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PubMed1992

Equal G and C contents in histone genes indicate selection pressures on mRNA secondary structure.

Protein-specific versus taxon-specific patterns of nucleotide frequencies were studied in histone genes. The third positions of codons have a (well-known) taxon-specific G+C level and a histone type-specific G/C ratio. This ratio counterbalances the G/C ratio in the first and second positions so that the overall G and C levels in the coding region become approximately equal. The compensation of the G/C ratio indicates a selection pressure at the mRNA level rather than a selection pressure or mutation bias at the DNA level or a selection pressure on codon usage. The structure of histone mRNAs is compatible with the hypothesis that the G/C compensation is due to selection pressures on mRNA secondary structure. Nevertheless, no specific motifs seem to have been selected, and the free energy of the secondary structures is only slightly lower than that expected on the basis of nucleotide frequencies.

Animals↗
PubMed1990

Chromatin structure of Drosophila melanogaster ribosomal genes.

The chromatin structure of ribosomal genes of D. melanogaster has been studied by crosslinking proteins to DNA. We found that a number of histone contacts with DNA through histidine in the approximately 1 kb-long region surrounding the transcription initiation site, coding regions and the region of 240 bp-long repeats from the intergenic spacers (Alu-repeats) were weakened as compared to the inactive chromatin of the type II insertion. A protein with the molecular mass of 50 kDa (p50), associated with all DNA sequences analysed, has been discovered. Another protein with molecular mass of about 70 kDa (p70) has been found to be specific only for the Alu-repeats.

Animals↗
PubMed1988

Histone acetylation: a step in gene activation.

Cellular ageing appears to consist mainly in a loss of adaptability and a progressive decrease in the capacity of the cell to maintain homeostasis. Such age related phenomenon can be the result of stochastic or of programmed events, and may occur through changes in the base pairs or coding of the DNA, through increasing levels of error in transcription and finally through alterations at the translation step of proteins synthesis. The purpose of this chapter is to present histone acetylation as a key event in the control of chromatin structure and transcription.

Acetylation↗
PubMed1982

Chicken histone H5: selection of a cDNA recombinant using an extended synthetic primer.

We describe the use of a synthetic primer to select a cDNA recombinant clone containing H5 coding sequences. The strategy used was as follows: 1. Prepare oligo(dT) cellulose-bound mRNA from chicken reticulocytes and select 11S-18S material from sucrose gradients. 2. Use this RNA fraction both to prepare a cDNA library and as a template for H5-specific cDNA synthesis using a synthetic primer. 3. Screen out most globin cDNA recombinants with oligo(dT)-primed globin cDNA. 4. Search for H5 recombinants using H5 specific cDNA and verify the identity by DNA sequencing. Our screening suggests an H5 mRNA abundance of about two parts per thousand in chicken reticulocyte poly(A)-containing RNA. The isolation of an H5 cDNA recombinant clone is an initial step in the study of H5 genes and their relationship to H1 and core histone genes.

Amino Acid Sequence↗
PubMed1999

Transcription of DNA templates associated with histone (H3 x H4)(2) tetramers.

To investigate the in vitro transcription by bacteriophage T7 RNA polymerase of oligonucleosomes lacking histone H2A x H2B dimers, templates were assembled from histone (H3 x H4)(2) tetramers with and without the complementary amount of H2A x H2B dimers and two different DNA species: pGEMEX-1, devoid of nucleosome positioning sequences, and T7-207-18, which contains downstream from the promoter 18 tandem repeats of a 207-bp positioning sequence. Assembly with core histone octamers affects pGEMEX-1 transcription mainly at the initiation level, while T7-207-18 is almost exclusively inhibited at the level of elongation. With both DNA templates and under different salt conditions, RNA synthesis is much more efficient on oligonucleosomes containing only (H3 x H4)(2) tetramers than on those with whole histone octamers. Under conditions promoting a low transcription rate, it is unambiguously shown with pGEMEX-1 that the block to initiation due to the presence of core histone octamers is substantially removed when (H3 x H4)(2) is substituted for the whole octamer. With T7-207-18, under assay conditions allowing transcription of the whole coding region of the naked DNA, analysis of the transcription products indicates that RNA elongation on the template containing (H3 x H4)(2) tetramers takes place as easily as on free DNA, in contrast with the significant inhibition observed in the presence of whole histone octamers.

