Changes in nucleosomal core histone variants during chicken development and maturation

Microheterogeneity in H1 histones and its consequences

The extent of microheterogeneity of H1 histones in individual higher organisms, without considering post-translational modifications, is such that five to eight molecular species can be recognized. The H1 variants differ among themselves in their ability to condense DNA and chromatin fragments, and they are non-uniformly distributed in chromatin. This review assembles data that support the notion that the differences in chromatin condensation (heterochromatization) observed through the microscope are maintained by the non-uniform distribution of H1 variants, and that this pattern of chromatin condensation may determine the dynamics of chromatin during replication and may represent the commitment aspect of differentiation. The differential response of the multiple H1 variants with regard to their synthesis and turnover is consistent with this notion.

Mouse histone H2A and H2B genes: four functional genes and a pseudogene undergoing gene conversion with a closely linked functional gene

The sequence of five mouse histone genes, two H2a and three H2b genes on chromosome 13 has been determined. The three H2b genes all code for different proteins, each differing in two amino acids from the others. The H2b specific elements present 5' to H2b genes from other species are present in all three mouse H2b genes. All three H2b genes are expressed in the same relative amounts in three different mouse cell lines and fetal mice. The H2b gene with the H2b specific sequence closest to the TATAA sequence is expressed in the highest amount. One of the H2a genes lacks the first 9 amino acids, the promoter region, the last 3 amino acids and contains an altered 3' end sequence. Despite these multiple defects, there is only one nucleotide change between the two H2a genes from codon 9 to 126. This indicates that a recent gene conversion has occurred between these two genes. The similarity of the nucleotide sequences in the coding regions of mouse histone genes is probably due to gene conversion events targeted precisely at the coding region.

Structure and organization of the chicken H2B histone gene family

The results of Southern blotting experiments confirm that the chicken H2B histone gene family contains eight highly homologous members. One or two more sequences which are considerably divergent from the others appear to exist in the chicken genome. Seven of the eight H2B genes have been cloned and sequenced. All seven genes fall in two histone gene clusters, but no common arrangement exists for the clusters themselves. Three different H2B protein variants are encoded by these seven genes. The nucleotide sequence homology among the genes within their coding sequences appears to exceed that required for the corresponding protein sequences, suggesting that histone H2B mRNA sequence and structure are both selected during evolution. An analysis of the 5' flanking sequence data reveals that these genes possess CCAAT and TATA boxes, elements commonly associated with genes transcribed by RNA polymerase II. In addition, these genes all share an H2B-specific element of the form: ATTTGCATA. The 3' sequences of these genes contain the hyphenated symmetrical dyad homology and downstream purine-rich sequence shared by histone genes in general.

Synthesis and ubiquitination of histones during myogenesis

One and two-dimensional polyacrylamide gel electrophoresis have revealed that cultures of postmitotic (G0) chicken skeletal myotube cells synthesize significant but reduced quantities of histone proteins as compared to their proliferating myoblast precursors. In addition, modulation of variant synthesis within the histone H2A and H3 classes may accompany myotube formation. That the histone bands contain no nonhistone contaminants was shown by exclusion of [3H]tryptophan. It is unlikely that these results reflect synthesis of histone by contaminating replicating cells, since a single treatment with cytosine arabinoside at the time of fusion effectively removed unfused cells while suppressing synthesis of DNA in the myotube cultures. The relatively sparse incorporation of label by major variants of the H2A class in dividing myoblasts was shown to be caused by heterogeneity due to phosphorylation and extensive ubiquitination, which decline at the time of myotube formation. As determined by quantitative Western-blotting, dividing myoblasts and myotubes contain an average of 1.0 and 0.4 molecules of ubiquitinated H2A (uH2A), respectively, per 10 nucleosomes.

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.

Sequences of four mouse histone H3 genes: implications for evolution of mouse histone genes

The sequences of four histone H3 genes coding for the replication variant proteins H3.1 and H3.2 have been determined. Three of these genes, two coding for H3.1 proteins and one for an H3.2 protein, are located on chromosome 13 and expressed at low levels. The fourth gene, encoding an H3.2 protein, is located on chromosome 3 and expressed at a high level. The coding regions of the three genes on chromosome 13 are more similar to each other than to the H3 gene on chromosome 3, and equally divergent from it, suggesting that either gene duplication or gene conversion has occurred since the genes were dispersed onto two chromosomes. A 14-base sequence including the CCAAT sequence and located 5' to the genes on chromosome 13 has been conserved. The histone H3 gene on chromosome 3 has multiple potential binding sites for the Sp1 transcription factor. The coding regions show greater than 95% conservation among the four genes. This is due to the strict pattern of codon usage and the presence of two long (greater than 60 base) regions of completely conserved nucleic acid sequence. These conserved regions in the coding sequence may have an important functional role at the mRNA or DNA level.

