Replacement variant histone genes contain intervening sequences

Histone supply: Multitiered regulation ensures chromatin dynamics throughout the cell cycle

Mendiratta et al. review the interplay between the different regulatory layers that affect the transcription and dynamics of distinct histone H3 variants along the cell cycle.

As the building blocks of chromatin, histones are central to establish and maintain particular chromatin states associated with given cell fates. Importantly, histones exist as distinct variants whose expression and incorporation into chromatin are tightly regulated during the cell cycle. During S phase, specialized replicative histone variants ensure the bulk of the chromatinization of the duplicating genome. Other non-replicative histone variants deposited throughout the cell cycle at specific loci use pathways uncoupled from DNA synthesis. Here, we review the particular dynamics of expression, cellular transit, assembly, and disassembly of replicative and non-replicative forms of the histone H3. Beyond the role of histone variants in chromatin dynamics, we review our current knowledge concerning their distinct regulation to control their expression at different levels including transcription, posttranscriptional processing, and protein stability. In light of this unique regulation, we highlight situations where perturbations in histone balance may lead to cellular dysfunction and pathologies.

Methods for Preparing Nucleosomes Containing Histone Variants

Histone variants are key epigenetic players that regulate transcription, repair, replication, and recombination of genomic DNA. Histone variant incorporation into nucleosomes induces structural diversity of nucleosomes, consequently leading to the structural versatility of chromatin. Such chromatin diversity created by histone variants may play a central role in the epigenetic regulation of genes. Each histone variant possesses specific biochemical and physical characteristics, and thus the preparation methods are complicated. Here, we introduce the methods for the purification of human histone variants as recombinant proteins, and describe the preparation methods for histone complexes and nucleosomes containing various histone variants. We also describe the detailed method for the preparation of heterotypic nucleosomes, which may function in certain biological phenomena. These methods are useful for biochemical, structural, and biophysical studies.

The histone variant H3.3 claims its place in the crowded scene of epigenetics

Histones are evolutionarily conserved DNA-binding proteins. As scaffolding molecules, they significantly regulate the DNA packaging into the nucleus of all eukaryotic cells. As docking units, they influence the recruitment of the transcriptional machinery, thus establishing unique gene expression patterns that ultimately promote different biological outcomes. While canonical histones H3.1 and H3.2 are synthetized and loaded during DNA replication, the histone variant H3.3 is expressed and deposited into the chromatin throughout the cell cycle. Recent findings indicate that H3.3 replaces the majority of canonical H3 in non-dividing cells, reaching almost saturation levels in a time-dependent manner. Consequently, H3.3 incorporation and turnover represent an additional layer in the regulation of the chromatin landscape during aging. In this respect, work from our group and others suggest that H3.3 plays an important function in age-related processes throughout evolution. Here, we summarize the current knowledge on H3.3 biology and discuss the implications of its aberrant dynamics in the establishment of cellular states that may lead to human pathology. Critically, we review the importance of H3.3 turnover as part of epigenetic events that influence senescence and age-related processes. We conclude with the emerging evidence that H3.3 is required for proper neuronal function and brain plasticity.

Identification of the amino acid residues responsible for stable nucleosome formation by histone H3.Y

Histone H3.Y is conserved among primates. We previously reported that exogenously produced H3.Y accumulates around transcription start sites, suggesting that it may play a role in transcription regulation. The H3.Y nucleosome forms a relaxed chromatin conformation with flexible DNA ends. The H3.Y-specific Lys42 residue is partly responsible for enhancing the flexibility of the nucleosomal DNA. To our surprise, we found that H3.Y stably associates with chromatin and nucleosomes in vivo and in vitro. However, the H3.Y residues responsible for its stable nucleosome incorporation have not been identified yet. In the present study, we performed comprehensive mutational analyses of H3.Y, and determined that the H3.Y C-terminal region including amino acid residues 124-135 is responsible for its stable association with DNA. Among the H3.Y C-terminal residues, the H3.Y Met124 residue significantly contributed to the stable DNA association with the H3.Y-H4 tetramer. The H3.Y M124I mutation substantially reduced the H3.Y-H4 association in the nucleosome. In contrast, the H3.Y K42R mutation affected the nucleosome stability less, although it contributes to the flexible DNA ends of the nucleosome. Therefore, these H3.Y-specific residues, Lys42 and Met124, play different and specific roles in nucleosomal DNA relaxation and stable nucleosome formation, respectively, in chromatin.

A subset of replication-dependent histone mRNAs are expressed as polyadenylated RNAs in terminally differentiated tissues

Histone proteins are synthesized in large amounts during S-phase to package the newly replicated DNA, and are among the most stable proteins in the cell. The replication-dependent (RD)-histone mRNAs expressed during S-phase end in a conserved stem-loop rather than a polyA tail. In addition, there are replication-independent (RI)-histone genes that encode histone variants as polyadenylated mRNAs. Most variants have specific functions in chromatin, but H3.3 also serves as a replacement histone for damaged histones in long-lived terminally differentiated cells. There are no reported replacement histone genes for histones H2A, H2B or H4. We report that a subset of RD-histone genes are expressed in terminally differentiated tissues as polyadenylated mRNAs, likely serving as replacement histone genes in long-lived non-dividing cells. Expression of two genes, HIST2H2AA3 and HIST1H2BC, is conserved in mammals. They are expressed as polyadenylated mRNAs in fibroblasts differentiated in vitro, but not in serum starved fibroblasts, suggesting that their expression is part of the terminal differentiation program. There are two histone H4 genes and an H3 gene that encode mRNAs that are polyadenylated and expressed at 5- to 10-fold lower levels than the mRNAs from H2A and H2B genes, which may be replacement genes for the H3.1 and H4 proteins.

