PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “Histone Code”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original 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
PubMed1997

Identification of proliferation-induced genes in Arabidopsis thaliana. Characterization of a new member of the highly evolutionarily conserved histone H2A.F/Z variant subfamily.

The changes in gene expression associated with the reinitiation of cell division and subsequent progression through the cell cycle in Arabidopsis thaliana cell-suspension cultures were investigated. Partial synchronization of cells was achieved by a technique combining phosphate starvation and a transient treatment with the DNA replication inhibitor aphidicolin. Six cDNAs corresponding to genes highly induced in proliferating cells and showing cell-cycle-regulated expression were obtained by the mRNA differential display technique. Full-length cDNA clones (cH2BAt and cH2AvAt) corresponding to two of the display products were subsequently isolated. The cH2BAt clone codes for a novel histone H2B protein, whereas the cH2AvAt cDNA corresponds to a gene encoding a new member of the highly conserved histone H2A.F/Z subfamily of chromosomal proteins. Further studies indicated that H2AvAt mRNA expression is tightly correlated with cell proliferation in cell-suspension cultures, and that closely related analogs of the encoded protein exist in Arabidopsis. The implications of the conservation of histone H2A.F/Z variants in plants are discussed.

Amino Acid Sequence↗
PubMed2004

Global position and recruitment of HATs and HDACs in the yeast genome.

Chromatin regulators play fundamental roles in the regulation of gene expression and chromosome maintenance, but the regions of the genome where most of these regulators function has not been established. We explored the genome-wide occupancy of four different chromatin regulators encoded in Saccharomyces cerevisiae. The results reveal that the histone acetyltransferases Gcn5 and Esa1 are both generally recruited to the promoters of active protein-coding genes. In contrast, the histone deacetylases Hst1 and Rpd3 are recruited to specific sets of genes associated with distinct cellular functions. Our results provide new insights into the association of histone acetyltransferases and histone deacetylases with the yeast genome, and together with previous studies, suggest how these chromatin regulators are recruited to specific regions of the genome.

Acetyltransferases↗
PubMed1981

Occurrence of the low-mobility H1 histones subfraction in embryonic, differentiated, and neoplastic tissues of the Syrian hamster.

Electrophoretically slow H1 histone subfractions with mobilities identical to that of the subfraction found in the Kirkman-Robbins hamster hepatoma chromatin have been shown to be present in 12-day hamster embryos and in a sarcoma-type hamster tumor induced by SV40. No subfractions of such mobility were found in hamster liver, regenerating liver, thymus, spleen, and a fast-growing transplantable amelanotic hamster melanoma. A suggestion is made that some defective mechanisms of differentiation may affect the regulation of expression of the genes coding for the H1 histone subfractions. The same mechanisms may possibly but not necessarily be connected with the molecular events leading to neoplastic growth.

Animals↗
PubMed2006

The Spt4p subunit of yeast DSIF stimulates association of the Paf1 complex with elongating RNA polymerase II.

The Paf1 complex (Paf1C) interacts with RNA polymerase II (Pol II) and promotes histone methylation of transcribed coding sequences, but the mechanism of Paf1C recruitment is unknown. We show that Paf1C is not recruited directly by the activator Gcn4p but is dependent on preinitiation complex assembly and Ser5 carboxy-terminal domain phosphorylation for optimal association with ARG1 coding sequences. Importantly, Spt4p is required for Paf1C occupancy at ARG1 (and other genes) and for Paf1C association with Ser5-phosphorylated Pol II in cell extracts, whereas Spt4p-Pol II association is independent of Paf1C. Since spt4Delta does not reduce levels of Pol II at ARG1, Ser5 phosphorylation, or Paf1C expression, it appears that Spt4p (or its partner in DSIF, Spt5p) provides a platform on Pol II for recruiting Paf1C following Ser5 phosphorylation and promoter clearance. spt4Delta reduces trimethylation of Lys4 on histone H3, demonstrating a new role for yeast DSIF in promoting a Paf1C-dependent function in elongation.

Chromatin Immunoprecipitation↗
PubMedDate not supplied

A new mini-transposon for in vivo protein epitope tagging: application to Burkholderia multivorans.

A short amino acid sequence coding for the mature Pseudomonas aeruginosa OprI lipoprotein was fused to a mini-Tn5 plasposon (mini-transposon with an origin of replication) with tetracycline resistance in order to generate in-frame fusion proteins after transposition. After conjugative transfer to Burkholderia multivorans, clones reacting with an anti-OprI mab were selected. In-frame OprI-tagged proteins were detected and identified for six clones. The six C-tagged proteins were detected by immunoblot. The different mutants had insertions into a histone H1-like coding gene, cspD, encoding a cold-shock protein, dsbC, encoding a putative outer membrane lipoprotein involved in thiol-disulfide exchange, paaE, a ferredoxin-NADPH reductase gene, a gene for the catabolism of propionate, and one encoding an unknown protein.