The beta-globin domain in immature chicken erythrocytes: enhanced solubility is coincident with histone hyperacetylation

A 60 minute exposure of chicken immature erythrocytes to n-butyrate shifts actively acetylated and deacetylated histones to hypermodified forms. Micrococcal nuclease digestion of nuclei from n-butyrate treated cells and subsequent fractionation of the chromatin releases 40-45% of the adult beta-globin (beta A) nucleohistone into a soluble fraction. This is an eleven fold enrichment over the soluble chromatin from untreated cells (Ferenz and Nelson (1985) Nucleic Acids Res. 13, 1977-1995). The enhanced beta A chromatin solubility and induced histone hyperacetylation are coincident. Removal of n-butyrate from the cell incubation medium allows rapid histone deacetylation and a striking reduction in beta A chromatin solubility. Chromatin from cells incubated in the absence of n-butyrate, or in medium containing 10 mM NaCl or 2% dimethylsulfoxide, does not exhibit histone hyperacetylation, or the acquired solubility of beta A chromatin. We show that the H4 histone co-isolated with the beta A DNA is in a hyperacetylated state and present evidence that the n-butyrate incubation increases the solubility of both coding and noncoding chromatin regions in the beta-globin domain.

Core histone variants and ubiquitinated histones 2A and 2B of rat cerebral cortex neurons

The pattern of non-allelic variants of core histones was investigated in terminally differentiated rat cerebral cortex neurons. At 30 days two major H2A variants are present, H2A.1 and .2, together with two minor components, .x and .z. H2B has two variants, H2B.1 and .2, and H3 presents three variants, H3.1, .2 and .3. The ubiquitinated adducts of all H2A and H2B variants can be recognised on two-dimensional electrophoresis as forming a pattern similar to that of the unmodified species. uH2A amounts to 12-14% of total H2A. All H2A variants appear to be equally modified. uH2B amounts to 1-2% of total H2B.

Genomic organization and nucleotide sequence of two distinct histone gene clusters from Xenopus laevis. Identification of novel conserved upstream sequence elements

We have performed a detailed analysis of the genomic organization and the nucleotide sequence of two distinct Xenopus laevis histone gene clusters totaling approximately 23.5 X 10(3) base-pairs. Each cluster contains at least one copy of each of the five histone genes. However, these genes are present in different arrangements within each cluster and different H1A, H2A and H2B proteins (variants) are encoded by the respective genes of each cluster. Southern blot analysis of genomic X. laevis DNA indicates that each cluster is a member of a distinct family of tandemly repeated histone gene clusters. A comparative analysis of the nucleotide sequences flanking the histone genes within these two clusters has revealed the presence of multiple conserved sequence elements that are specific for each histone gene class and located at preferred upstream positions. Several of these elements correspond to sequences that are known to be required for maximal transcription of the corresponding genes. Most of these sequence elements have not been identified previously, although we find that many of them are present at corresponding locations upstream of histone genes from other organisms. We suggest that the conserved upstream sequence elements may play an important role in the expression of histone genes in vivo.

Replacement variant histone genes contain intervening sequences

The nucleotide sequences of two chicken histone genes encoding replacement variant H3.3 polypeptides are described. Unlike the replication variant genes of chickens (and almost all other organisms), these genes contain intervening sequences; introns are present in both genes in the 5' noncoding and coding sequences. Furthermore, the replacement variant histone mRNAs are post-transcriptionally polyadenylated. The locations, but not the sizes, of the two introns within the coding segments of the two genes have been exactly conserved, whereas the intron positions in their respective 5' flanking regions differ. Although both H3.3 genes predict the identical histone polypeptide sequence, they are as different from one another as each of them is from a more common replication variant H3.2 gene in silent base substitutions within the coding sequences. Thus, the H3.3 polypeptide sequence has been precisely maintained over a great evolutionary period, suggesting that this class of histones performs a strongly selected biological function. Although replacement variant histones can account for more than 50% of the total H3 protein in the nuclei of specific chicken tissues, the steady-state level of H3.3 mRNA is nearly the same (and is quite low) in all tissues and ages of animals examined. These properties suggest novel mechanisms for the control of the basal histone biosynthesis which takes place outside of the S phase of the cell cycle.

Age-dependent changes in the level of a 34 kDa DNA-binding protein in developing chick embryo liver

The relative amounts of a DNA-binding protein of 34 kDa increased during the early stages of development of chick embryo liver. The content of this protein reached a maximum in 18-19-day-old embryonic livers and decreased afterwards in older embryonic and post-natal chick livers. The 34 kDa polypeptide is the major DNA-binding protein (DBP) of embryonic liver and it preferentially binds to single-stranded DNA. The quantity of the 34 kDa DBP was relatively very low in embryonic muscle, heart and brain.