Animals↗
PubMed1983

Nucleotide sequences of H1 histone genes from Xenopus laevis. A recently diverged pair of H1 genes and an unusual H1 pseudogene.

Four clones containing H1 histone gene sequences were previously isolated from a Xenopus laevis genomic library (1) and we now present the complete nucleotide sequences of these H1 genes and their flanking regions. Two of these genes code for minor H1 proteins, probably H1C, when expressed in the oocyte transcription/translation system and are present on clones with almost identical overall organization. However, at the nucleotide level these genes differ in showing base insertions and deletions, as well as substitutions. A third gene sequence which is more related to the major X. laevis H1A, corresponds to the 3' two thirds of an H1 gene. This gene has in place of a 5' coding region at least 1800 bp of apparently noncoding sequence, some of which is A-T rich. The junction does not correspond to the consensus sequence of an intron/exon boundary and therefore this H1 sequence is more likely to represent a pseudogene. Comparisons of the coding and flanking regions of these X. laevis H1 genes indicate the kind of differences which can occur among H1 subtypes within a species. A region of homology noted in the 3' noncoding portion of vertebrate histone genes is discussed in relation to the mechanism of termination of transcription.

Amino Acid Sequence↗
PubMed1983

In vivo incorporation of Drosophila H2a histone into mammalian chromatin.

Hybrid prokaryotic/eukaryotic expression vectors have been used to introduce Drosophila histone genes into CV-1 African green monkey tissue culture cells. Transfection of CV-1 cells with Drosophila genes under the control of insect DNA promoter sequences results in low level expression of histone genes. On the other hand, when the Drosophila H2a gene is juxtaposed downstream from the long terminal repeat sequence of Rous sarcoma virus (RSV) expression of the insect gene is considerably more efficient; both 3' polyadenylated insect histone messenger RNA and putative Drosophila H2a histone protein can be readily detected in the transduced cells. Using this RSV/H2a vector, we have been able to demonstrate the presence of Drosophila H2a histone in monomer nucleosome preparations isolated from transfected CV-1 cells. These results suggest the feasibility of 'remodeling' cellular chromatin in vivo in precisely defined ways. The techniques described may be generally applicable to other genes coding for chromosomal proteins.

Animals↗
PubMed1990

Organization and transcription of Volvox histone-encoding genes: similarities between algal and animal genes.

The nucleotide sequences of two non-allelic histone H2A-H2B gene loci of the green alga Volvox carteri have been determined. Each locus contains a divergently arranged H2A-H2B gene pair. The encoded proteins differ in one (H2A) and 16 positions (H2B), respectively. The coding regions are separated by short intercistronic segments (256 bp and 298 bp) containing TATA boxes and a central tandem repeat of a conserved 20-bp element as the putative histone-specific transcription signals. The 3'-untranslated regions exhibit a characteristic 3'-palindrome and weakly conserved spacer elements. Transcription in one gene locus was shown to initiate 48 bp upstream from H2A and 59 bp upstream from H2B. Contrary to higher plants, V. carteri histone mRNAs are nonpolyadenylated. S1 mapping and Northern-blotting experiments indicated that V. carteri histone mRNAs are terminated at the 3'-palindrome by the same mechanism that operates in vertebrates and sea urchins.

Amino Acid Sequence↗
PubMed2003

Phosphorylation of RNA polymerase II CTD regulates H3 methylation in yeast.

