin remodeling machines, that co-operate to assemble DNA and histone proteins into chromatin. The current understanding of how histone chaperones and ATP-dependent remodeling machines coordinately assemble chromatin in vitro will be discussed, together with the growing body of genetic evidence that supports the role of histone chaperones in the cell.

Replication of minichromosomes in Saccharomyces cerevisiae is sensitive to histone gene copy number and strain ploidy

We have characterized a defect in the mitotic transmission of plasmid minichromosomes in yeast strains deleted for the more highly expressed pair of histone H3 and H4 genes. Several observations indicate that an impairment in DNA replication contributes to the decrease in minichromosome stability. First, the maintenance of ARS plasmids that lack centromeres was also defective. Second, the addition of multiple ARS elements suppressed the defect in plasmid maintenance. Third, a synergistic increase in plasmid loss rate was seen when a plasmid containing an inefficient mutated ARS was tested in a strain deleted for histone genes, implying an interaction between ARS activity and the histone gene deletion. These results support the existence of a histone-dependent step in the initiation of DNA replication. We find that the stability of native chromosomes is not affected in strains deleted for histone genes. We propose that reduced histone H3 and H4 protein decreases the efficiency of initiation at ARS elements on plasmids and chromosomes, but that the presence of multiple origins on chromosomes compensates for the reduced efficiency. We find that decreased minichromosome stability is suppressed by increases in strain ploidy. The greater stability due to ploidy increases is not due to a relative increase in the expression of histone genes. We discuss models for the effect of strain ploidy on minichromosome maintenance.

The anatomy of a hypoxic operator in Saccharomyces cerevisiae

Aerobic repression of the hypoxic genes of Saccharomyces cerevisiae is mediated by the DNA-binding protein Rox1 and the Tup1/Ssn6 general repression complex. To determine the DNA sequence requirements for repression, we carried out a mutational analysis of the consensus Rox1-binding site and an analysis of the arrangement of the Rox1 sites into operators in the hypoxic ANB1 gene. We found that single base pair substitutions in the consensus sequence resulted in lower affinities for Rox1, and the decreased affinity of Rox1 for mutant sites correlated with the ability of these sites to repress expression of the hypoxic ANB1 gene. In addition, there was a general but not complete correlation between the strength of repression of a given hypoxic gene and the compliance of the Rox1 sites in that gene to the consensus sequence. An analysis of the ANB1 operators revealed that the two Rox1 sites within an operator acted synergistically in vivo, but that Rox1 did not bind cooperatively in vitro, suggesting the presence of a higher order repression complex in the cell. In addition, the spacing or helical phasing of the Rox1 sites was not important in repression. The differential repression by the two operators of the ANB1 gene was found to be due partly to the location of the operators and partly to the sequences between the two Rox1-binding sites in each. Finally, while Rox1 repression requires the Tup1/Ssn6 general repression complex and this complex has been proposed to require the aminoterminal regions of histones H3 and H4 for full repression of a number of genes, we found that these regions were dispensable for ANB1 repression and the repression of two other hypoxic genes.

Sth1p, a Saccharomyces cerevisiae Snf2p/Swi2p homolog, is an essential ATPase in RSC and differs from Snf/Swi in its interactions with histones and chromatin-associated proteins

The essential Sth1p is the protein most closely related to the conserved Snf2p/Swi2p in Saccharomyces cerevisiae. Sth1p purified from yeast has a DNA-stimulated ATPase activity required for its function in vivo. The finding that Sth1p is a component of a multiprotein complex capable of ATP-dependent remodeling of the structure of chromatin (RSC) in vitro, suggests that it provides RSC with ATP hydrolysis activity. Three sth1 temperature-sensitive mutations map to the highly conserved ATPase/helicase domain and have cell cycle and non-cell cycle phenotypes, suggesting multiple essential roles for Sth1p. The Sth1p bromodomain is required for wild-type function; deletion mutants lacking portions of this region are thermosensitive and arrest with highly elongated buds and 2C DNA content, indicating perturbation of a unique function. The pleiotropic growth defects of sth1-ts mutants imply a requirement for Sth1p in a general cellular process that affects several metabolic pathways. Significantly, an sth1-ts allele is synthetically sick or lethal with previously identified mutations in histones and chromatin assembly genes that suppress snf/swi, suggesting that RSC interacts differently with chromatin than Snf/Swi. These results provide a framework for understanding the ATP-dependent RSC function in modeling chromatin and its connection to the cell cycle.