Replacement variant histone genes contain intervening sequences

The nucleotide sequences of two chicken histone genes encoding replacement variant H3.3 polypeptides are described. Unlike the replication variant genes of chickens (and almost all other organisms), these genes contain intervening sequences; introns are present in both genes in the 5' noncoding and coding sequences. Furthermore, the replacement variant histone mRNAs are post-transcriptionally polyadenylated. The locations, but not the sizes, of the two introns within the coding segments of the two genes have been exactly conserved, whereas the intron positions in their respective 5' flanking regions differ. Although both H3.3 genes predict the identical histone polypeptide sequence, they are as different from one another as each of them is from a more common replication variant H3.2 gene in silent base substitutions within the coding sequences. Thus, the H3.3 polypeptide sequence has been precisely maintained over a great evolutionary period, suggesting that this class of histones performs a strongly selected biological function. Although replacement variant histones can account for more than 50% of the total H3 protein in the nuclei of specific chicken tissues, the steady-state level of H3.3 mRNA is nearly the same (and is quite low) in all tissues and ages of animals examined. These properties suggest novel mechanisms for the control of the basal histone biosynthesis which takes place outside of the S phase of the cell cycle.

Differential expression of two clusters of mouse histone genes

The mouse histone mRNAs coded for by three different cloned DNA fragments have been characterized. Two of these cloned DNA fragments, MM221 and MM291, located on chromosome 13, code for H3, H2b and H2a histone mRNAs, which are expressed at low levels in cultured mouse cells and fetal mice. The other DNA fragment, MM614, located on chromosome 3, codes for an H3 and an H2a mRNA, which are expressed at high levels in these cells. The mRNAs for each histone protein share common coding region sequences, while the untranslated regions of all the genes have diverged significantly, as judged by S1 nuclease mapping. Amino acid substitutions in some H3, H2a and H2b proteins are detected as internal cleavages in the S1 nuclease maps. All of these genes code for replication variant histone mRNAs, which are regulated in parallel with DNA synthesis.

Histones in protistan evolution

The potential of comparative studies on histones for use in protistan evolution is discussed, using algal histones as specific examples. A basic premise for the importance of histones in protistan evolution is the observation that these proteins are completely absent in prokaryotes (and cytoplasmic organelles), but with few exceptions, the same five major histone types are found in all higher plants and animals. Since the histone content of the algae and other protists is not constant, some of these organisms may represent transition forms between the prokaryotic and eukaryotic modes of packaging the genetic material. Comparative studies of protistan histones may thus be of help in determining evolutionary relationships. However, several problems are encounter with protistan histones, including difficulties in isolating nuclei, proteolytic degradation, anomalous gel migration of histones, and difficulties in histone identification. Because of the above problems, and the observed variability in protistan histones, it is suggested that several criteria be employed for histone identification in protists.

Differences in the mode of iodination of H2a variants in chromatin

Modification of H2a variants with radioactive iodine was used to study under different ionic conditions the accessibility of their tyrosine residues in chromatin, in monosomes and when free in solution. The modification of tyrosine 57 in the hydrophobic part of H2a was found responsible for the appearance of new fractions with a reduced electrophoretic mobility in the presence of Trition X 100, detected only by autoradiography (radioactive "ghosts"). At low ionic strength a very small number of molecules were iodinated in chromatin, the modification affecting only their hydrophobic region. At moderate ionic strength the tyrosine residues near the N-terminal region of the molecule were predominantly modified. In chromatin the accessibility of the tyrosine residues of H2a1 was much greater than that of H2a2, a difference not observed with free histones.

Specific alterations in the pattern of histone-3 synthesis during conversion of human leukemic cells to terminally differentiated cells in culture

The presence of nano- to micromolar concentrations of 12-0-tetradecanoyl-phorbol-13-acetate (TPA) in suspension cultures of human promyelocytic leukemia cells, HL-60, or human monocytic leukemia cells, THP-1, resulted in the appearance of macrophage-like cells attached to the substratum. The terminally TPA-differentiated cells continued to synthesize histones at a low rate even though DNA replication had ceased. The pattern of synthesis of histone variants in differentiated cells differed from that in undifferentiated cells and resembled that of quiescent or density-arrested cells. In undifferentiated cells, all three histone-H3 variants are synthesized, while in quiescent cells, only the H3.3 variant is synthesized. When TPA-differentiated macrophages were placed in normal medium, the pattern of histone synthesis was not altered, thus substantiating previous findings that the differentiation is irreversible. Further, TPA-differentiated macrophages and macrophages isolated from a normal human donor exhibited identical pattern of histone synthesis. Altogether, the results indicate that changes in the synthetic rates of histones during the TPA-induced maturation of human leukemic cells is not directly due to TPA or terminal cell differentiation per se but is due to the cessation of cell proliferation and DNA replication.

