Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Histone Code”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 433 records · Page 24Linked to original sources
PubMed1994

The pattern of histone H4 expression in the tomato shoot apex changes during development.

Two histone H4 cDNA clones were isolated from a tomato (Lycopersicon esculentum Mill.) shoot-tip cDNA library using a heterologous probe from barley (Hordeum vulgare L.). Both cDNAs, which are 81% identical in the coding region, are polyadenylated and belong to a small gene family in the tomato genome. Histone H4 message is abundant in young tissues and rare in older tissues. In the shoot apical meristem, the distribution of H4-expressing cells changes during development. In a juvenile vegetative apex, H4 message is detectable in the central region and the peripheral parts of the meristem. In a mature vegetative apical meristem, H4-expressing cells are localized in the peripheral zone extending into the provascular strands and the rib meristem whereas the central zone is almost devoid of H4 mRNA. After floral transition, H4 mRNA is found throughout the floral meristem, indicating a second change in the pattern of H4 expression. The observed changes in H4 expression are indicative of changes in the distribution of mitotic activity in the shoot apical meristem during plant development. In addition, H4-expressing cells were found to occur frequently in clusters, which may indicate a partial synchronization of cell divisions in the shoot apex.

Amino Acid Sequence↗
PubMed1997

Developmental and tissue expression patterns of histone macroH2A1 subtypes.

MacroH2A is a novel nucleosomal core histone that contains a large nonhistone region and a region that closely resembles a full length histone H2A. We have cloned a cDNA that contains the entire coding region of macroH2A1.2, one of the two identified subtypes of macroH2A1. MacroH2A1.2 was found to differ from the other known subtype, macroH2A1.1, in a single segment of the nonhistone region. MacroH2A1 specific antibodies revealed relatively high levels of both subtypes in adult liver and kidney. MacroH2A1.1 was much lower in fetal liver and kidney in comparison to their adult counterparts, and was not detected in adult thymus and testis, tissues with active cell division and differentiation. Both subtypes were present at very low levels or absent from mouse embryonic stem cells maintained in an undifferentiated state by growth in the presence of leukemia inhibitory factor. MacroH2A1.2 increased when the embryonic stem cells were induced to differentiate in vitro, while macroH2A1.1 remained undetectable. These results support the idea that macroH2A1.1 and macroH2A1.2 are functionally distinct, and suggest that changes in their expression may play a role in developmentally regulated changes in chromatin structure and function.

Animals↗
PubMed1987

Unusual features of transcribed and translated regions of the histone H4 gene family of Tetrahymena thermophila.

The complete DNA sequence is presented of H4-II, the second of the pair of histone H4 genes of the ciliated protozoan, Tetrahymena thermophila. Both H4 genes code for the same protein. Codon usage in these and other Tetrahymena genes is severely restricted and is similar to that in yeast. Flanking regions are AT-rich (greater than or equal to 75%), relative to coding sequences (approximately 45% GC). Except for small, similarly positioned homologies, flanking sequences of the two genes are different. Canonical sequences in higher eukaryotic promoters are not obvious in these genes. Instead, short, localized, base composition eccentricities characterize the 5' flanking sequences of all Tetrahymena genes analyzed. The consensus, P yP u(A)3-4 ATGG initiates translation in these and all other known Tetrahymena genes. Nuclear transcripts and messages of both growing and starved cells begin at multiple sites, mainly at the first or second A residue following a pyrimidine. The palindrome typical of histone message 3' termini in higher organisms is not present. Downstream of both genes are sequences similar to the processing/polyadenylation signal of higher eukaryotes, although the unique 3' ends are not those predicted by the location of the signals.

Amino Acid Sequence↗
PubMed1978

Reiterated genes with varying location in intercalary heterochromatin regions of Drosophila melanogaster polytene chromosomes.

The localization of two cloned D. melanogaster DNA fragments in polytene chromosomes was determined by means of in situ hybridization. These different fragments (Dm 225 and Dm 234B) are present in the genome in hundreds copies and contain genes whose transcription yields two different classes in abundant mRNA (Ilyin et al., 1976, 1977; Tchurikov et al., 1978). About 20--30 sites of these genes are demonstrable in the polytene chromosomes of a given stock. There are small but significant variations in the number and localization of these sites among individuals of the same stock. On the other hand, different stocks of D. melanogaster have an utterly different distribution of revealed hybridization sites in the polytene chromosomes. The location of both fragments (Dm 225 and Dm 234) was found to be virtually identical within any given stock of D. melanogaster. 69 sites for localization of Dm 225 or Dm 234 genes were detected in the chromosomes of 11 individuals studied. At least 50 (and up to 62) of them coincide with intercalary heterochromatin regions which are known to be characterized by ectopic pairing, late replication and the presence of "weak spots" in the chromosome. The ability of Dm225 and Dm 234 to code for the "abundant" classes of messenger RNA (Ilyin et al., 1976) and the fact that their location may coincide with the histone and ribosomal genes suggest that intercalary heterochromatin regions are "nests" containing various types of actively transcribable tandem-repeated genes coding for common "household" cell functions.