Histone methylation is now realized to be a pivotal regulator of gene transcription. Although recent studies have shed light on a trans-histone regulatory pathway that controls H3 Lys 4 and H3 Lys 79 methylation in Saccharomyces cerevisiae, the regulatory pathway that affects Set2-mediated H3 Lys 36 methylation is unknown. To determine the functions of Set2, and identify factors that regulate its site of methylation, we genomically tagged Set2 and identified its associated proteins. Here, we show that Set2 is associated with Rbp1 and Rbp2, the two largest subunits of RNA polymerase II (RNA pol II). Moreover, we find that this association is specific for the interaction of Set2 with the hyperphosphorylated form of RNA pol II. We further show that deletion of the RNA pol II C-terminal domain (CTD) kinase Ctk1, or partial deletion of the CTD, results in a selective abolishment of H3 Lys 36 methylation, implying a pathway of Set2 recruitment to chromatin and a role for H3 Lys 36 methylation in transcription elongation. In support, chromatin immunoprecipitation assays demonstrate the presence of Set2 methylation in the coding regions, as well as promoters, of genes regulated by Ctk1 or Set2. These data document a new link between histone methylation and the transcription apparatus and uncover a regulatory pathway that is selective for H3 Lys 36 methylation.

DNA Methylation↗
PubMed1997

Accuracy of histone H3 messenger RNA in situ hybridization for the assessment of cell proliferation in human tissues.

Histone H3 mRNA in situ hybridization was compared to a reference method, iododeoxyuridine (IdUrd) immunohistochemistry of tissues labeled in vivo, as a means for assessing the proportion of S-phase cells (labeling index, LI) in oral tumor and normal mucosa. Paraffin sections from 16 patients with oral squamous cell carcinoma were studied. Patients received an IdUrd infusion before the biopsy was taken. Tissue sections were coded before counting the percentages of S-phase cells. A high correlation was found between the results obtained by the two techniques. The average histone H3 and IdUrd LIs of the tumors were 28.5 +/- 2.4% and 29.2 +/- 2.7%, respectively (P = 0.85), with a Spearman correlation coefficient r = 0.95 (P < 0. 0001). The histone H3 LI of the basal layer of normal mucosa was 3.1 +/- 0.8%, whereas the IdUrd LI was 2.7 +/- 0.9% (P = 0.74), with r = 0.78 (P = 0.004). In the suprabasal layers, these parameters were 21. 3 +/- 2.3% and 23.9 +/- 3.2%, respectively (P = 0.56), with r = 0.93 (P < 0.0001). In sections stained for both histone H3 and IdUrd, most cells were double labeled, with very few cells containing only one of the labels. In some specimens, large areas of H3-stained cells did not contain IdUrd-labeled cells, suggesting that during the IdUrd infusion, the precursor did not reach these areas. Two specimens were histone H3 negative. They were also negative when hybridized with beta-actin probe, indicating degradation of mRNAs in these samples. The results of this study demonstrate that the histone H3 mRNA in situ hybridization performed in human formalin-fixed, paraffin-embedded tissues provides the same data as does labeling the tumors in vivo with halogenated pyrimidine.

Biopsy↗
PubMed1986

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.

Acetylation↗
PubMedDate not supplied

Cloning and analysis of the Kluyveromyces lactis TRP1 gene: a chromosomal locus flanked by genes encoding inorganic pyrophosphatase and histone H3.

The TRP1 gene of the yeast Kluyveromyces lactis has been cloned from a genomic library by complementation of the Saccharomyces cerevisiae trp1-289 mutation. The gene was located within the clone by transposon mutagenesis and the coding region identified by DNA sequencing. This has indicated that K. lactis TRP1 encodes a 210-amino acid polypeptide which shows 53% identity to the homologous S. cerevisiae protein. The K. lactis TRP1 gene has been disrupted by substituting the S. cerevisiae URA3 gene for a large part of the TRP1 coding sequence. Replacement of the chromosomal TRP1 locus with this construction has enabled the production of non-reverting trp1- strains of K. lactis, while a genetic analysis of the disrupted allele confirmed that the TRP1 gene had been cloned. DNA sequencing has also shown that the K. lactis TRP1 sequence is flanked by genes encoding inorganic pyrophosphatase and histone H3, which we have designated IPP and HHT1 respectively. Hybridization studies have shown that in common with S. cerevisiae, K. lactis has two copies of the histone H3 gene. Each H3 gene is closely linked to a gene encoding histone H4 and in both yeast species the IPP gene is tightly linked to one of the histone gene pairs.

