Complete nucleotide sequence of a chicken H2b histone gene

Characterization of nucleosomes consisting of the human testis/sperm-specific histone H2B variant (hTSH2B)

We have reported earlier the occurrence of a specific histone H2B variant in human testis and sperm. Here we have structurally characterized this protein, its association with the rest of the histone octamer, and its effects on the nucleosome structure. We show that a reconstituted octamer consisting of hTSH2B and a stoichiometric complement of histones H2A, H3, and H4 exhibits a lower stability compared to the reconstituted native counterpart consisting of H2B. In contrast, the hTSH2B containing octamers are able to form nucleosome core particles which are structurally and dynamically indistinguishable from those reconstituted with octamers consisting of only native histones. Furthermore, the presence of hTSH2B in the nucleosome does not affect its ability to bind to linker histones.

Change of liver function in hypertrophying lobe of rabbit liver after portal branch ligation

Preoperative portal embolization (PE) is useful for the prevention of postoperative liver failure after extended hepatectomy. However, clinical evaluation of liver function in the hypertrophying lobe after PE has not been studied. Here we report functional changes in the hypertrophying lobe using a 80% portal-branch-ligation rabbit model. Liver function was evaluated by the expression of liver-specific genes detected by Northern blot analysis and plasma disappearance rate of indocyanine green (ICG). The weight of the unligated lobe after portal ligation increased about twofold on the 7th postoperative day (POD) and about threefold on the 14th POD. The mRNA levels of the liver-specific genes (albumin, aldolase B, and tyrosine aminotransferase) in the unligated lobe decreased to about 50% on the 1st POD and returned to the preoperative levels on the 7-14th POD. In contrast, the expression of histone H2B mRNA increased on the 3rd-7th POD. The plasma disappearance rate of ICG (K-ICG) in the rabbit that has only the unligated lobe did not significantly change during the first 7 days, but then improved and recovered to 80% of that in the rabbit that has whole liver on the 14th POD. These results indicate that liver function of the hypertrophying lobe after portal branch ligation does not increase during the first 7 days despite an increase in liver weight. This finding suggests that the compensatory hypertrophying liver is enlarging without functional augmentation in the early period after PE.

Cell adhesion to substratum and activation of tyrosine kinases are essentially required for G1/S phase transition in BALB/c 3T3 fibroblasts

Cell adhesion to substratum and activation of tyrosine kinases are essential for the progression of cell cycle through G1 phase in mammalian cells. The kinetic studies of mouse BALB/c 3T3 fibroblasts showed that serum was no longer required for the progression of G1/S phase transition. In contrast, cell adhesion was essentially required in late G1 phase, especially at the period of G1/S transition. Among the kinase inhibitors used to elucidate the signal transduction caused by cell adhesion, tyrosine kinase inhibitors, genistein and herbimycin A, blocked the G1/S transition most effectively when cells were exposed to the inhibitors at the period of G1/S transition. Cell adhesion was not critically required for cells to undergo DNA synthesis once they had passed the G1/S boundary, and the effects of tyrosine kinase inhibitors on the progression of S phase were also not critical. The expressions of histone H2B and dihydrofolate reductase (DHFR) genes (S phase specific genes) and also the transcription factor E2F-1 gene (an activator of DHFR gene) were suppressed when cells were cultured without adhesion or exposed to the tyrosine kinase inhibitors. These results suggest that cell adhesion to substratum plays an important role in the G1/S phase transition of mouse BALB/c 3T3 fibroblasts through the activation of tyrosine kinases other than growth factor receptor-tyrosine kinases.

Cell cycle synchrony in the developing chicken lens epithelium

Synchronous oscillations of DNA synthesis and histone 2B mRNA expression occur during normal development of 13- to 16-day-old embryonic chicken lens epithelium. At least four cycles were observed with peak values of DNA synthesis and histone 2B mRNA 5 to 10 times greater than baseline values. Fourier analysis of DNA synthesis identified a statistically significant oscillatory period of 18 hr, the approximate length of the cell cycle at this age. Minor components of 7-9 and 12 hr were also identified in the data sets. Lenses labeled with 3H-thymidine and analyzed by autoradiography at 13.8 days of embryogenesis revealed more than twice the number of labeled nuclei at this time than in lenses labeled 9 hr later; histone 2B mRNA followed this same pattern. These findings demonstrate that a significant population of cells is synchronized with respect to the cell cycle in the developing lens epithelium in ovo. The temporal pattern of mitosis may be the basis of the fiber cell architecture and consequent lens transparency.

Alterations in the structural gene and the expression ofp53 in rat liver tumors induced by aflatoxin B1

Rat hepatocellular carcinomas (HCCs) induced by aflatoxin B1 (AFB) treatment were examined for changes in the p53 tumor suppressor gene and in p53 suppressor gene expression. A high proportion of HCCs (nine of 11 tumors in six of eight animals) exhibited new p53 restriction fragments, indicating genomic alterations of one of the p53 alleles. Each tumor with an altered p53 restriction-fragment pattern exhibited a new fragment in one of two size classes (3 kb or 7 kb with EcoRI digestion) that were missing portions of the 3' end of the p53 gene. These findings indicate that apparently similar genomic rearrangements or deletions occurred independently in AFB-induced tumors. When compared with nontumor liver tissue from the same animal, the tumors with p53 gene alterations showed dramatically reduced levels of p53 mRNA and protein and greatly increased levels of histone H2B and retinoblastoma tumor suppressor (Rb) mRNA. In two HCCs showing no evidence of p53 restriction-fragment alterations, mutant p53 protein was detected. Mutant protein was also detected in two liver samples containing an adenoma and altered foci. These data suggest that alterations of the p53 tumor suppressor gene are involved in the induction of rat HCC by AFB.