Human X-linked Intellectual Disability Factor CUL4B Is Required for Post-meiotic Sperm Development and Male Fertility

In this study, we demonstrate that an E3-ubiquitin ligase associated with human X-linked intellectual disability, CUL4B, plays a crucial role in post-meiotic sperm development. Initially, Cul4b(Δ)/Y male mice were found to be sterile and exhibited a progressive loss in germ cells, thereby leading to oligoasthenospermia. Adult Cul4b mutant epididymides also contained very low numbers of mature spermatozoa, and these spermatazoa exhibited pronounced morphological abnormalities. In post-meiotic spermatids, CUL4B was dynamically expressed and mitosis of spermatogonia and meiosis of spermatocytes both appeared unaffected. However, the spermatids exhibited significantly higher levels of apoptosis during spermiogenesis, particularly during the acrosome phase through the cap phase. Comparative proteomic analyses identified a large-scale shift between wild-type and Cul4b mutant testes during early post-meiotic sperm development. Ultrastructural pathology studies further detected aberrant acrosomes in spermatids and nuclear morphology. The protein levels of both canonical and non-canonical histones were also affected in an early spermatid stage in the absence of Cul4b. Thus, X-linked CUL4B appears to play a critical role in acrosomal formation, nuclear condensation, and in regulating histone dynamics during haploid male germ cell differentiation in relation to male fertility in mice. Thus, it is possible that CUL4B-selective substrates are required for post-meiotic sperm morphogenesis.

Tissue-specific expression of histone H3 variants diversified after species separation

Background

The selective incorporation of appropriate histone variants into chromatin is critical for the regulation of genome function. Although many histone variants have been identified, a complete list has not been compiled.

Results

We screened mouse, rat and human genomes by in silico hybridization using canonical histone sequences. In the mouse genome, we identified 14 uncharacterized H3 genes, among which 13 are similar to H3.3 and do not have human or rat counterparts, and one is similar to human testis-specific H3 variant, H3T/H3.4, and had a rat paralog. Although some of these genes were previously annotated as pseudogenes, their tissue-specific expression was confirmed by sequencing the 3′-UTR regions of the transcripts. Certain new variants were also detected at the protein level by mass spectrometry. When expressed as GFP-tagged versions in mouse C2C12 cells, some variants were stably incorporated into chromatin and the genome-wide distributions of most variants were similar to that of H3.3. Moreover, forced expression of H3 variants in chromatin resulted in alternate gene expression patterns after cell differentiation.

Conclusions

We comprehensively identified and characterized novel mouse H3 variant genes that encoded highly conserved amino acid sequences compared to known histone H3. We speculated that the diversity of H3 variants acquired after species separation played a role in regulating tissue-specific gene expression in individual species. Their biological relevance and evolutionary aspect involving pseudogene diversification will be addressed by further functional analysis.

Electronic supplementary material

The online version of this article (doi:10.1186/s13072-015-0027-3) contains supplementary material, which is available to authorized users.

Contribution of the two genes encoding histone variant h3.3 to viability and fertility in mice

Histones package DNA and regulate epigenetic states. For the latter, probably the most important histone is H3. Mammals have three near-identical H3 isoforms: canonical H3.1 and H3.2, and the replication-independent variant H3.3. This variant can accumulate in slowly dividing somatic cells, replacing canonical H3. Some replication-independent histones, through their ability to incorporate outside S-phase, are functionally important in the very slowly dividing mammalian germ line. Much remains to be learned of H3.3 functions in germ cell development. Histone H3.3 presents a unique genetic paradigm in that two conventional intron-containing genes encode the identical protein. Here, we present a comprehensive analysis of the developmental effects of null mutations in each of these genes. H3f3a mutants were viable to adulthood. Females were fertile, while males were subfertile with dysmorphic spermatozoa. H3f3b mutants were growth-deficient, dying at birth. H3f3b heterozygotes were also growth-deficient, with males being sterile because of arrest of round spermatids. This sterility was not accompanied by abnormalities in sex chromosome inactivation in meiosis I. Conditional ablation of H3f3b at the beginning of folliculogenesis resulted in zygote cleavage failure, establishing H3f3b as a maternal-effect gene, and revealing a requirement for H3.3 in the first mitosis. Simultaneous ablation of H3f3a and H3f3b in folliculogenesis resulted in early primary oocyte death, demonstrating a crucial role for H3.3 in oogenesis. These findings reveal a heavy reliance on H3.3 for growth, gametogenesis, and fertilization, identifying developmental processes that are particularly susceptible to H3.3 deficiency. They also reveal partial redundancy in function of H3f3a and H3f3b, with the latter gene being generally the most important.

The mRNP remodeling mediated by UPF1 promotes rapid degradation of replication-dependent histone mRNA

Histone biogenesis is tightly controlled at multiple steps to maintain the balance between the amounts of DNA and histone protein during the cell cycle. In particular, translation and degradation of replication-dependent histone mRNAs are coordinately regulated. However, the underlying molecular mechanisms remain elusive. Here, we investigate remodeling of stem-loop binding protein (SLBP)-containing histone mRNPs occurring during the switch from the actively translating mode to the degradation mode. The interaction between a CBP80/20-dependent translation initiation factor (CTIF) and SLBP, which is important for efficient histone mRNA translation, is disrupted upon the inhibition of DNA replication or at the end of S phase. This disruption is mediated by competition between CTIF and UPF1 for SLBP binding. Further characterizations reveal hyperphosphorylation of UPF1 by activated ATR and DNA-dependent protein kinase upon the inhibition of DNA replication interacts with SLBP more strongly, promoting the release of CTIF and eIF3 from SLBP-containing histone mRNP. In addition, hyperphosphorylated UPF1 recruits PNRC2 and SMG5, triggering decapping followed by 5'-to-3' degradation of histone mRNAs. The collective observations suggest that both inhibition of translation and recruitment of mRNA degradation machinery during histone mRNA degradation are tightly coupled and coordinately regulated by UPF1 phosphorylation.

