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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.
J Mol Evol 1986
PMID:Sequences of four mouse histone H3 genes: implications for evolution of mouse histone genes. 302 55

Sea urchin and rodent genomes have been posited to evolve rapidly as indicated by divergences in single copy nuclear DNA sequences. We have examined whether the synonymous substitution rates of three highly conserved genes, beta-tubulin, histone H4, and histone H3, adhere to these high genomic substitution rates by comparing sequences between two sea urchins, Strongylocentrotus purpuratus and Lytechinus pictus, and between rodents and humans. Whereas the rate of change between the 3' untranslated regions of the beta-tubulin cDNA of S. purpuratus (Sp-beta 1), sequenced in this study, and of L. pictus (Lp-beta 3) was consistent with the overall rate of change estimated from previous DNA hybridization results between these species, the synonymous substitution rates for the carboxyl domains of these beta-tubulins, as well as for the late histones H4 and H3, were significantly depressed. In contrast, synonymous nucleotide substitution rates between rodents and between rodent and human for the carboxyl domain proper of identical beta-tubulin isotypes and for histone H4 and H3.1 did not differ from the overall rate of change for the rodent genomes. Moreover, an analysis of paralogous human and mouse beta-tubulin sequences supported the conclusion that the synonymous substitution rates in the mouse were higher than those in the human. Differences in constraint on evolutionary change were not evident strictly from the conserved amino acid sequences and base compositions of these genes. Other constraining influences seemed more relevant to the departure of the synonymous substitution rates of the sea urchin beta-tubulin and histone coding regions from the average genomic rate.
J Mol Evol 1988
PMID:Synonymous nucleotide substitution rates of beta-tubulin and histone genes conform to high overall genomic rates in rodents but not in sea urchins. 313 88

The haploid genome of Saccharomyces cerevisiae contains two nonallelic sets of histone H3 and H4 gene pairs, termed the copy I and copy II loci. The structures of the mRNA transcripts from each of these four genes were examined by nuclease protection and primer extension mapping. For each gene, several species of mRNAs were identified that differed in the lengths of their 5' and 3' untranslated regions. The cell cycle accumulation pattern of the H3 and H4 mRNAs was determined in cells from early-exponential-growth cultures fractionated by centrifugal elutriation. The RNA transcripts from all four genes were regulated with the cell division cycle, and transcripts from the nonallelic gene copies showed tight temporal coordination. Cell cycle regulation did not depend on selection of a particular histone mRNA transcript since the ratio of the multiple species from each gene remained the same across the division cycle. Quantitative measurements showed significant differences in the amounts of mRNA expressed from the two nonallelic gene sets. The mRNAs from the copy II H3 and H4 genes were five to seven times more abundant than the mRNAs from the copy I genes. There was no dosage compensation in the steady-state levels of mRNA when either set of genes was deleted. In particular, there was no increase in the amount of copy I H3 or H4 transcripts in cells in which the high-abundance copy II genes were deleted.
Mol Cell Biol 1988 Feb
PMID:Comparison of the structure and cell cycle expression of mRNAs encoded by two histone H3-H4 loci in Saccharomyces cerevisiae. 328 Sep 73

Wheat embryo histone H3 has been isolated and purified and the elucidation of the complete amino-acid sequence is described. Peptides were generated by cleavages with CNBr, S. aureus V8 proteinase, endoproteinase Lys-C and trypsin. The peptides were purified by HPLC and the sequence determined by solid-state and gas-phase sequencing methodology. The amino-acid sequence of the protein is identical to pea embryo histone H3 and the sequence deduced from the nucleotide sequence of a wheat embryo histone gene (Tabata T. et al. (1984) Mol. Gen. Genet. 196, 397-400).
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PMID:The primary structure of histone H3 from wheat. 328 55

The unfolding of nucleosome cores in transcriptionally active chromatin uncovers the sulfhydryl groups of histone H3, making them accessible to SH-reagents. This has suggested that nucleosomes from active genes could be retained selectively on organomercurial/agarose columns. When nucleosomes released from rat liver nuclei by limited digestion with micrococcal nuclease were passed through an Hg affinity column, a run-off fraction of compact, beaded nucleosomes was separated from a retained nucleosome fraction. Although both contained monomer-length DNA and a full complement of core histones, histones in the retained fraction were hyperacetylated. Dot blot hybridizations showed the Hg-bound nucleosome fraction to be enriched in DNA sequences transcribed by hepatocytes (serum albumin and transferrin genes), while a brain-specific gene (preproenkephalin) was not retained, but appeared in the nucleosomes of the run-off fraction. The results are discussed in light of other evidence linking hyperacetylation of histones H3 and H4 to conformational changes at the middle of the nucleosome core.
J Mol Biol 1987 Jul 20
PMID:Affinity chromatographic purification of nucleosomes containing transcriptionally active DNA sequences. 365 49