Amino Acid Sequence↗
PubMedDate not supplied

[Gradient condensation of chromatin in ribosomal genes of Drosophila melanogaster].

The organization of chromatin in D. melanogaster ribosomal repeats with and without insertions was studied. We have shown earlier that upon digestion with micrococcal nuclease a "non-transcribed" intergenic spacer produces unusual chromatin particles containing DNA fragments 200-280 b.p. in length. These particles sediment like H1-containing nucleosomes, are stable only in the presence of polyamines, and are probably bound to some non-histone protein. The content of core histones and H1 in different regions of ribosomal genes has been studied by two-dimensional electrophoresis of chromatin particles and by "protein-image" hybridization. The content of histones and respectively the degree of chromatin condensation increase in the following order: the 1kb-long region surrounding the initiation site is practically free of histones less than the region of 240 b.p. repeats from the intergenic spacer, containing homologies with the ribosomal promotor less than coding region preceding the usual site of insertions less than coding region lying behind this site less than inactive type II ribosomal insertion. Therefore, the region of the beginning of transcription of most ribosomal genes is in an active conformation, even though at least 75% of the genes are repressed. Ribosomal insertions are in a compact, repressed form. We suggest that their inhibitory action on the transcription of corresponding genes at the molecular level is similar to the position effect of heterochromatic regions at the chromosomal level.

Animals↗
PubMed1989

In vivo protein binding sites and nuclease hypersensitivity in the promoter region of a cell cycle regulated human H3 histone gene.

The chromatin structure and protein-DNA interactions of a cell cycle regulated human H3 histone gene have been examined at different levels of resolution. Using traditional Southern blot analysis we have investigated the accessibility of the H3 coding region and its flanking sequences to DNase I, S1 nuclease and restriction endonuclease digestion. Using the native genomic blotting method recently developed in our laboratory, two sites of protein-DNA interaction in the proximal 240 bp of the promoter region of this H3 gene were established. Further in vivo analysis of protein-DNA binding sites in intact cells by genomic sequencing revealed, with single nucleotide resolution, the guanine contacts and footprints of the proteins bound to the promoter. The relative locations of protein-DNA interactions in this H3 gene are similar to those identified in vivo and in vitro in a cell cycle dependent human H4 histone gene. The proteins complexed with the H3 histone gene promoter can be dissociated between 0.16 and 0.28 M NaCl. The protein-DNA contacts persist throughout the cell cycle and thus may have a functional relationship with the basal level of transcription of this H3 gene that occurs during and outside of S phase.

Base Sequence↗
PubMed1980

Transcriptional fidelity of histone genes injected into Xenopus oocyte nuclei.

Previous work has indicated that at least some of the genetic information required for the expression of sea urchin histone genes is recognized following injection of the gene repeat (h22) into Xenopus oocyte nuclei. The ability to elicit the expression of cloned genes and their sequence-manipulated counterparts is proving invaluable in analysing the molecular details of gene expression. Direct injection of such genes into Xenopus oocyte nuclei remains one of the simplest methods for obtaining such expression and a remarkable degree of transcriptional fidelity has been demonstrated using this system with RNA polymerase III genes, and to a lesser extent with rDNAs transcribed by RNA polymerase I. In the case of polymerase II genes there is ample evidence for coupled transcription-translation, but the degree of transcriptional fidelity involved may, as has recently been shown for the ovalbumin gene, be minimal. However, clearly if the oocyte is to be used to investigate transcriptional regulation of such genes, transcriptional fidelity defined as the production of correct RNA termii, rather than the production of 'functional mRNAs' (ref. 15), must pertain. Here we demonstrate such fidelity in the expression of all five Psammechinus miliaris histone genes comprising a repeat unit. However, we find large quantitative variations in the levels of synthesis of the individual correct termini and hence of the mRNAs. In addition to the mRNAs, species with no detectable counterparts in the sea urchin are generated off the coding strand, as are heterogeneous noncoding species.