Rapid degradation of replication-dependent histone mRNAs largely occurs on mRNAs bound by nuclear cap-binding proteins 80 and 20

The translation of mammalian messenger RNAs (mRNAs) can be driven by either cap-binding proteins 80 and 20 (CBP80/20) or eukaryotic translation initiation factor (eIF)4E. Although CBP80/20-dependent translation (CT) is known to be coupled to an mRNA surveillance mechanism termed nonsense-mediated mRNA decay (NMD), its molecular mechanism and biological role remain obscure. Here, using a yeast two-hybrid screening system, we identify a stem-loop binding protein (SLBP) that binds to a stem-loop structure at the 3′-end of the replication-dependent histone mRNA as a CT initiation factor (CTIF)-interacting protein. SLBP preferentially associates with the CT complex of histone mRNAs, but not with the eIF4E-depedent translation (ET) complex. Several lines of evidence indicate that rapid degradation of histone mRNA on the inhibition of DNA replication largely takes place during CT and not ET, which has been previously unappreciated. Furthermore, the ratio of CBP80/20-bound histone mRNA to eIF4E-bound histone mRNA is larger than the ratio of CBP80/20-bound polyadenylated β-actin or eEF2 mRNA to eIF4E-bound polyadenylated β-actin or eEF2 mRNA, respectively. The collective findings suggest that mRNAs harboring a different 3′-end use a different mechanism of translation initiation, expanding the repertoire of CT as a step for determining the fate of histone mRNAs.

Identification of G1-regulated genes in normally cycling human cells

Background

Obtaining synchronous cell populations is essential for cell-cycle studies. Methods such as serum withdrawal or use of drugs which block cells at specific points in the cell cycle alter cellular events upon re-entry into the cell cycle. Regulatory events occurring in early G1 phase of a new cell cycle could have been overlooked.

Methodology and Findings

We used a robotic mitotic shake-off apparatus to select cells in late mitosis for genome-wide gene expression studies. Two separate microarray experiments were conducted, one which involved isolation of RNA hourly for several hours from synchronous cell populations, and one experiment which examined gene activity every 15 minutes from late telophase of mitosis into G1 phase. To verify synchrony of the cell populations under study, we utilized methods including BrdU uptake, FACS, and microarray analyses of histone gene activity. We also examined stress response gene activity. Our analysis enabled identification of 200 early G1-regulated genes, many of which currently have unknown functions. We also confirmed the expression of a set of genes candidates (fos, atf3 and tceb) by qPCR to further validate the newly identified genes.

Conclusion and Significance

Genome-scale expression analyses of the first two hours of G1 in naturally cycling cells enabled the discovery of a unique set of G1-regulated genes, many of which currently have unknown functions, in cells progressing normally through the cell division cycle. This group of genes may contain future targets for drug development and treatment of human disease.

Regulated degradation of replication-dependent histone mRNAs requires both ATR and Upf1

Eukaryotic cells coordinately regulate histone and DNA synthesis. In mammalian cells, most of the regulation of histone synthesis occurs post-transcriptionally by regulating the concentrations of histone mRNA. As cells enter S phase, histone mRNA levels increase, and at the end of S phase they are rapidly degraded. Moreover, inhibition of DNA synthesis causes rapid degradation of histone mRNAs. Replication-dependent histone mRNAs are the only metazoan mRNAs that are not polyadenylated. Instead, they end with a conserved stem-loop structure, which is the only cis-acting element required for coupling regulation of histone mRNA half-life with DNA synthesis. Here we show that regulated degradation of histone mRNAs requires Upf1, a key regulator of the nonsense-mediated decay pathway, and ATR, a key regulator of the DNA damage checkpoint pathway activated during replication stress.

Differential expression of human replacement and cell cycle dependent H3 histone genes

Histones are the major protein component of chromatin. Except H4, all histone classes consist of several subtypes. The H3 family includes two replacement histone genes, H3.3A and H3.3B, which both encode the same protein and are expressed independently from the cell cycle. Since the two genes encode an identical protein, we analyzed whether they are differentially expressed. Therefore we cloned, sequenced and characterized the regulatory structures of the H3.3A gene and compared these with the corresponding regions in the H3.3B gene. In contrast to the H3.3B promoter, the promoter region of the H3.3A gene revealed neither a TATA nor any CCAAT boxes but an initiator element and several SP1 binding sequence motifs within an overall GC-rich sequence. Northern blot analysis of RNA from six human cell lines revealed that every cell line expressed each of the H3 isoform genes H3.1, H3.3A and H3.3B. In contrast, analysis of total RNA from human tissues showed a differential expression of the H3 isoform genes. The H3.3 genes are essentially only expressed in adult tissue, whereas the H3.1 gene is transcribed just in fetal tissue. The functional relevance of the elements identified by sequence analysis was established using a reporter gene assay with deletion constructs of the H3.3A promoter. In this assay a 256 bp fragment was sufficient for the full promoter activity and three promoter segments, each containing SP1 binding motifs, contribute to the H3.3A gene expression. The possible functional relevance of the differences between the two H3.3 genes in structure and expression is discussed.

The replacement H3.3 histone gene in Paracentrotus lividus sea urchin: structure and regulatory elements

We have isolated the Paracentrotus lividus sea urchin H3.3 histone gene and characterized the nucleotide sequences of the gene and its proximal promoter. Band shift experiments showed that two cAMP/PMA responsive elements (CRE/TRE), present in the proximal promoter, bind nuclear factors present in embryos at the blastula and gastrula stages (CRE1) and at the blastula stage (CRE2). The putative H3.3 coding region activating sequences (CRAS) failed to bind nuclear factors while the corresponding elements of the two replication-dependent genes (H3L and late H3) clearly recognized nuclear proteins. These results suggest some role of the CRE/TRE elements but not CRAS elements in the transcriptional regulation of the replication-independent histone genes in invertebrates.

Replication-dependent histone gene expression is related to Cajal body (CB) association but does not require sustained CB contact

Interactions between Cajal bodies (CBs) and replication-dependent histone loci occur more frequently than for other mRNA-encoding genes, but such interactions are not seen with all alleles at a given time. Because CBs contain factors required for transcriptional regulation and 3' end processing of nonpolyadenylated replication-dependent histone transcripts, we investigated whether interaction with CBs is related to metabolism of these transcripts, known to vary during the cell cycle. Our experiments revealed that a locus containing a cell cycle-independent, replacement histone gene that produces polyadenylated transcripts does not preferentially associate with CBs. Furthermore, modest but significant changes in association levels of CBs with replication-dependent histone loci mimic their cell cycle modulations in transcription and 3' end processing rates. By simultaneously visualizing replication-dependent histone genes and their nuclear transcripts for the first time, we surprisingly find that the vast majority of loci producing detectable RNA foci do not contact CBs. These studies suggest some link between CB association and unusual features of replication-dependent histone gene expression. However, sustained CB contact is not a requirement for their expression, consistent with our observations of U7 snRNP distributions. The modest correlation to gene expression instead may reflect transient gene signaling or the nucleation of small CBs at gene loci.

