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Studies on histone oligomers. IV. Reassociation of chromatin from histones of various conformations.

Chicken erythrocyte chromatin, whole or (H1,H5)-depleted, was dissociated in 2 M NaCl in the presence or absence of 5 M urea at pH 8 or pH 5, and reconstituted by decreasing the concentration of NaCl and urea. The reassociated products were characterized by their solubilities in 0.1 mM EDTA, micrococcal nuclease digestion, cross-linking of histones, and fractionation of histone oligomers by solubility in ammonium sulfate solution. In the absence of urea, the nucleosome structure and the histone octamer were reconstituted perfectly at both pH 5 and pH 8. When chromatin was exposed to urea, no nucleosome structure or histone octamer was obtained at pH 5 either decreasing the concentration of salt first or that of urea first. At pH 8, the chromatin structure was regained fairly well by decreasing the concentration of urea first, but only partially by decreasing the concentration of salt first. Solubility in 0.1 mM EDTA was found to be a good criterion for monitoring the proper reassociation of chromatin.

Animals↗

Phosphoserines on maize CENTROMERIC HISTONE H3 and histone H3 demarcate the centromere and pericentromere during chromosome segregation.

We have identified and characterized a 17- to 18-kD Ser50-phosphorylated form of maize (Zea mays) CENTROMERIC HISTONE H3 (phCENH3-Ser50). Immunostaining in both mitosis and meiosis indicates that CENH3-Ser50 phosphorylation begins in prophase/diplotene, increases to a maximum at prometaphase-metaphase, and drops during anaphase. Dephosphorylation is precipitous (approximately sixfold) at the metaphase-anaphase transition, suggesting a role in the spindle checkpoint. Although phCENH3-Ser50 lies within a region that lacks homology to any other known histone, its closest counterpart is the phospho-Ser28 residue of histone H3 (phH3-Ser28). CENH3-Ser50 and H3-Ser28 are phosphorylated with nearly identical kinetics, but the former is restricted to centromeres and the latter to pericentromeres. Opposing centromeres separate in prometaphase, whereas the phH3-Ser28-marked pericentromeres remain attached and coalesce into a well-defined tether that binds the centromeres together. We propose that a centromere-initiated wave of histone phosphorylation is an early step in defining the two major structural domains required for chromosome segregation: centromere (alignment, motility) and pericentromere (cohesion).

Amino Acid Sequence↗

Loading of Arabidopsis centromeric histone CENH3 occurs mainly during G2 and requires the presence of the histone fold domain.

The centromeric histone H3 (CENH3) substitutes histone H3 within the nucleosomes of active centromeres in all eukaryotes. CENH3 deposition at centromeres is needed to assemble the kinetochore, a complex of conserved proteins responsible for correct chromosome segregation during nuclear division. Histones of regular nucleosomes are loaded during replication in S phase, while CENH3 deposition deviates from this pattern in yeast, human, and Drosophila melanogaster cells. Little is known about when and how CENH3 targets centromeric loci. Therefore, we determined the location and quantity of recombinant enhanced yellow fluorescent protein (EYFP)-CENH3 in mitotic root and endopolyploid leaf nuclei of transgenic Arabidopsis thaliana cells. Our data indicate significant loading of A. thaliana CENH3 during G2 (before splitting into sister kinetochores) rather than during the S or M phase of the cell cycle. The histone fold domain of the C-terminal part of CENH3 is sufficient to target A. thaliana centromeres. A. thaliana EYFP-CENH3 can recognize and target three different centromeric repeats of Arabidopsis lyrata but not field bean (Vicia faba) centromeres.

Amino Acid Sequence↗

Analysis of binding interactions between histone core complex and simian virus 40 DNA. A comparison of acetylated versus non-acetylated histone core complexes.

The interactions of acetylated and non-acetylated core complex histones with simian virus 40 (SV40) DNA 1 have been analyzed. A modified filter-binding assay utilizing micrococcal nuclease, which allows quantification of histone octamer binding to DNA has been developed. Using this assay it was determined that both non-acetylated core complex histones ad core complex histones acetylated with acetyl adenylate to levels existing in vivo bind cooperatively to SV40 DNA 1. Although both interactions are cooperative, the magnitude of the cooperativity parameter, omega, is significantly less in the acetylated case. This difference in cooperativity is in contrast to the nearly identical intrinsic association constant, K, observed in both cases.