Melatonin decreases mRNA for histone H4 in thymus of young rats

The antiproliferative properties of melatonin have been previously demonstrated for several normal and tumoral tissues. In a recent report we have shown that melatonin is able to inhibit programmed cell death in thymus both, in vivo and in vitro. Given that other authors have related programmed cell death and cell proliferation and that no previous reports on melatonin and cell division exist on thymus, we decide to study the possible antiproliferative effect of melatonin in this organ measured as the levels of mRNA for the histone H4. We found that melatonin inhibits cell division on thymus when administered chronically both, at high (500 microg/body weight) and low (50 microg/body weight) dose. We also found a circadian rhythm of the mRNA for histone H4, opposed to the one previously described for melatonin, supporting the negative regulation by this hormone of cell division on thymus. A single dose of melatonin (50 microg/body weight) was not able to decrease the levels of mRNA for H4 in the time-points studied but after two hours of its administration. Finally, we report the inhibitory effect of melatonin in the cell proliferation of Harderian gland, brain, lung and kidney.

Genetic dissection of histone function

Mutational analysis is an essential tool for understanding the functions of genes within a living organism. The budding yeast Saccharomyces cerevisiae provides an excellent model system for dissecting the genetics of histone function at the molecular and cellular levels. A simple gene organization, plus a wide variety of genetic strategies, makes it possible to directly manipulate a specific histone gene in vitro and then examine the expression of mutant alleles in vivo. Recent methods for manipulating the yeast histone genes have been designed to facilitate both side-directed analysis of structure/function relationships and unbiased screens targeted at specific functional pathways. The conservation of histone and nucleosome structure throughout evolution means that the principles discovered through genetic studies in yeast will be broadly applicable to the chromatin of more complex eukaryotes.

Interactions of transcriptional regulators with histones

Tremendous advances in the study of chromatin have revealed new classes of transcriptional regulators distinct from classical DNA-binding proteins. Many previously described transcription factors, coactivators, and adaptors are regulators of chromatin structure, interacting directly with the core histone proteins or with nucleosomes. This review describes a method used by our laboratory to examine the interactions of regulatory proteins with the core histone proteins. Far-Western analysis uses a protein probe to detect interactions with histones immobilized on membranes. Variations of this technique can detect the acetylation state of the interacting histones and whether the interaction occurs through the globular domain or the amino-terminal "tail" domain. In addition, we discuss complementary techniques for confirming histone-regulatory protein interactions.

Temperature-Sensitive Plant Cells with Shunted Indole-3-Acetic Acid Conjugation

Cells of henbane (Hyoscyamus muticus L.) grow indefinitely in culture without exogenous auxin. Cells of its temperature-sensitive variant XIIB2 grow like the wild type at 26[deg]C but die rapidly at 33[deg]C unless auxin is added to the medium. Despite this temperature-sensitive auxin auxotrophy, XIIB2 produces wild-type amounts of indole-3-acetic acid (IAA). IAA is the predominant auxin and is important for plant growth and development. Since the IAA production of the variant is functional, we investigated whether the synthesis or degradation of IAA metabolites, possibly active auxins themselves, is altered. The IAA metabolites were IAA-aspartate (IAAsp) and IAA-glucose. The wild type converted IAA mainly to IAAsp, whereas the variant produced mainly IAA-glucose. Exogenous auxin corrected the shunted IAA metabolism of the variant. The half-life of labeled IAAsp in the variant was reduced 21-fold, but in the presence of exogenous auxin it was not different from the wild type. The temperature sensitivity of XIIB2 was also corrected by supplying IAAsp. Pulse-chase experiments revealed that henbane rapidly metabolizes IAAsp to compounds not identical to IAA. The data show that the variant XIIB2 is a useful tool to study the function of IAA conjugates to challenge the popular hypothesis that IAA conjugates are merely slow-release storage forms of IAA.