Evolutionarily distinct classes of S27 ribosomal proteins with differential mRNA expression in rat hypothalamus

Using an in situ hybridization screen for cDNA clones of brain region-specific mRNAs, we isolated a rat transcript that encodes a ribosomal protein S27. Searching GenBank DNA databases, we found two S27 protein isoforms. One isoform, encoded by multiple genes, is extant in archaea and eukarya, but not bacteria. The second isoform appears to be recently evolved because it has been identified only in mammals. Multiple transcripts encode each isoform and exhibit different tissue expression patterns throughout rat brain and periphery, with abundant expression in the hypothalamus. In situ hybridization studies revealed predominant expression of S27(1) in distinct hypothalamic nuclei, such as the paraventricular, supraoptic, suprachiasmatic, arcuate, and circularis nuclei, whereas expression of S27(2) mRNA was discretely expressed in select neurons of the periventricular and supraoptic nuclei. Combined with the genetic evidence that S27 has extraribosomal functions in plants, the complexity of S27 biology observed here may suggest auxiliary functions for S27 proteins in the mammalian nervous system.

Formation of the 3' end of histone mRNA

All metazoan messenger RNAs, with the exception of the replication-dependent histone mRNAs, terminate at the 3' end with a poly(A) tail. Replication-dependent histone mRNAs end instead in a conserved 26-nucleotide sequence that contains a 16-nucleotide stem-loop. Formation of the 3' end of histone mRNA occurs by endonucleolytic cleavage of pre-mRNA releasing the mature mRNA from the chromatin template. Cleavage requires several trans-acting factors, including a protein, the stem-loop binding protein (SLBP), which binds the 26-nucleotide sequence; and a small nuclear RNP, U7 snRNP. There are probably additional factors also required for cleavage. One of the functions of the SLBP is to stabilize binding of the U7 snRNP to the histone pre-mRNA. In the nucleus, both U7 snRNP and SLBP are present in coiled bodies, structures that are associated with histone genes and may play a direct role in histone pre-mRNA processing in vivo. One of the major regulatory events in the cell cycle is regulation of histone pre-mRNA processing, which is at least partially mediated by cell-cycle regulation of the levels of the SLBP protein.

Histone gene expression and chromatin structure during spermatogenesis

The chromatin of male germ cells is restructured throughout spermatogenesis. Analysis of differential histone protein patterns at specific stages of spermatogenesis may contribute towards an understanding of the changes in chromatin structure and function during this differentiation process. The most striking changes in histone patterns occur at the stage of pachytene spermatocytes when most of the linker H1 histones are replaced by the testis specific subtype H1t. In addition, replacement of core histone subtypes is observed at this stage. These structural changes precede the reorganization of chromatin at haploid stages when histones are replaced first by transition proteins and then by protamines.

One allele of the major histone gene cluster is enough for cell proliferation of the DT40 chicken B cell line

Thirty-nine of the 44 chicken histone genes are located in a major histone gene cluster of 110 kb, the others residing in four separate regions. We generated a heterozygous chicken DT40 mutant, 1/2 delta110 kb, devoid of one allele of the cluster, using gene targeting techniques. Analyses of the mutant revealed that the growth rate of DT40 cells was unchanged even in the absence of one allele of the cluster. Moreover, analyses involving a RNase protection assay, SDS-PAGE or Triton-acid-urea-PAGE revealed not only that in the 1/2 delta110 kb mutant the steady-state levels of total mRNAs of gene families H1, H2A, H2B, H3 and H4 remained constant, but also that the amounts of histones H1, H2A, H2B, H3 and H4 were not changed. A comparison by 2D-PAGE revealed no changes in total cellular protein patterns of the mutant. These observations demonstrate that all the histone gene families have the inherent ability to compensate for the disruption of one allele of the gene cluster, with no influence on cell functions.

Differential expression of the murine histone genes H3.3A and H3.3B

The histone family of proteins is subdivided into two major groups: the main type histones, which are synthesized in coordination with DNA replication during the S-phase of the cell cycle, and the replacement histones, which can be synthesized in the absence of DNA replication substituting main type histone isoforms. Accumulation of replacement histone variants has been observed in several terminally differentiated tissues that have stopped cell division. The replacement subtype of the H3 class is termed H3.3. This protein is encoded by two different genes (H3.3A and H3.3B) that both code for the same amino acid sequence, but differ in nucleotide sequences and gene organization. This has been shown for human and avian H3.3A and H3.3B genes and for a murine H3.3B cDNA. In an attempt to define patterns of replacement histone H3.3 gene expression during male germ cell differentiation, we have constructed mouse testicular cDNA libraries and have isolated cDNAs corresponding to the murine H3.3A and H3.3B genes. Using probes specific for these two different genes we show by RNase protection analysis and by nonradioactive in situ hybridization with testis sections that H3.3A mRNA is present in pre- and postmeiotic cells, whereas expression of the H3.3B gene is essentially restricted to cells of the meiotic prophase.

H3.3A variant histone mRNA containing an alpha-globin insertion: modulated expression during mouse gametogenesis correlates with meiotic onset

Replacement-variant H3.3 histones have been isolated and sequenced in different eukaryotes, but no functional H3.3A gene has been characterized in the mouse so far. We have cloned an H3.3A cDNA from a mouse fetal ovary library, differentially screened with testis versus somatic cDNA probes. We showed this gene contains a region homologous to the reverse and complementary alpha-globin gene. We believe such a structure could have been generated by retroposition during the evolution of both globin and histone gene families. The sequence coding for H3.3A is 76.6% homologous to the mouse H3.3B gene at the nucleotide level and differs in only one amino acid at the protein level. The high degree of homology between these genes and the H3.3 variant histones from other eukaryotes reveals the conservation of these replication-independent class of histones throughout evolution. Analysis of gene expression reveals a developmental regulation concurrent with meiotic progression, with the highest level of transcript detection coincident with meiotic onset during both oogenesis and spermatogenesis.