Animals↗
PubMed1982

Active chromatin.

Active genes are packaged into an altered nucleosome structure forming a chromosomal domain defined by increased sensitivity to nucleases. This structure, reflecting a potential for transcription, contains sites hypersensitive to nuclease digestion adjacent to the coding regions and may also be distinguished by specific non-histone proteins, variant or modified histones or modified DNA. Its formation, by unfolding of a tightly packed chromatin fibre by factors which might affect DNA supercoiling, may be the first step in gene activation.

Animals↗
PubMed1997

Structural characteristics of two wheat histone H2A genes encoding distinct types of variants and functional differences in their promoter activity.

To investigate the regulation of plant histone H2A gene expression, we isolated two H2A genes (TH254 and TH274) from wheat, which encode two variants of H2A. Both genes had an intron in the coding region. In the promoters, some characteristic sequences, such as Oct and Nona motifs, which are conserved among plant histone genes, were located in a short region (about 120 bp) upstream from the putative TATA box. Transient expression analyses of promoter activity with H2A-GUS fusion genes using tobacco protoplasts revealed novel types of positive cis-acting sequences in the TH254 promoter: a direct repeat of a 13 bp sequence (AGTTACATTATTG) and a stretch composed of an AT-rich sequence (ATATAGAAAATTAAAA) and a G-box (CACGTG). Quantitative S1 assay of the mRNA amounts from the TH254/GUS and TH274/GUS chimeric genes in stably transformed and cell cycle-synchronized tobacco cell lines showed that the promoters of both genes contained at least one cis-acting element responsible for S phase-specific expression. Histochemical analysis of transgenic tobacco plants carrying the chimeric genes showed that the promoters of the two H2A genes were active in developing seedlings and flower organs but were regulated in a different manner.

Amino Acid Sequence↗
PubMed1994

Isolation of a new H3.3 histone variant cDNA of P. lividus sea urchin: sequence and embryonic expression.

A cDNA encoding a new H3 histone variant has been isolated from a Paracentrotus lividus sea urchin embryo cDNA library. The encoded protein is identical to the H3.3 histone subtype identified in other species, with the difference that E replaces D at position 81. The clone corresponds to a transcript of about 1.6 kb, not dependent on DNA replication, present in the unfertilized egg and at all stages of embryonic development. The coding part of the cDNA cross-reacts also with a 0.5 kb H3 late histone mRNA.

Animals↗
PubMedDate not supplied

Characteristics of human sperm chromatin structure following an episode of influenza and high fever: a case study.

Semen samples from a fertile patient presenting with influenza and a 1-day fever of 39.9 degrees C were obtained and analyzed at 18-66 days postfever (dpf) for sperm nuclear proteins, DNA stainability, free thiols (-SH), and susceptibility to DNA denaturation in situ. At 18 dpf, 36% of sperm demonstrated denatured DNA as measured by the sperm chromatin structure assay (SCSA), and decreased to 23% by 39 dpf. Samples at 33 and 39 dpf contained 49% and 30%, respectively, of cells with increased DNA stainability (HIGRN). A unique sperm nuclear protein band migrating between histones and protamines on acid-urea gels appeared at 33 and 39 dpf and nearly disappeared by 52 dpf. Amino acid sequencing of the first 8 N-terminal residues identified this protein as the precursor to protamine 2. The protamine P1 and P2 ratio remained normal, whereas the histone to protamine ratio increased slightly at 33 to 39 dpf. Flow cytometric measurements of nuclear -SH groups revealed the greatest reduction in free nuclear thiols at 33 dpf, and returned to normal by 45 dpf. The time of appearance of the unprocessed protamine 2 precursor and the relative increase in histone suggest a fever-related disruption of the synthesis of mRNA that codes for a P2 processing enzyme or enzymes. Increased DNA staining is likely due to the increased histone/protamine ratio. This case study demonstrates that fever/influenza can have latent effects on sperm chromatin structure and may result in transient release of abnormal sperm.