Progression into the first meiotic division is sensitive to histone H2A-H2B dimer concentration in Saccharomyces cerevisiae

The yeast Saccharomyces cerevisiae contains two genes for histone H2A and two for histone H2B located in two divergently transcribed gene pairs: HTA1-HTB1 and HTA2-HTB2. Diploid strains lacking HTA1-HTB1 (hta1-htb1 delta/hta1-htb1 delta, HTA2-HTB2/HTA2-HTB2) grow vegetatively, but will not sporulate. This sporulation phenotype results from a partial depletion of H2A-H2B dimers. Since the expression patterns of HTA1-HTB1 and HTA2-HTB2 are similar in mitosis and meiosis, the sporulation pathway is therefore more sensitive than the mitotic cycle to depletion of H2A-H2B dimers. After completing premeiotic DNA replication, commitment to meiotic recombination, and chiasma resolution, the hta1-htb1 delta/hta1-htb1 delta, HTA2-HTB2/HTA2-HTB2 mutant arrests before the first meiotic division. The arrest is not due to any obvious disruptions in spindle pole bodies or microtubules. The meiotic block is not bypassed in backgrounds homozygous for spo13, rad50 delta, or rad9 delta mutations, but is bypassed in the presence of hydroxyurea, a drug known to inhibit DNA chain elongation. We hypothesize that the deposition of H2A-H2B dimers in the mutant is unable to keep pace with the replication fork, thereby leading to a disruption in chromosome structure that interferes with the meiotic divisions.

Nucleosome assembly by a complex of CAF-1 and acetylated histones H3/H4

Chromatin assembly factor 1 (CAF-1) assembles nucleosomes in a replication-dependent manner. The small subunit of CAF-1 (p48) is a member of a highly conserved subfamily of WD-repeat proteins. There are at least two members of this subfamily in both human (p46 and p48) and yeast cells (Hat2p, a subunit of the B-type H4 acetyltransferase, and Msi1p). Human p48 can bind to histone H4 in the absence of CAF-1 p150 and p60. p48, also a known subunit of a histone deacetylase, copurifies with a chromatin assembly complex (CAC), which contains the three subunits of CAF-1 (p150, p60, p48) and H3 and H4, and promotes DNA replication-dependent chromatin assembly. CAC histone H4 exhibits a novel pattern of lysine acetylation that overlaps with, but is distinct from, that reported for newly synthesized H4 isolated from nascent chromatin. Our data suggest that CAC is a key intermediate of the de novo nucleosome assembly pathway and that the p48 subunit participates in other aspects of histone metabolism.

The major cytoplasmic histone acetyltransferase in yeast: links to chromatin replication and histone metabolism

We have isolated the predominant cytoplasmic histone acetyltransferase activity from Saccharomyces cerevisiae. This enzyme acetylates the lysine at residue 12 of free histone H4 but does not modify histone H4 when packaged in chromatin. The activity contains two proteins, Hat1p and Hat2p. Hat1p is the catalytic subunit of the histone acetyltransferase and has an intrinsic substrate specificity that modifies lysine in the recognition sequence GXGKXG. The specificity of the enzyme in the yeast cytoplasm is restricted relative to recombinant Hat1p suggesting that it is negatively regulated in vivo. Hat2p, which is required for high affinity binding of the acetyltransferase to histone H4, is highly related to Rbap48, which is a subunit of the chromatin assembly factor, CAF-1, and copurifies with the human histone deacetylase HD1. We propose that the Hat2p/Rbap48 family serve as escorts of histone metabolism enzymes to facilitate their interaction with histone H4.

Histone H3 amino terminus is required for telomeric and silent mating locus repression in yeast

Heterochromatin is a cytologically visible form of condensed chromatin capable of repressing genes in eukaryotic cells. For the yeast Saccharomyces cerevisiae, despite the absence of observable heterochromatin, there is genetic and chromatin structure data which indicate that there are heterochromatin-like repressive structures. Genes experience position effects at the silent mating loci and the telomeres, resulting in a repressed state that is inherited in an epigenetic manner. The histone H4 amino terminus is required for repression at these loci. Additional studies have indicated that the histone H3 N terminus is not important for silent mating locus repression, but redundancy of repressive elements at the silent mating loci may be responsible for masking its role. Here we report that histone H3 is required for full repression at yeast telomeres and at partially disabled silent mating loci, and that the acetylatable lysine residues of H3 play an important role in silencing.

Histone structure and function

The past year has seen major advances in our understanding of histone and nucleosome structure and function. Direct DNA mapping and thermodynamic experiments have finally provided conclusive evidence that the histones impose an altered helical pitch on the DNA as it is wrapped on the surface of the core histone octamer. Further, it is now clear that lysine acetylation in the amino-terminal domains of histones H3 and H4 can alter the topology of the DNA in chromatin and probably influence its higher-order folding. Genetic experiments reported in the past year have provided a wealth of new information on histone structure and function, including the identification of the peptide domain of histone H4 that is necessary for permanent gene repression, the confirmation that nucleosome structure is critical for centromere function, and evidence that histone acetylation plays a significant role in chromosome dynamics.