A solitary human H3 histone gene on chromosome 1

A solitary histone H3 gene encoding a novel H3 protein sequence has been isolated. This H3 gene maps to chromosome 1 (1q42), whereas we have shown previously that the majority of the human histone genes form a large cluster on chromosome 6 (6p21.3). In addition, a small cluster has been described at 1q21. The clustered histone genes are expressed during the S-phase of the cell cycle, hence their definition as replication-dependent histone genes. In contrast, expression of replacement histone genes is essentially cell-cycle independent; they are solitary genes and map outside the major clusters. The newly described H3 gene maps outside all known histone gene clusters and varies by four amino acid residues from the consensus mammalian H3 structure. In contrast to other solitary histone genes, this human H3 gene shows the consensus promoter and 3' flanking portions that are typical for replication-dependent genes.

Targeted disruption of H2B-V encoding a particular H2B histone variant causes changes in protein patterns on two-dimensional polyacrylamide gel electrophoresis in the DT40 chicken B cell line

The chicken H2B gene family comprises eight members (H2B-I to H2B-VIII), which are all located in two major histone gene clusters. All of them have been shown to encode four different protein variants (classes I to IV). In the DT40 chicken B cell line, the H2B-V gene, encoding the class III H2B variant, constituted about 10% of the total intracellular mRNA from all the H2B genes. To study the nature of this particular variant in vivo, we generated heterozygous (H2B-V, +/-) and homozygous (H2B-V, -/-) DT40 mutants by targeted integration. The remaining H2B genes were shown to be expressed more in these mutants than in the wild-type cell lines. The growth rate of DT40 cells was unchanged in the absence of the H2B-V gene. Two-dimensional polyacrylamide gel electrophoresis showed that the protein patterns were, on the whole, similar between the wild-type and homozygous cell lines. However, within this constant background, some cellular proteins disappeared or decreased quantitatively in the homozygous mutants, and several other proteins increased or newly appeared. These results suggest that the class III H2B variant participates negatively or positively in regulation of the expression of particular genes that encode the proteins that vary in DT40 cells. This type of regulation is possibly mediated through alterations in nucleosome structure over the restricted regions involving the putative genes of the DT40 genome.

Structure and expression of histone H3.3 genes in Drosophila melanogaster and Drosophila hydei

We demonstrate that in Drosophila melanogaster the histone H3.3 replacement variant is encoded by two genes, H3.3A and H3.3B. We have isolated cDNA clones for H3.3A and cDNA and genomic clones for H3.3B. The genes encode exactly the same protein but are widely divergent in their untranslated regions (UTR). Both genes are expressed in embryos and adults; they are expressed in the gonads as well as in somatic tissues of the flies. However, only one of them, H3.3A, shows strong testes expression. The 3' UTR of the H3.3A gene is relatively short (approximately 250 nucleotides (nt)). H3.3B transcripts can be processed at several polyadenylation sites, the longest with a 3' UTR of more than 1500 nt. The 3' processing sites, preferentially used in the gonads and somatic tissues, are different. We have also isolated the Drosophila hydei homologues of the two H3.3 genes. They are quite similar to the D. melanogaster genes in their expression patterns. However, in contrast to their vertebrate counterparts, which are highly conserved in their noncoding regions, the Drosophila genes display only limited sequence similarity in these regions.

Isolation and characterization of the gene encoding histone H2A from Trypanosoma cruzi

In the present paper we report the isolation and characterization of the sequence of two genomic DNA fragments coding for the histone H2A of Trypanosoma cruzi. An analysis of the predicted amino acid sequence shows the presence of the amino-terminal motif characteristic of the H2A histones proteins and the Lys-Lys motif reported to be the site for the ubiquitin attachment. Southern blots of total parasite DNA probed with the H2A sequence suggested that the T. cruzi histone H2A gene is encoded in two independent gene clusters. The molecular karyotyping of the parasite indicated that these two clusters locate in a single chromosome of about 700 kb in length. The T. cruzi H2A mRNA is polyadenylated as are the basal histone mRNAs of higher eukaryotes and the histone mRNAs of yeast. By polymerase chain reaction amplification and sequencing and by S1 mapping we determined respectively the 5' and 3' end of the gene showing that the miniexon is added to the mRNA 71 nucleotides upstream of the ATG initiation codon and that the polyadenylation site locates in nucleotide position 773-775 close to invert repeats.

Identification of conserved potential regulatory sequences of the protamine-encoding P1 genes from ten different mammals

In order to detect regulatory conserved DNA elements within the protamine 1-encoding gene (P1) promoter, we have sequenced this region from the rat, guinea pig, gorilla, orangutan, anubis baboon and red monkey P1 genes and compared it to the homologous human, bull, boar and mouse nucleotide (nt) sequences. We demonstrate the presence of a consensus sequence, HSMCYTCAYAAT (Prot1C: protamine 1 consensus), from nt position -64 to position -53 in all P1 genes whose promoter sequences are now known. We also show that sequences similar to Prot1C are found in the promoter region of other testis-specific genes, such as the transition protein 1-encoding gene promoter which is thought to have derived from the P1 genes. The relevance of this conserved element in the expression of P1 genes is strongly supported by the recent demonstration of a mouse testis trans-acting factor [Tet-1; Tamura et al., J. Biol. Chem. 267 (1992) 4327-4332] which binds and matches in the mouse the first 11 bp of the corresponding consensus Prot1C sequence reported here. Another highly conserved element (TGTGAGG) has been identified 20 +/- 3 nt upstream from Prot1C. This sequence forms a perfect palindrome with the central 7 nt of Prot1C and is absent in the homologous region of other genes. Further upstream, at positions -113 to -132, a third highly conserved region is present (MATGCCCATATWTGGRCAYG) which is similar to the c-fos SRE (serum-response element) and contains the central core common to all SREs. This element has not been found in the homologous region of other sperm-specific genes.(ABSTRACT TRUNCATED AT 250 WORDS)

cDNA sequence and expression of an intron-containing histone H2A gene from Norway spruce, Picea abies

We have isolated a cDNA clone corresponding to a histone H2A gene from Norway spruce, Picea abies (L.) Karst. The clone was isolated on the basis of the preferential expression of the corresponding gene during germination. The identification of the clone was based on the high degree of nucleotide sequence identity (60-65%) to a range of eukaryotic histone H2A genes and the presence of a 9 amino acids long sequence identical to the conserved 'H2A box' in the deduced amino acid sequence. Like other plant histone genes, the spruce histone H2A gene encodes a polyadenylated transcript. Further, the spruce gene contains an intervening sequence of 891 bp in the coding region. The presence of introns is typical of a distinct class of replication-independent histone genes in other eukaryotes. However, the sequence of the spruce gene and its high expression in mitotically active tissues such as the apical meristem, strongly suggests that it belongs to the class of replication-dependent histone genes. This is the first documentation of an intervening sequence in this class of histone genes and the finding implies that introns were present in the ancestral histone H2A gene before the divergence of the two classes of histone genes.