Amino Acid Sequence↗
PubMed1987

Retropseudogenes for human chromosomal protein HMG-17.

The human genome contains multiple copies of sequences homologous to the cDNA coding for non-histone chromosomal protein HMG-17. To study the mechanism of generation and dispersion of the HMG-17 multigene family a human genomic library was screened and 70 clones isolated and studied by Southern transfer and restriction site analysis. The results suggest that most of the clones contain unique sequences. Sequence analysis of two genomic clones indicates that they contain elements typical of processed retropseudogenes. Even though both sequences contained open reading frames the sequences lacked introns, were flanked by short, direct repeats and lacked elements associated with functional genes. The sequences of the two pseudogenes were 85% homologous to each other and each was 90% homologous to the human cDNA. Based on the sequence difference in the open reading frame between the pseudogenes and the cDNA it can be estimated that the sequences arose approximately ten million years ago from a common precursor. The present paper, which is the first study on genes coding for this nucleosomal binding protein, indicates that the HMG-17 multigene family is the largest known human retropseudogene family.

Base Sequence↗
PubMed1981

A model of evolutionary base substitutions and its application with special reference to rapid change of pseudogenes.

A model of evolutionary base substitutions that can incorporate different substitutional rates between the four bases and that takes into account unequal composition of bases in DNA sequences is proposed. Using this model, we derived formulae that enable us to estimate the evolutionary distances in terms of the number of nucleotide substitutions through comparative studies of nucleotide sequences. In order to check the validity of various formulae, Monte Carlo experiments were performed. These formulae were applied to analyze data on DNA sequences from diverse organisms. Particular attention was paid to problems concerning a globin pseudogene in the mouse and the time of its origin through duplication. We obtained a result suggesting that the evolutionary rates of substitution in the first and second codon positions of the pseudogene were roughly 10 times faster than those in the normal globin genes; whereas, the rate in the third position remained almost unchanged. Application of our formulae to histone genes H2B and H3 of the sea urchin showed that, in each of these genes, the rate in the third codon position is tremendously higher than that in the second position. All of these observations can easily and consistently be interpreted by the neutral theory of molecular evolution.

Animals↗
PubMed1996

Histones associated with non-nucleosomal rat ribosomal genes are acetylated while those bound to nucleosome-organized gene copies are not.

Acetylation of histones bound to rat rRNA genes has been studied relative to their organization in chromatin, either as canonical nucleosomes, containing the inactive copies, or as anucleosomal nonrepeating structures, corresponding to the transcribed genes (Conconi, A., Widmer, R. M., Koller, T., and Sogo, J. M. (1989) Cell 57, 753-761). Nuclei from butyrate-treated rat tumor cells were irradiated with a UV laser to cross-link proteins to DNA, and the purified covalent complexes were immunofractionated by an antibody that specifically recognized the acetylated histones. Upon probing with sequences coding for mature rat 28 S RNA, DNA of the antibody-bound complexes was 5-20-fold enriched relative to the total rat DNA. Since the laser cross-links histones to DNA in both active and inactive genes, one cannot distinguish which one of them, or both, are bound to acetylated histones. Alternatively, purified mononucleosomes were immunofractionated, but DNA from the antibody-bound monosomes was not enriched in coding rDNA. Taken together, these results suggest that nucleosome-organized rRNA genes are bound to nonmodified histones and that the acetylated histones are associated with the active, anucleosomal gene copies.

Acetylation↗
PubMed1983

Structure of a cluster of mouse histone genes.

The four mouse histone genes (2 H3 genes, an H2b gene and an H2a gene) present in a cloned 12.9 kilobase fragment of DNA have been completely sequenced including both 5' and 3' flanking regions. These genes are expressed in cultured mouse cells and the 3' and 5' ends of the mRNA have been determined by S1 nuclease mapping. These genes code for a minor fraction of the histone mRNAs expressed in cultured mouse cells. They comprise at most 5-8% of the total histone mRNA of each type. The two H3 genes code for H3.2 and H3.1 histone proteins, while the H2b gene codes for an H2b.1 protein with a single amino acid change (val-leu) at position 18. Only the 3' portion of the H2a gene is contained in the clone and there is an amino acid change (alanine-proline) at position 126. Comparison of the 5' and 3' flanking sequences reveals a conserved sequence at the 3' end of the mRNA which forms a hairpin loop structure. The codon usage in the genes is non-random and there has been no discrimination against CG doublets in the coding region of the genes.

Amino Acid Sequence↗
PubMed2005

Immunoglobulin locus silencing and allelic exclusion.