Acetylation↗

Conformation studies of histone H1(0) in comparison with histones H1 and H5.

The class of lysine-rich histones, H1, found in most eukaryotic cells is largely replaced by another class of lysine-rich histones, H5, in avian and other erythrocytes. Erythrocytes are transcriptionally inert and this state has been attributed to the presence of H5. Although there are many sequence differences between H1 and H5 both molecules have very similar structures with three well-defined domains: a flexible basic N-terminal region, an apolar globular central region and a flexible basic C-terminal region. The lengths of the N-terminal regions are different for H1 and H5 whereas the lengths of the central and C-terminal regions are very similar. Considerable interest attaches to the findings that another type of mammalian lysine-rich histone H1(0) has an apolar region exhibiting considerable sequence homology (70%) with the central globular region of H5. The abundance of H1 in cells has been found to correlate inversely with their mitotic activities. Conformational studies using high-resolution nuclear magnetic resonance and optical spectroscopy have been made of H1 and its conformational behaviour has been compared with those of H1 and H5. H1 has been found to contain a central globular region of similar size to those found in H1 and H5. However, the conformation and stability of the globular domain of H1 are very similar to the globular region of H5 rather than H1. H1 appears to be a hybrid containing a major feature of the H5 histone. The globular regions of H1 and H5 are known to bind to a specific site on the nucleosome sealing off two turns of DNA. It is proposed that H1 binds to the same site.

Amino Acid Sequence↗

Proteolytic digestion studies of chromatin core-histone structure. Identification of limit peptides from histone H2B.

Trypsin digestion of chicken erythrocyte chromatin results in a well-defined set of limit peptides derived from the core histones (P1-P5). Two peptides running in sodium dodecyl sulphate gel electrophoresis at the positions of P2 and P3 have been identified as histone H2B residues 21-125 and 24-125. No C-terminal residues are therefore lost from histone H2B. The N-terminal sequence removed correlates well with that having low sequence conservation and not with that showing the greatest basicity. The same correlation was reported previously by us for histone H2A.

Amino Acid Sequence↗

Conserved eukaryotic histone-fold residues substituted into an archaeal histone increase DNA affinity but reduce complex flexibility.

Although the archaeal and eukaryotic nucleosome core histones evolved from a common ancestor, conserved lysine residues are present at DNA-binding locations in all four eukaryotic histones that are not present in the archaeal histones. Introduction of lysine residues at the corresponding locations into an archaeal histone, HMfB, generated a variant with increased affinity for DNA that formed more compact complexes with DNA. However, these complexes no longer facilitated the circularization of short DNA molecules and had lost the flexibility to wrap DNA alternatively in either a negative or positive supercoil.

Amino Acid Sequence↗

Histone H2A.X gene transcription is regulated differently than transcription of other replication-linked histone genes.

Histone H2A.X is a replication-independent histone H2A isoprotein species that is encoded by a transcript alternatively processed at the 3' end to yield two mRNAs: a 0.6-kb mRNA ending with the stem-loop structure characteristic of the mRNAs for replication-linked histone species, and a second, polyadenylated 1.6-kb mRNA ending about 1 kb further downstream (C. Mannironi, W. M. Bonner, and C. L. Hatch, Nucleic Acids Res. 17:9113-9126, 1989). Of the two, the 0.6-kb H2A.X stem-loop mRNA predominates in many cell lines, indicating that the presence of two types of mRNA may not completely account for the replication independence of H2A.X protein synthesis. The ambiguity is resolved by the finding that the level of the 0.6-kb H2A.X mRNA is only weakly downregulated during the inhibition of DNA replication and only weakly upregulated during the inhibition of protein synthesis, while the levels of other replication-linked mRNAs are strongly down- or upregulated under these two conditions. Analysis of the nuclear transcription rates of specific H2A genes showed that while the rates of transcription of replication-linked H2A genes decreased substantially during the inhibition of DNA synthesis and increased substantially during the inhibition of protein synthesis, the rate of H2A.X gene transcription decreased slightly under both conditions. These differences in transcriptional regulation between the H2A.X gene and other replication-linked histone genes are sufficient to account for the differences in regulation of their respective stem-loop mRNAs.