A human histone H2B.1 variant gene, located on chromosome 1, utilizes alternative 3' end processing

A variant human H2B histone gene (GL105), previously shown to encode a 2300 nt replication independent mRNA, has been cloned. We demonstrate this gene expresses alternative mRNAs regulated differentially during the HeLa S3 cell cycle. The H2B-Gl105 gene encodes both a 500 nt cell cycle dependent mRNA and a 2300 nt constitutively expressed mRNA. The 3' end of the cell cycle regulated mRNA terminates immediately following the region of hyphenated dyad symmetry typical of most histone mRNAs, whereas the constitutively expressed mRNA has a 1798 nt non-translated trailer that contains the same region of hyphenated dyad symmetry but is polyadenylated. The cap site for the H2B-GL105 mRNAs is located 42 nt upstream of the protein coding region. The H2B-GL105 histone gene was localized to chromosome region 1q21-1q23 by chromosomal in situ hybridization and by analysis of rodent-human somatic cell hybrids using an H2B-GL105 specific probe. The H2B-GL105 gene is paired with a functional H2A histone gene and this H2A/H2B gene pair is separated by a bidirectionally transcribed intergenic promoter region containing consensus TATA and CCAAT boxes and an OTF-1 element. These results demonstrate that cell cycle regulated and constitutively expressed histone mRNAs can be encoded by the same gene, and indicate that alternative 3' end processing may be an important mechanism for regulation of histone mRNA. Such control further increases the versatility by which cells can modulate the synthesis of replication-dependent as well as variant histone proteins during the cell cycle and at the onset of differentiation.

Genes encoding a histone H3.3-like variant in Arabidopsis contain intervening sequences

Two genes encoding a particular H3 histone variant were isolated from Arabidopsis thaliana. These genes differ from the H3 genes previously cloned from Arabidopsis and other plants by several interesting properties: (1) the two genes are located close to each other; (2) their coding regions are interrupted by two or three small introns, the two closest to the initiation codon being located at the same place in the two genes; (3) another, long intron is located in the 5'-untranslated region just before the initiation codon of gene I as deduced from the sequence of several corresponding cDNAs, and very likely also of gene II; (4) these genes do not show preferential expression in organs containing meristematic tissues contrary to the classical intronless replication-dependent histone genes, thus suggesting that their expression is not replication-dependent; (5) the protein encoded by both genes is the same and corresponds to a minor H3 variant highly conserved among all the plant species studied up to now. All these characteristics are common with the animal replication-independent H3.3 histone genes and it is assumed that the genes described here are the first example of the equivalent H3.3 gene family in plants. Interestingly, the promoter regions of the two genes have the same general structure as the Arabidopsis intronless genes. Possible implications on the regulation of H3 genes expression are discussed.

Arabidopsis thaliana H1 histones. Analysis of two members of a small gene family

We have isolated two Arabidopsis thaliana cDNA clones that encodes different H1 histone proteins. The H1-1 and H1-2 proteins are 274 and 273 amino acids in length, respectively. Unlike the H1 histones within a single animal species, the two plant H1 proteins share little sequence similarity outside the protein's central globular domain. Within the globular domain, a pentapeptide that is extremely well conserved in animal H1 histones, is not found in either of the plant proteins. Southern blot analysis suggests that A. thaliana has only three H1 histone genes. A genomic clone encoding the H1-1 protein was isolated and the protein-coding region was found to consist of two exons separated by a 104-bp intron. The site of transcriptional initiation of the H1-1 gene was mapped by primer-extension analysis and a conserved octamer motif, identical to that observed in most plant core histone genes that have been characterized to date, was found 101 nucleotides upstream of the presumed transcription-initiation site. The 3' portion of the gene encoding H1-2 was also isolated and sequenced. When the 3'-flanking regions of the two H1 genes were compared, several highly conserved sequences were observed that might be convergently transcribed relative to the histone genes.

A Drosophila melanogaster H3.3 cDNA encodes a histone variant identical with the vertebrate H3.3

A cDNA encoding an H3.3 histone variant in Drosophila melanogaster predicts a protein with an amino acid (aa) sequence identical with that in vertebrates. The D. melanogaster H3.3 nucleotide (nt) sequence has diverged significantly from that of both the H3.3 gene of vertebrates and the H3.1 gene of D. melanogaster, largely through third nt changes in its codons. The perfect H3.3 aa sequence conservation between organisms as phylogenetically divergent as vertebrates and flies suggests that the H3.3 histone variant itself is an important structural component of chromatin, apart from the value of its replication-independent expression pattern.

Normal transitions in synthesis of replacement histones H2A.Z and H3.3 during differentiation of dystrophic myotube cells. A brief note

We previously reported that differentiating G0 myotube cells cultured from normal chicken embryos exhibit a histone synthesis pattern that is highlighted by transitions in the expression of the minor replacement variants H3.3 and perhaps H2A.Z (Wunsch and Lough, Dev. Biol. 119 (1987) 94-99). Because these proteins may be synthesized to maintain chromatin structure during the differentiation and maturation of the skeletal muscle fiber, it was of interest to determine whether they are made at normal levels during the differentiation of dystrophic muscle. To this end, the synthesis of histone proteins in cultured myoblasts and myotubes from normal and dystrophic avian embryos has been characterized by two-dimensional polyacrylamide gel electrophoresis and fluorography. Proliferating myoblasts (day 1) as well as two stages of differentiating myotubes (days 3, 4) exhibited histone synthesis patterns that were indistinguishable when comparing normal and dystrophic cells. It is noteworthy that this study also revealed that, in both cell types, the change in H2A.Z synthesis during the myoblast/myotube transition was remarkable, increasing from approximately 20% of the non-ubiquitinated H2As in myoblasts to 80% in myotubes. Also, gel staining patterns and immunoblotting detected no differences in the degree of histone ubiquitination between normal and dystrophic cells. These findings indicate that, up to this point in dystrophic differentiation, neither the synthesis nor ubiquitination of histones are perturbed.