Exonuclease III digests DNA sequentially from the 3' end. This enzyme is used to analyse the location of nucleosomes on DNA fragments containing a particular 145 base-pair (bp) sequence. When one of these fragments is assembled into chromatin and digested with exonuclease, a strong and persistent pause in digestion is detected at a single location. That this pause is due to the enzyme encountering a nucleosome is suggested, firstly, by its absence from digests of free DNA and, secondly, by the detection of a corresponding pause on the other strand. The two pauses, 146 bp apart, specify the location of a single precisely positioned nucleosome on the DNA fragment. This position corresponds exactly to one of two possible positions of the 145 bp sequence identified previously. A fragment containing only about 80 bp of the original 145 bp continues to position itself in the nucleosome like the parent sequence. Therefore, some of the sequence can be replaced with different DNA without affecting nucleosome positioning. Further exonuclease III analysis of an extensive set of deletions demonstrates that a central region of about 40 bp is essential for positioning the 145 bp sequence. When deletions advance into this region from either side, only a very small proportion of the DNA remains in the original position on the nucleosome. Therefore, the two short lengths of DNA at the edges of the region must each contain all or part of an essential nucleosome-positioning signal. These two critical sequences are symmetrically located across the nucleosome dyad and interact with the same region of histone H3. The sequence TGC occurs at the same place in both sequences; otherwise they are dissimilar.
J Mol Biol 1986 May 05
PMID:Deletion analysis of a DNA sequence that positions itself precisely on the nucleosome core. 378 73

The expression of c-myb in normal human T lymphocytes directly derived from a normal subject and not adapted to continuous growth in culture was found to be markedly increased after phytohemagglutinin stimulation. In the same cells, the expression of c-myc mRNA is a much earlier event compared with the appearance of c-myb mRNA, which takes place soon after that of histone H3 mRNA. The increase in c-myb expression was not due to a particular T-lymphocyte subset, as shown by in situ hybridization assays.
Mol Cell Biol 1985 Oct
PMID:Activation of c-myb expression by phytohemagglutinin stimulation in normal human T lymphocytes. 391 38

In order to understand how the phosphorylation of histones affects the chromatin structure, we used electron microscopy, sedimentation velocity, circular dichroism and electric birefringence to monitor the salt-induced filament reversible solenoid transition of phosphorylated and native chromatin. Phosphorylation in vitro of chicken erythrocyte chromatin by cyclic-AMP-dependent protein kinase from porcine heart led to the modification of the histones H3 and H5 only, which were modified at a level of one phosphate and about three phosphate groups per molecule, respectively. In contrast to circular dichroism and sedimentation studies, which tend to suggest that phosphorylation of H3 and H5 does not affect chromatin structure, electron microscopy reveals that phosphorylation causes a relaxation of structure at low ionic strength. Electric birefringence and relaxation time measurements clearly prove that local structural changes are induced in chromatin: we observe a decrease of the steady-state birefringence with the appearance of a negative contribution in the signal and a marked increase of the flexibility of fibres. The component with the negative birefringence presents very short relaxation times, like those exhibited by small DNA fragments or individual nucleosomes. Two possibilities are then suggested. First, the conformational change is consistent with what would be expected from the presence of DNA segments loosely associated with the core histone H3. That the length of such segments could correspond to about one to two base-pairs per nucleosome strongly suggests that phosphorylation induces changes affecting some specific H3-DNA interactions only. This result could corroborate previous observations indicating that the N-terminal region of H3, where the site of phosphorylation is located, plays a decisive role in maintaining the superstructure of chromatin. Second, phosphorylation could introduce hinge points between each nucleosome. In this case, the negative birefringence results from partial orientation of the swinging nucleosomes. A possible mode of action of phosphorylation might be to weaken structural restraints imposed by histone H3, thus facilitating further condensation of chromatin.
J Mol Biol 1985 Nov 20
PMID:Histone phosphorylation in native chromatin induces local structural changes as probed by electric birefringence. 408 98

The gene for histone H3 from the yeast Saccharomyces cerevisiae was placed under the control of the lac promoter of Escherichia coli by fusing the H3 coding sequence to that of beta-galactosidase. The gene was shown to be transcribed in vivo, but its product was not detected in cell extracts. However, synthesis of the fused polypeptide was detected in an in vitro transcription-translation system derived from E. coli. Proteolytic degradation of the newly synthesized polypeptides may be the cause of their apparent absence in the in vivo experiment.
J Mol Biol 1983 Aug 15
PMID:Synthesis of yeast histone 3 in an Escherichia coli cell-free system. 635 Jun 5

The complete DNA sequences of two loci encoding H3 and H4 histones in Saccharomyces cerevisiae have been determined. Each locus contains one H3 and one H4 gene. The genes at each locus are divergently transcribed and the coding sequences are separated by 646 base-pairs at one locus and 676 base-pairs at the other. The H3 genes code for identical histone H3 proteins and the H4 genes code for identical histone H4 proteins. The yeast proteins differ from histones H3 and H4 of calf by 15 and 8 amino acid substitutions, respectively, and these differences are largely confined to the carboxy-terminal halves of the proteins. The genes demonstrate a bias in synonymous codon usage similar to that noted for other yeast genes. This bias is confined to the coding sequences of the genes and is specific for the reading frame encoding the proteins. The coding sequence of each gene is flanked on both sides by DNA with an A + T content of 70 to 80%. Possible regulatory sequences are located relative to the 5' and 3'-termini of the histone H3 and H4 RNA transcripts.
J Mol Biol 1983 Sep 25
PMID:DNA sequences of yeast H3 and H4 histone genes from two non-allelic gene sets encode identical H3 and H4 proteins. 635 83


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