Animals↗
PubMed1993

Two histone H1-encoding genes of the green alga Volvox carteri with features intermediate between plant and animal genes.

Southern hybridization indicated the presence of at least two and possibly four histone H1-encoding genes occurring as singlets in the Volvox carteri genome. Two of these genes, H1-I and H1-II, have been cloned and characterized. Their coding sequences are each interrupted by three introns, but only the position of the second intron is identically conserved in both H1-I and H1-II. The encoded 260-amino-acid (aa) (H1-I) and 240-aa (H1-II) polypeptides possess the typical tripartite organization of animal H1 histones, with variable N- and C-terminal domains flanking a conserved 'globular' DNA-binding domain. Extensive differences in their variable regions suggest that H1-I and H1-II (62% identity) represent two isotypes with different functions. A prominent KAPKAP-KAA motif in the H1-I N-terminal region, similarly seen in single H1 variants of a mosquito and a nematode, has a putative function in packing condensed subtypes of chromatin. Different from higher plants, but like animals, the H1 genes of V. carteri possess a typical 3' palindrome for mRNA processing, resulting in non-polyadenylated mRNAs. Transcription initiates 33 nucleotides (nt) (H1-I) and 26 nt (H1-II) downstream of typical TATA boxes. A putative 20-bp conserved enhancer element upstream of each TATA box closely resembles the consensus sequence associated with the nucleosomal histone-encoding genes in V. carteri [Müller et al., Gene 93 (1990) 167-175] and suggests stringent regulation. Accordingly, transcription of H1 was shown to be restricted to late embryogenesis, when new flagella are produced. We discuss the inferred accessory role of histone H1 proteins in stabilizing axonemal microtubules, as has been recently observed in sea urchin flagella [Multigner et al., Nature 360 (1992) 33-39].

Amino Acid Sequence↗
PubMed1986

Normal stoichiometry of histone dimer sets is necessary for high fidelity of mitotic chromosome transmission.

To identify gene products that function stoichiometrically in mitotic chromosome transmission, genes were cloned on high copy number plasmids and transformed into yeast cells, and the transformants were examined for an increase in the frequency of mitotic chromosome loss or recombination resulting from the gene imbalance. When either pair of the yeast histone genes H2A and H2B, or H3 and H4 was present on high copy number plasmids, both chromosomes V and VII exhibited an increased frequency of chromosome loss. The rate of chromosome loss was not elevated when the histone genes were present on single copy plasmids, when their transcription from high copy plasmids was repressed, or when frame-shift mutations were present in the coding sequence. This method for the identification of genes circumvents some of the limitations of traditional mutational analysis and yields the cloned gene.

Aneuploidy↗
PubMed1994

Isolation and characterization of two replication-dependent mouse H1 histone genes.

Mice contain at least seven nonallelic forms of the H1 histones, including the somatic variants H1a-e and less closely related variants H1 degrees and H1t. The mouse H1 degrees and H1c (H1var.1) genes were isolated and characterized previously. We have now isolated, sequenced and studied the expression properties of two additional mouse H1 genes, termed H1var.2 and H1var.3. Extensive amino acid and nucleotide sequence comparisons were made between the two genes and other mammalian H1 histone genes. A high degree of nucleotide sequence identity was seen between the H1var.2, rat H1d and human H1b genes, even well beyond the coding region, indicating that these genes are likely homologues. Unlike the previously characterized mouse H1var.1 gene which produces both nonpolyadenylated and polyadenylated mRNAs, the H1var.2 and H1var.3 genes produce only typical, replication dependent, nonpolyadenylated mRNAs.

Amino Acid Sequence↗