Sequence, organization and expression of the core histone genes of Aspergillus nidulans

The core histone gene family of Aspergillus nidulans was characterized. The H2A, H2B and H3 genes are unique in the A. nidulans genome. In contrast there are two H4 genes, H4.1 and H4.2. As previously reported for the H2A gene (May and Morris 1987) introns also interrupt the other core histone genes. The H2B gene, like the H2A gene, is interrupted by three introns, the H3 and H4.1 gene are each interrupted by two introns and the H4.2 gene contains one intron. The position of the single intron in H4.2 is the same as that the first intron of the H4.1 gene. The H2A and H2B genes are arranged as a gene pair separated by approximately 600 bp and are divergently transcribed. The H3 and H4.1 genes are similarly arranged and are separated by approximately 800 bp. The H4.2 gene is not closely linked to either the H2A-H2B or H3-H4.1 gene pairs. Using pulse field gel electrophoresis an electrophoretic karyotype was established for A. nidulans. This karyotype was used to assign the H3-H4.1 gene pair and the H4.2 gene to linkage group VIII and the H2A-H2B gene pair to either linkage group III or VI. The abundance of each of the histone messenger RNAs was determined to be cell cycle regulated but the abundance of the H4.2 mRNA appears to be regulated differently from the others.

Histone variant patterns during vertebrate embryogenesis and limb development

Two-dimensional gel electrophoresis was used to examine the relative content of core histone variants during early chicken embryogenesis and at selected stages of hindlimb development. Nuclei from stage 19 limb buds displayed a pattern similar to whole embryos at stage 1, at which time all of the known avian histone variants, including the minor isoprotein H3.3, were detected. Variant ratios did not change during limb development, up to stage 29. However, the portion of H2A variants migrating as ubiquitinated conjugates increased more than twofold during limb development, advancing from 4.5% of the total H2A proteins at stage 19 to 12% at stage 29.

Histone genes in Physarum polycephalum: transcription and analysis of the flanking regions of the two H4 genes

The histone H4 multigene family of Physarum polycephalum consists of two genes, H41 and H42. Both genes have an unusual structure in that they are interrupted by a small intron. The structure of the P. polycephalum H4 genes is discussed and compared to the structure of histone genes of other organisms. S1 nuclease analysis was used to map the 5' and 3' ends of the histone H4 messengers. We show that the histone H4 genes have a hybrid structure; they are interrupted by an intervening sequence, as in replacement variant histone genes of higher eukaryotes, but their 5' and 3' noncoding regions have the properties of replication-dependent histone genes: the 5' and 3' leader and trailer sequences are short, possess a 3'-hyphenated dyad symmetry element, and a CAGA sequence is found 3' to the hyphenated hairpin structure. This report also provides evidence that both genes are expressed in late G2 phase as well as in S phase and that their expression is temporally coordinated and quantitatively similar during the cell cycle.

The 5' splice site: phylogenetic evolution and variable geometry of association with U1RNA

The 5' splice site sequences of 3294 introns from various organisms (1-672) were analyzed in order to determine the rules governing evolution of this sequence, which may shed light on the mechanism of cleavage at the exon-intron junction. The data indicate that, currently, in all organisms, a common sequence 1GUAAG6U and its derivatives are used as well as an additional sequence and its derivatives, which differ in metazoa (G/1GUgAG6U), lower eucaryotes (1GUAxG6U) and higher plants (AG/1GU3A). They all partly resemble the prototype sequence AG/1GUAAG6U whose 8 contigous nucleotides are complementary to the nucleotides 4-11 of U1RNA, which are perfectly conserved in the course of phylogenetic evolution. Detailed examination of the data shows that U1RNA can recognize different parts of 5' splice sites. As a rule, either prototype nucleotides at position -2 and -1 or at positions 4, 5 or 6 or at positions 3-4 are dispensable provided that the stability of the U1RNA-5' splice site hybrid is conserved. On the basis of frequency of sequences, the optimal size of the hybridizable region is 5-7 nucleotides. Thus, the cleavage at the exon-intron junction seems to imply, first, that the 5' splice site is recognized by U1RNA according to a "variable geometry" program; second, that the precise cleavage site is determined by the conserved sequence of U1RNA since it occurs exactly opposite to the junction between nucleotides C9 and C10 of U1RNA. The variable geometry of the U1RNA-5' splice site association provides flexibility to the system and allows diversification in the course of phylogenetic evolution.

An Auxin-Regulated Gene of Arabidopsis thaliana Encodes a DNA-Binding Protein

We have isolated a single-copy gene from the plant Arabidopsis thaliana, called dbp, which encodes a lysine-rich, DNA-binding protein. The Dbp protein has a molecular weight and a composition resembling histone H1. When the dbp gene was expressed in bacteria, the protein product bound DNA nonspecifically. The dbp gene is expressed constitutively in all parts of the plant but is induced five times above this basal level in apical zones. In vitro hormone-depletion experiments showed that the expression in the shoot apex could be induced by exogenous auxin. In situ hybridizations in the root apex indicated that the expression of dbp is enhanced in the region of cell division.

Histone gene expression during sea urchin spermatogenesis: an in situ hybridization study

The expression of testis-specific and adult somatic histone genes in sea urchin testis was investigated by in situ hybridization. The testis-specific histone genes (Sp H2B-1 of Strongylocentrotus purpuratus and Sp H2B-2 of Lytechinus pictus) were expressed exclusively in a subset of male germ line cells. These cells are morphologically identical to replicating cells pulse-labelled with 3H-thymidine. Genes coding for histones expressed in adult somatic and late embryo cells (H2A-beta for S. purpuratus and H3-1 for L. pictus) were expressed in the same germ line cells, as well as in the supportive cells (nutritive phagocytes) of the gonad. All histone mRNAs detected in the male germ lineage declined precipitously by the early spermatid stage, before cytoplasmic reduction. The data suggest that both testis-specific and adult somatic histone genes are expressed in proliferating male germ line cells. Testis-specific gene expression is restricted to spermatogonia and premeiotic spermatids, but somatic histone expression is not. The decline of histone mRNA in nondividing spermatids is not merely a consequence of cytoplasmic shedding, but probably reflects mRNA turnover.