Lymphocytes are characterised by monoclonal expression of antigen receptors. This is achieved by silencing of one of two homologous antigen receptor alleles, a process known as allelic exclusion. This process is regulated both before and after V(D)J recombination, by a variety of mechanisms. These include nuclear localisation, changes in chromatin structure and histone modifications, non-coding sense and antisense RNA transcription, epigenetic alterations at the DNA level, feedback signalling from expressed alleles, locus contraction and decontraction, recruitment to heterochromatin. This review will focus on recent advances in the immunoglobulin heavy and kappa light chain loci. The current picture is of a complex, temporally ordered sequence of events, in which these loci share many contributory mechanisms, but clear and intriguing differences are emerging.

Alleles↗
PubMedDate not supplied

Chromatin structure and dynamics: functional implications.

In eucaryotes, DNA packaging into nucleosomes and its organization in a chromatin fiber generate constraints for all processes involving DNA, such as DNA-replication, -repair, -recombination, and -transcription. Transient changes in chromatin structure allow overcoming these constraints with different requirements in regions where processes described above are initiated. Mechanisms involved in chromatin dynamics are complex. Multiprotein complexes which can contain histone-acetyltransferase, -deacetylase, -methyltransferase or -kinase activities are targeted by regulatory factors to precise regions of the genome. These enzymes have been shown to modify histone-tails within specific nucleosomes. Post-translational modifications of histone-tails constitute a code that is thought to contribute to the nucleosome or to the chromatin fiber remodeling, either directly, or through the recruitment of other proteins. Other multiprotein complexes, such as ATP-dependent remodeling complexes, play an essential role in chromatin fiber dynamics allowing nucleosome sliding and redistribution on the DNA. We will focus here on the chromatin structure and its consequences for DNA damaging, replication, repair, and transcription and we will discuss the mechanisms of chromatin remodeling.

Acetyltransferases↗
PubMed2004

Plants contain a high number of proteins showing sequence similarity to the animal SUV39H family of histone methyltransferases.

The SET domain, first identified within and named after proteins encoded by three Drosophila genes [Su(var)3-9, E(z), and Trithorax], is recognized as a signature motif for histone methyltransferases that are involved in epigenetic processes. The SUV39H family of SET domain proteins methylate specifically the residue lysine 9 of histone H3, creating a code for gene silencing. This family of proteins contain at their C termini a unique catalytic domain consisting of pre-SET, SET, and post-SET domains. Sequence homology-based searches identified 15 Arabidopsis, 14 maize, and 12 rice proteins that can be assigned to the SUV39H family. These high numbers in plants are in marked contrast to the situation in animals, in which each species appears to contain only two to three proteins of this family. Our phylogenetic analyses revealed that plant proteins can be classified into seven orthology groups. Representative members of each group can be found in single plant species, suggesting that different group members are evolutionarily conserved to perform specific functions.

Animals↗
PubMed2005

Role of histone modifications in marking and activating genes through mitosis.

The global inhibition of transcription at the mitotic phase of the cell cycle occurs together with the general displacement of transcription factors from the mitotic chromatin. Nevertheless, the DNase- and potassium permanganate-hypersensitive sites are maintained on potentially active promoters during mitosis, helping to mark active genes at this stage of the cell cycle. Our study focuses on the role of histone acetylation and H3 (Lys-4) methylation in the maintenance of the competency of these active genes during mitosis. To this end we have analyzed histone modifications across the promoters and coding regions of constitutively active, inducible, and inactive genes in mitotic arrested cells. Our results show that basal histone modifications are maintained during mitosis at promoters and coding regions of the active and inducible RNA polymerase II-transcribed genes. In addition we have demonstrated that, together with H3 acetylation and H3 (Lys-4) methylation, H4 (Lys-12) acetylation at the coding regions contributes to the formation of a stable mark on active genes at this stage of the cell cycle. Finally, analysis of cyclin B1 gene activation during mitosis revealed that the former occurs with a strong increase of H3 (Lys-4) trimethylation but not H3 or H4 acetylation, suggesting that histone methyltransferases are active during this stage. These data demonstrate a critical role of histone acetylation and H3 (Lys-4) methylation during mitosis in marking and activating genes during the mitotic stage of the cell cycle.

Acetylation↗
PubMed1980

Silent nucleotide substitutions during evolution.

Silent nucleotide substitutions in evolution are found by comparing homologous sequences of DNA from different organisms. Silent changes are common in the third bases of codons, so that no changes takes place in the specified amino acid. Silent changes average about half of the total nucleotide substitutions during evolution of protein-coding regions of genes. Nucleotide substitutions also take place during evolution in non-coding regions of DNA, such as in intervening sequences and in sequences that precede and follow codon regions in genes. Deletions and additions from events of recombination, in addition to nucleotide substitutions, are common in these non-coding regions.

Animals↗