Base Sequence↗

3' end processing of Drosophila melanogaster histone pre-mRNAs: requirement for phosphorylated Drosophila stem-loop binding protein and coevolution of the histone pre-mRNA processing system.

Synthetic pre-mRNAs containing the processing signals encoded by Drosophila melanogaster histone genes undergo efficient and faithful endonucleolytic cleavage in nuclear extracts prepared from Drosophila cultured cells and 0- to 13-h-old embryos. Biochemical requirements for the in vitro cleavage are similar to those previously described for the 3' end processing of mammalian histone pre-mRNAs. Drosophila 3' end processing does not require ATP and occurs in the presence of EDTA. However, in contrast to mammalian processing, Drosophila processing generates the final product ending four nucleotides after the stem-loop. Cleavage of the Drosophila substrates is abolished by depleting the extract of the Drosophila stem-loop binding protein (dSLBP), indicating that both dSLBP and the stem-loop structure in histone pre-mRNA are essential components of the processing machinery. Recombinant dSLBP expressed in insect cells by using the baculovirus system efficiently complements the depleted extract. Only the RNA-binding domain plus the 17 amino acids at the C terminus of dSLBP are required for processing. The full-length dSLBP expressed in insect cells is quantitatively phosphorylated on four residues in the C-terminal region. Dephosphorylation of the recombinant dSLBP reduces processing activity. Human and Drosophila SLBPs are not interchangeable and strongly inhibit processing in the heterologous extracts. The RNA-binding domain of the dSLBP does not substitute for the RNA-binding domain of the human SLBP in histone pre-mRNA processing in mammalian extracts. In addition to the stem-loop structure and dSLBP, 3' processing in Drosophila nuclear extracts depends on the presence of a short stretch of purines located ca. 20 nucleotides downstream from the stem, and an Sm-reactive factor, most likely the Drosophila counterpart of vertebrate U7 snRNP.

Amino Acid Sequence↗

Analysis of histone gene expression in adult tissues of the sea urchins Strongylocentrotus purpuratus and Lytechinus pictus: tissue-specific expression of sperm histone genes.

We analyzed the histone mRNA population found in several adult tissues of the sea urchin Strongylocentrotus purpuratus and in testis of Lytechinus pictus. Unique species of H1 and H2b mRNAs encoding the sperm-specific histone subtypes can be found exclusively in testis RNA. S. purpuratus contains two distinct testis-specific H1 transcripts, while L. pictus contains one such transcript. Each of these mRNAs is larger than either early or late embryonic H1 mRNAs. Other somatic adult tissues contain transcripts derived from members of the late embryonic H1 histone gene family. S. purpuratus contains one H2b transcript found exclusively in testis, while L. pictus contains two such H2b mRNAs. Similarly, in tissues other than testis, late H2b transcripts were found. While there is no sperm-specific H2a protein, a limited set of late histone H2a genes encoding primarily the H2a-beta subtype is expressed in testis. The majority of the H2a protein found in diploid adult tissues is also the H2a-beta subtype; however, the size of the H2a transcripts differs between testis and other tissues. We conclude that different members of the late H2a gene family are differentially expressed in embryos and adult tissues. We prepared and characterized cDNA clones encoding the sperm-specific H2b protein as well as the H2a-beta protein found in testis.

Amino Acid Sequence↗

Uteroplacental insufficiency induces site-specific changes in histone H3 covalent modifications and affects DNA-histone H3 positioning in day 0 IUGR rat liver.