Cell Nucleus↗
PubMed1985

Structure of a duck H3 variant histone gene: a H3 subtype with four cysteine residues.

A duck recombinant DNA phage library was screened for H3 histone genes, and the sequence of a variant H3 gene, which appears not to be part of a histone gene cluster, has been determined. As derived from the nucleotide sequence, this gene codes for a 135-amino acid (aa) protein (as any other H3) and shows 10 aa substitutions compared with most published H3 structures. Six of these aa changes are based on one nucleotide (nt) substitutions in arginine codons. This results in three new histidines and, in addition to the highly conserved cysteine at position 110, three more cysteines are found in this H3 histone subtype.

Amino Acid Sequence↗
PubMed1989

Differential use of termination codons in ciliated protozoa.

Sequence analysis of genes in four species of ciliated protozoa and analysis of tRNAs in Tetrahymena has demonstrated that TAG and TAA encode glutamine or glutamic acid in these organisms and TGA is the only stop codon. Thus, it has generally been assumed that all ciliates use a nonuniversal genetic code in which TGA acts as the sole termination codon. We have sequenced the linear DNA molecules that carry an actin gene and a beta-tubulin gene from the ciliate Euplotes crassus. These genes are shown to use TAA as a termination codon based on homology to known actin and beta-tubulin gene sequences. In addition, we have sequenced a portion of the 3' terminus of the E. crassus H4 histone gene and show that it also uses TAA as a termination codon. These data indicate that the timing of genetic code changes in the ciliates must be reconsidered.

Actins↗
PubMed2002

Requirement of Hos2 histone deacetylase for gene activity in yeast.

Histone deacetylases, typified by class I Rpd3 in the yeast Saccharomyces cerevisiae, have historically been associated with gene repression. We now demonstrate that Hos2, another member of the class I family, binds to the coding regions of genes primarily during gene activation, when it specifically deacetylates the lysines in H3 and H4 histone tails. Moreover, Hos2 is preferentially associated with genes of high activity genome-wide. We also show that Hos2 and an associated factor, Set3, are necessary for efficient transcription. Therefore, our data indicate that, in contrast to other class I histone deacetylases, Hos2 is directly required for gene activation.

Acetylation↗
PubMed1991

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.

Amino Acid Sequence↗
PubMed1998

The biochemical and phenotypic characterization of Hho1p, the putative linker histone H1 of Saccharomyces cerevisiae.

There is currently no published report on the isolation and definitive identification of histone H1 in Saccharomyces cerevisiae. It was, however, recently shown that the yeast HHO1 gene codes for a predicted protein homologous to H1 of higher eukaryotes (Landsman, D. (1996) Trends Biochem. Sci. 21, 287-288; Ushinsky, S. C., Bussey, H. , Ahmed, A. A., Wang, Y., Friesen, J., Williams, B. A., and Storms, R. K. (1997) Yeast 13, 151-161), although there is no biochemical evidence that shows that Hho1p is, indeed, yeast histone H1. We showed that purified recombinant Hho1p (rHho1p) has electrophoretic and chromatographic properties similar to linker histones. The protein forms a stable ternary complex with a reconstituted core di-nucleosome in vitro at molar rHho1p:core ratios up to 1. Reconstitution of rHho1p with H1-stripped chromatin confers a kinetic pause at approximately 168 base pairs in the micrococcal nuclease digestion pattern of the chromatin. These results strongly suggest that Hho1p is a bona fide linker histone. We deleted the HHO1 gene and showed that the strain is viable and has no growth or mating defects. Hho1p is not required for telomeric silencing, basal transcriptional repression, or efficient sporulation. Unlike core histone mutations, a hho1Delta strain does not exhibit a Sin or Spt phenotype. The absence of Hho1p does not lead to a change in the nucleosome repeat length of bulk chromatin nor to differences in the in vivo micrococcal nuclease cleavage sites in individual genes as detected by primer extension mapping.

Amino Acid Sequence↗
PubMed1988

A new family of repetitive, retroposon-like sequences in the genome of the rainbow trout.

We have identified a new family of interspersed, moderately repetitive DNA elements, termed the RSg-1 family, in the genome of the rainbow trout. Two of the elements examined here are situated upstream of sequences which code for trout nuclear proteins; a protamine gene (p101) and the clustered histone H4 gene. Sequence comparison of various RSg-1 elements indicated a high degree of nucleotide sequence homology between different members of the family. These repetitive elements exhibit well defined 3' ends which contain poly(A) segments preceded by the consensus polyadenylation signal AATAAA. Sequences flanking the 3' end of the poly(A) tract also conform to a consensus sequence. A similar sequence is also found flanking the 5' terminus of the element in the protamine clone p101, and thus may represent a target-site duplication generated upon insertion of the element into the genome. These characteristics, together with the heterogeneous nature of the 5' ends of the elements, are reminiscent of processed pseudogenes and retroposons such as the mammalian L1 family of interspersed repetitive elements.