Regulation of nucleosomal core histone variant levels in differentiating murine erythroleukemia cells

During hexamethylenebis(acetamide)-induced terminal differentiation of murine erythroleukemia (MEL) cells in vitro, the histone variant proportions undergo changes similar to those observed in vivo in terminally differentiating cells of the young mouse. Thus, there is a rapid increase in the relative amounts of the variants H2A.1 and H2B.2 in parallel with the increase in the number of hemoglobin-producing cells and the sharp decrease in the growth rate. We show that the changes in variant proportions are not associated with slower growth per se but are most likely due to differential changes in the rates of variant synthesis as a result of commitment to terminal differentiation. In addition, we observed an inducer-specific increase in the rate of synthesis and the relative amount of the minor H2A variant 4, well before hemoglobin accumulation. We also present evidence that H2A and H2B histones are synthesized and incorporated into chromatin at a significant rate even when DNA synthesis is inhibited, suggesting turnover of these histones. H2A and H2B turnover can be detected directly even in exponentially growing cells. H2A.1 and H2B.2 have higher turnover rates than H2A.2 and H2B.1, respectively, in exponentially growing cells, a difference which is even more pronounced in induced cells. The magnitude of the differential turnover is not sufficient to account for the changes in the histone variant proportions in the short life of induced MEL cells but could explain the slow accumulation of H2A.2, H2B.1, and H3.3 in nondividing adult tissues of the mouse.

Transcriptionally active chromatin

Eukaryotic chromatin has a dynamic, complex hierarchical structure. Active gene transcription takes place on only a small proportion of it at a time. While many workers have tried to characterize active chromatin, we are still far from understanding all the biochemical, morphological and compositional features that distinguish it from inactive nuclear material. Active genes are apparently packaged in an altered nucleosome structure and are associated with domains of chromatin that are less condensed or more open than inactive domains. Active genes are more sensitive to nuclease digestions and probably contain specific nonhistone proteins which may establish and/or maintain the active state. Variant or modified histones as well as altered configurations or modifications of the DNA itself may likewise be involved. Practically nothing is known about the mechanisms that control these nuclear characteristics. However, controlled accessibility to regions of chromatin and specific sequences of DNA may be one of the primary regulatory mechanisms by which higher cells establish potentially active chromatin domains. Another control mechanism may be compartmentalization of active chromatin to certain regions within the nucleus, perhaps to the nuclear matrix. Topological constraints and DNA supercoiling may influence the active regions of chromatin and be involved in eukaryotic genomic functions. Further, the chromatin structure of various DNA regulatory sequences, such as promoters, terminators and enhancers, appears to partially regulate transcriptional activity.

Histone variants of the insect Plodia interpunctella during metamorphosis

The pattern of histone variants from the meal moth Plodia interpunctella was compared to the mouse histone variant pattern. Plodia contains histones which comigrate on two dimensional gels with H3.2, H3.3, H4 and H2A.Z in mouse. Plodia H2A.1 and H2B.1 migrate somewhat differently from the respective mouse histones. Comparison of the iodinated tryptic peptides of H2A.1 and H2A.Z from mouse and Plodia showed that the H2A.Z proteins have two iodinated peptides that comigrate in the two species and three more that are different. The H2A.1 proteins in the two species have one iodinated peptide which comigrates and two more which migrate very close to each other. The histone variants from three developmental stages, larval, pupal and adult of Plodia interpunctella were also identified and compared. The same histone variant pattern is found through all stages of development. It is concluded that histone gene expression does not change during metamorphosis in Plodia .

A minireview of microheterogeneity in H1 histone and its possible significance

Subtypes of H1 histone vary in primary structure, and the higher organisms that have been studied each seem to have about a half-dozen subtypes. The proportions of these subtypes vary with the progress of differentiation as seen in embryonic development, hormonally induced changes, spermatogenesis, and terminal differentiation. The H1 subtypes differ among themselves in their ability to condense DNA and small chromatin fragments. They have the potential, therefore, of causing different parts of the chromatin to be condensed to different degrees.

Fate of newly synthesized histones in G1 and G0 cells

We have shown that quiescent cells as well as those in the G1 phase of the cell cycle synthesize histones at a reduced but significant rate. Now, we show that the histones synthesized during G0 and G1 are stably incorporated into nuclei soon after synthesis. Micrococcal nuclease digestion of nuclei isolated from cells in G0 and G1 revealed that the specific histone variants synthesized in these different physiological states are found associated with DNA as nucleosomes. Nucleosomes were separated by polyacrylamide gel electrophoresis in a reducing buffer so that histone spot morphology, particularly that of the H3s was improved.