Uteroplacental insufficiency and subsequent intrauterine growth retardation (IUGR) increase the risk of adult onset insulin resistance and dyslipidemia in humans and rats. IUGR rats are further characterized by postnatal alterations in hepatic PPAR-gamma coactivator (PGC-1) and carnitine-palmitoyl-transferase I (CPTI) expression, as well as overall hyperacetylation of histone H3. However, it is unknown whether the histone H3 hyperacetylation is site specific or relates to the changes in gene expression previously described in IUGR rats. We therefore hypothesized that uteroplacental insufficiency causes site-specific modifications in hepatic H3 acetylation and affects the association of acetylated histone H3 with PGC-1 and CPTI promoter sequences. Uteroplacental insufficiency was used to produce asymmetrical IUGR rats. IUGR significantly increased acetylation of H3 lysine-9 (H3/K9), lysine-14 (H3/K14), and lysine-18 (H3/K18) at day 0 of life, and these changes occurred in association with decreased nuclear protein levels of histone deacetylase 1 (HDAC1) and HDAC activity. Chromatin immunoprecipitation using acetyl-H3/K9 antibody and day 0 chromatin revealed that uteroplacental insufficiency affected the association between acetylated H3/K9 and the promoters of PGC-1 and CPTI, respectively, in IUGR liver. At day 21 of life, the neonatal pattern of H3 hyperacetylation persisted only in the IUGR males. We conclude that uteroplacental insufficiency increases H3 acetylation in a site-specific manner in IUGR liver and that these changes persist in male IUGR animals. The altered association of the PGC-1 and CPTI promoters with acetylated H3/K9 correlates with previous reports of IUGR altering the expression of these genes. We speculate that in utero alterations of chromatin structure contribute to fetal programming.

Animals↗

Isolation and characterization of protein A24, a "histone-like" non-histone chromosomal protein.

In earlier studies, the nucleolar levels of protein A24 were found to be markedly decreased in the nucleolar hypertrophy induced by thioacetamide or during liver regeneration (Ballal, N.R., Goldknopf, I.L., Goldberg, D.A., and Busch, H. (1974) Life Sci. 14, 1835-1845; Ballal, N.R., Kang, Y.-J., Olson, M.O.-J., and Busch, H.J. Biol. Chem. 250, 5921-5925). To determine the role of protein A24, methods were developed for its isolation in highly purified form. Milligram quantities of highly purified protein A24 were isolated from the 0.4 N H2SO4-soluble proteins of calf thymus chromatin by exclusion chromatography on Sephadex G-100, followed by preparative polyacrylamide gel electrophoresis. Protein A24 was highly purified as shown by its migration as a single spot on two-dimensional polyacrylamide gel electrophoresis, its single NH2-terminal amino acid, methionine, and the production of approximately 50 peptides by tryptic digestion. Like histones 2A, 2B, 3, and 4. A24 was extractable from chromatin with 0.4 N H2SO4 or 3 M NaCl/7 M urea, but unlike most non-histone proteins or histone 1, protein A24 was not extracted with 0.35 M NaCl, 0.5 M HClO4, or 0.6 M NaCl. Protein A24 was present in only 1.9% of the total amount of histones 2A, 2B, 3 and 4; its molecular weight is 27,000.

Amino Acids↗

Isolation of four core histones from human sperm chromatin representing a minor subset of somatic histones.

Using high performance liquid chromatography we have successfully purified four core histones from mature human sperm chromatin. The H2A variants present in sperm (H2A.X and limited H2A.Z) have been shown previously to be minor variants in somatic chromatin. The histones are highly modified as evidenced by extensive acetylation and an as yet uncharacterized multicharge modification of H2B. Based on our data, we conclude that histone proteins are a minor component of each mature spermatozoa. Given the unique nature of the histone variants present in sperm, we propose that this chromatin component has a specific function and may possibly facilitate the programming of genes which will be active in early development.

Amino Acids↗

Chemical cross-linking of H1 histone to the nucleosomal histones.