Animals↗
PubMedDate not supplied

[The loss of CpC dinucleotides from DNA. II. Methylated and non-methylated genes of vertebrates].

The frequencies of neighboring b.p. in more than 1100 genes of vertebrates in the EMBL bank (1000 kb) have been analysed. It has been found that the majority of such genes exhibit a lack of CpG duplexes and an excess of TpG+CpA. The loss of CpG may indicate that the major part of these sites in the genome is methylated and has been subjected to the pressure of CpG----TpG+CpA mutations. The methylated genes grouped into compartment M+ are represented by a fraction of repeated sequences and by genes of the most rapidly diverging families of proteins (globins, immunoglobulins, structural proteins, etc.). The genes of this compartment are characterized by a correlation between the G+C content and the value of CpG-suppression. A group of genes has been detected in which the CpG mutation process has gone so far that nearly all of these dinucleotides have disappeared from DNA. Judging by the value of CpG-suppression, these genes, grouped in the Mo+ compartment, used to be strongly methylated before. However, in the now extant vertebrates they have fully depleted their CpG reserve and for this reason lost the methylation capacity. Transitions in methylated CpG may be one of the sources of spontaneous mutagenesis resulting in the enhanced genetic instability of the cell. A gene compartment has been detected with an intermediate level of CpG deficiency; this compartment has been designated as M+. In these genes only a few of the available CpGs have been steadily methylated (and subjected to mutation). It has been found that the genome of vertebrates contains a specific CpG-rich fraction which exhibits no CpG-suppression, irrespective of the overall content of G+C. Probably, CpG sites have persisted unmethylated throughout the existence of these genes. We suggest them to constitute a M- compartment. This compartment comprises the genes of tRNA and rRNA (5S, 5.8S, 18S, 28S) and small nuclear RNAs U2-U6, as well as the genes of core histones, some enzymes, viruses and 5'-flanking sequences of certain protein-coding genes. In the genome of vertebrates, the genes of the evolutionary most conserved proteins and RNAs have not undergone methylation. A list of genes, belonging to different compartments of the vertebrate genome, is given. Compartment Mo+ constitutes 19%, M(+)--35%, M(+/-)--28% and M(-)--8% of all the vertebrate genes studied. Possible mechanisms, protecting the functionally most significant genes of vertebrates from methylation, and discussed.

Animals↗
PubMed1978

Aspects of the regulation of histone genes.

Sequencing of cloned histone DNA of the sea urchin Psammechinus miliaris has confirmed the map of the histone genes obtained earlier by rather less refined techniques. Sequencing of spacer has revealed that it is unlikely to code for protein. Some interesting sequences in the prelude regions to the structural genes have been found. The technique of injecting DNA into the germinal vesicle of the Xenopus oocyte has been greatly simplified, so that now many of the parameters governing the transcription of the injected genes can be investigated. Some mRNA-like molecules appear when circular histone DNA is inserted into the oocyte nucleus. We are cautiously optimistic that the technique can be further developed and will provide a useful tool for the study of the molecular mechanisms governing the expression of structural genes coding for proteins.

Animals↗
PubMed1990

Transcription factor USF from duck erythrocytes transactivates expression of the histone H5 gene in vitro by interacting with an intragenic sequence.

The duck histone H5 gene contains a 12 base pair (bp) sequence motif within the coding region, which shows homology in 10 out of 12 bp with the consensus sequence of the USF binding site in the Ad2ML-promoter. The functional equivalent of transcription factor USF, partially purified from whole cell extracts of duck erythrocytes (EUSF), was shown to interact with this intragenic sequence. Electrophoretic mobility shift analyses revealed the selective formation of a complex between this protein fraction and the duck H5 gene. Footprint assays with DNase I delineated specific binding to the intragenic sequence outlined above. Moreover this protein fraction, containing EUSF, transactivates the expression of the duck H5 gene in vitro and elimination of the USF-consensus sequence leads to a loss of stimulation but retains the basic transcription of the gene. These results suggest an as yet unknown functional role of EUSF in the expression of the H5 gene of the duck.

Animals↗