A proposal for a possible role of nucleosome positioning in the evolutionary adjustment of introns

1. Prokaryotes and yeast have mostly intronless genes, whereas the presence of a large number of extended introns are characteristic of the genes of of multicellular eukaryotic organisms which, however, as an exception also have a few intronless genes. 2. According to the current view, the lack of introns in prokaryotic organisms and yeast is due to the selective pressure of a short cell division time. On the other hand, the presence of introns in multicellular eukaryotic organisms is explained by the lack of selective forces against them. 3. In the present hypothesis it is proposed that introns were used as tools in the course of evolution for the organization of eukaryotic genes within the repeating units of nucleosomes, since the distinct DNA conformations of the nucleosome core particle and of the linker region, respectively, represent a constraint for the positioning of genes. 4. Recently it was shown that initiation of transcription is inhibited when the promoter sequence is within a nucleosome. 5. Since the nucleosomal organization of DNA leads to a severely deformed DNA helix and recognition of sequences by regulatory proteins is likely to depend on the conformation of the double helix, it is postulated that for the different sizes of eukaryotic genes which have to be organized within repeating units of nucleosomes, introns provided the flexibility of adjustment for the positioning of regulatory sequences, by drifting in length, sequence and position.

Temporal changes in PO and MBP gene expression after crush-injury of the adult peripheral nerve

The crush-injured sciatic nerve provides a model to study Schwann cell regulation of myelin gene expression during the process of demyelination and remyelination. In order to investigate the possible transcriptional regulation of myelin gene expression, the quantity, quality and translational efficiency of PO (the major myelin glycoprotein) and MBP (the myelin basic proteins) coding messages were investigated as a function of time following crush-injury of the adult rat sciatic nerve. Northern blot analysis indicated that the size of the PO and MBP transcripts remain unchanged in the distal segments of crushed sciatic nerves at 1, 2, 4, 7, 10, 14 and 21 days after crush-injury. Dot-blot analysis showed a sharp drop in levels of PO and MBP coding transcripts 1 day after crush-injury with the lowest steady-state levels at 4-7 days. Message levels were found to increase after 7 days, the highest increase in levels of message was found to be between 10 and 14 days. The highest steady-state level of both transcripts was observed at 21 days. In vitro translation and immunoprecipitation of PO-translated products from various stages of crush-injury also indicated this trend. The pattern of gene expression of PO- and MBP-coding transcripts parallel each other and follow the pattern of demyelination and remyelination. The results are also consistent with our previous interpretation which suggests that PO and MBP gene expression is regulated at the level of transcription and that these two genes might be coordinately expressed. Western blot analysis of PO protein from these stages revealed a similar decrease and then increase in the levels of the protein.(ABSTRACT TRUNCATED AT 250 WORDS)

Modulation of histone H3 variant synthesis during the myoblast-myotube transition of chicken myogenesis

We have previously reported that nucleosomal histones are synthesized by cultured, postmitotic myotube cells at 9-29% of the rate in their dividing myoblast precursors (A. M. Wunsch, A. L. Haas, and J. Lough, 1987, Dev. Biol. 119, 85-93). In that study, histones were separated by two-dimensional polyacrylamide gels containing 8 M urea in the first-dimension to optimally separate variants of the H2A class. To separate and compare synthesis of variants in the H2B and H3 classes during myogenesis, 5.75 M urea has been used in the first dimension. Although no changes in the H2B variant pattern were discerned, a dramatic change in H3 variant synthesis was detected, in which a predominance of H3.2 synthesis in dividing myoblasts was almost completely replaced by a lower level of H3.3 synthesis after myotube formation. With increasing differentiation, H3.2 synthesis became undetectable, while H3.3 synthesis continued. Control experiments indicated that these results were not mediated by replicating cells in the myotube cultures, the effects of cytosine arabinoside, or contaminating non-histone proteins. These results suggest that histone H3.2 is replaced by histone H3.3 in nucleosomes during skeletal muscle maturation.

The unique histone H2A gene of Aspergillus nidulans contains three introns

The histone H2A gene of the filamentous fungus Aspergillus nidulans has been cloned and sequenced. There is a single H2A gene in the genome of A. nidulans, and it contains three introns. The introns are 51 nucleotides (nt), 56 nt and 50 nt in length and split codons for amino acids (aa) 18, 48 and 116 of the predicted protein. The transcriptional start and termination points have been determined using an S1 nuclease protection assay. The predicted protein is 132 aa residues in length and surprisingly has a threonine after the initiator methionine instead of the usual serine. The sequence of the predicted histone H2A protein is compared to histone H2A proteins from Schizosaccharomyces pombe, Saccharomyces cerevisiae and calf thymus. Comparison of the amino acid sequence to these other H2A proteins shows that the divergence of amino acid sequences between H2A proteins is found in two clustered sites.

Characterization of mouse H3.3-like histone genes

We designed a strategy to select genomic clones of mouse replication-independent H3.3 histone genes. We obtained three clones which met our selection criteria for being H3.3 genes. Upon sequencing two of these clones we found that they were unlike previously isolated chicken H3.3 clones: they code for several unpredicted amino acid substitutions and contain no introns in the coding regions. We showed by S1 nuclease assays that these genes are protected by mRNAs that have expression characteristics of H3.3 mRNA. The protection data and nucleotide sequence analysis show that the H3.3 transcripts can be processed at one of four cleavage/polyadenylation sites. We show that these genes probably evolved through reverse transcription intermediates, and are processed pseudogenes which are no longer under selective pressure. The 5' and 3' transcribed, nontranslated sequences show extensive homology to those of a human cDNA clone, and we suggest that these sequences may be required for appropriate regulation of expression of H3.3 genes.