When whole steer kidney nuclei were treated with dimethyl-3,3'-dithiobisproprionimidate, N,N'-bis(2-carboxyimidomethyl) tartaramide dimethyl ester, or 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide under approximately physiological ionic conditions, H1 histone was cross-linked to each of the four histones in the nucleosome core. The carbodiimide reagent, which introduces no atoms between the amino acid side chains being joined, seemed to give the same result as did the longer di-imidate cross-linking reagents. When conditions were optimized for the production of of H1-containing dimers, the total yield of H1-core histone heterodimers was nearly equal to the yield of H1 homodimers. Naturally occurring H1 dimers and cross-linked heterodimers of high mobility group proteins 14 and 17 with H1 and core histones were also observed.

Animals↗

[Histone H1 from the herring Clupea harengus pallasi testis structurally resembling histone H5].

Erythrocyte- and testis-specific fractions of the lysine-rich histone of herring Clupea harengus pallasi were studied. Electrophoretically purified fractions were cleaved at residues of tyrosine and phenylalanine. The fragments thus obtained and intact proteins were investigated by the method of incomplete succinylation which permitted one to determine the number of lysine residues, the total number of arginine and histidine residues and the molecular length of polypeptides. It has been found that the testis-specific fraction has in its C-terminal half of the molecule 15 arginine residues and a high proportion of basic amino acid residues (0,49) and thereby resembles the histone H5 of birds and fishes. The N-terminal half of this fraction however is close to the somatic variants of lysine-rich histones by the number of arginine residues and by the proportion of basic amino acid residues. To the author's knowledge, the testis-specific fraction of the lysine-rich histone in fishes are described for the first time.

Amino Acid Sequence↗

[Histones of Salmonidae fishes. Comparative study of histones from different species and intraspecies variability of Oncorhynchus nerka H1].

The comparative electrophoretic properties of erythrocyte histones from 7 Salmonidae species were investigated. Using Na-SDS gel electrophoresis, it was shown that all the species studied possess the erythrocyte-specific fraction of histone H5. High resolution gel electrophoresis in acetic acid--urea gels demonstrated differences in the subfractional composition of histone H1 from erythrocytes and liver of O. nerka. The analysis of the sample of 40 individuals from the same population revealed the existence of intraspecies polymorphism in histone H1 subfractional composition.

Animals↗

A histone H4-specific methyltransferase. Properties, specificity and effects on nucleosomal histones.

A histone H4-specific methyltransferase was purified 80-100-fold from nuclei of calf lymphocytes and from calf thymus. Some biochemical properties of the enzyme are described. The enzyme transfers in vitro methyl groups from S-adenosylmethionine preferentially to the lysine residue 20 of histone H4. This is the major in vivo methylation site of H4. DNA-bound or nucleosomal H4 is not methylated in vitro. We have used methylated and unmodified H4 (in the presence of sufficient quantities of the other core histones) for nucleosome reconstitution in vitro and have not found significant differences in the efficiencies of assembly.

Amino Acids↗

Regulation of the histone H3K36 methyltransferase Set2 by the histone chaperone Spt6.

Histone H3 lysine 36 methylation is a conserved histone modification that is critical for maintaining eukaryotic transcriptional fidelity and genomic stability. In Saccharomyces cerevisiae, this modification is catalyzed by Set2, an ortholog of the mammalian H3K36 methyltransferase SETD2. Previous genetic, biochemical, and structural studies showed that Set2 activity is repressed by a Set2 autoinhibitory domain (AID) and that activation requires the direct binding of the histone chaperone Spt6. To study the role of Spt6 and Set2 autoinhibition in vivo, we have isolated and analyzed multiple classes of Spt6 and Set2 mutants. Our results suggest an autoinhibited form of Set2 in which the catalytic domain (CD) is bound by the AID. In strong agreement with our genetic results, biophysical experiments demonstrate that the CD and AID physically interact, and that the autoinhibition mutants disrupt this interaction. Finally, RNA sequencing and chromatin immunoprecipitation and sequencing studies show the importance of the Set2-Spt6 interaction for transcription and H3K36 methylation genome-wide. Taken together, our results support a model in which Set2 exists in an inactive, autoinhibited state in vivo through direct CD-AID interactions, with binding by Spt6 required to release the autoinhibition.

Saccharomyces cerevisiae Proteins↗