Expression of c-myc, c-raf-1, and c-Ki-ras in azaserine-induced pancreatic carcinomas and growing pancreas in rats

We examined the pattern of expression of several proto-oncogenes during nonneoplastic growth and in acinar cell neoplasms in the rat pancreas. The levels of c-myc, c-raf-1, and c-Ki-ras mRNAs were increased in regenerating pancreata following surgical partial pancreatectomy and following administration of camostat. We also investigated proto-oncogene expression associated with the progression of pancreatic cancers in azaserine-treated rats. Injection of a single dose (30 mg/kg) of azaserine (O-diazoacetyl-L-serine) to 14-d-old rats leads to a variety of neoplastic lesions in the rat pancreas. Total RNA was isolated from lesions in various stages of tumor progression, including adenomas, carcinomas in situ, and invasive carcinomas. We observed increased expression of c-myc, c-raf-1, and c-Ki-ras in azaserine-induced adenomas and carcinomas. Actin expression was also increased in these tissues, whereas amylase expression was variable. However, when compared to the normal growing pancreas, the level of proto-oncogene expression in the adenomas and carcinomas was disproportionate to the degree of cellular division in those tissues. Thus, the alterations induced by azaserine apparently caused a deregulated increase in expression of cellular oncogenes associated with growth regulation.

Conserved organization of an avian histone gene cluster with inverted duplications of H3 and H4 genes

The organization of histone gene clusters of the duck Cairina moschata was studied in the DNA inserts of two recombinant phage that overlap and feature identical histone gene arrangements but differ in sequence details and in the extent of repetition of an AT-rich motif in one of the nontranscribed spacer regions. These few but substantial differences between otherwise nearly identical histone gene groups suggest that we have independently isolated alleles of the same site of the duck genome or that this gene arrangement occurs (with slight variations) more than once per haploid genome. Within the histone gene cluster described, H3 and H4 genes are duplicated (with inverted orientation), whereas one H1 gene is flanked by single H2A and H2B genes. The arrangement of duck histone genes described here is identical to a subsection of the chicken genome but differs from any other published histone gene cluster.

Histones and their modifications

Histones constitute the protein core around which DNA is coiled to form the basic structural unit of the chromosome known as the nucleosome. Because of the large amount of new histone needed during chromosome replication, the synthesis of histone and DNA is regulated in a complex manner. During RNA transcription and DNA replication, the basic nucleosomal structure as well as interactions between nucleosomes must be greatly altered to allow access to the appropriate enzymes and factors. The presence of extensive and varied post-translational modifications to the otherwise highly conserved histone primary sequences provides obvious opportunities for such structural alterations, but despite concentrated and sustained effort, causal connections between histone modifications and nucleosomal functions are not yet elucidated.

Histone H4 and H2B genes in rainbow trout (Salmo gairdnerii)

The complete nucleotide sequence of the 3.0-kb BamH I-Sst I restriction fragment contained within the rainbow trout genomic clone lambda TH2 has been determined. This region contains the rainbow trout H4 and H2B histone genes and 5' and 3' flanking and spacer sequences, and represents the 5' half of the histone-gene cluster; the remaining half has been characterized previously. The genes are uninterrupted, and are transcribed from the same strand. The protein sequence of H4, as determined from the nucleic acid sequence, is the same as that derived for other vertebrate H4 proteins, although comparison of nucleotide sequences shows a great deal of sequence divergence, especially in the third base position. The amino acid sequence of H2B, though largely homologous to those of other vertebrate H2B proteins, displays some characteristic differences in primary structure. Consensus sequences noted in many other eukaryotic genes, as well as histone-specific consensus sequences, have been identified. An unusual feature of the spacer region between the H4 and H2B genes is the presence of a duplicated sequence 87 bp in length. The 5' and 3' ends of each repeat are complementary, and each repeat contains smaller repeated sequences internally, as well as a possible cruciform structure.

Crystallographic structure of the octameric histone core of the nucleosome at a resolution of 3.3 A

The structure of the (H2A-H2B-H3-H4)2 histone octamer has been determined by means of x-ray crystallographic techniques at a resolution of 3.3 angstroms. The octamer is a prolate ellipsoid 110 angstroms long and 65 to 70 angstroms in diameter, and its general shape is that of a rugby ball. The size and shape are radically different from those determined in earlier studies. The most striking feature of the histone octamer is its tripartite organization, that is, a central (H3-H4)2 tetramer flanked by two H2A-H2B dimers. The DNA helix, placed around the octamer in a path suggested by the features on the surface of the protein, appears like a spring holding the H2A-H2B dimers at either end of the (H3-H4)2 tetramer.

Applicability of superhelical model for regulation of gene expression

The superhelical model for regulation of gene expression was tested in 41 structural genes of eukaryotes, viruses and plasmids, and in the primer RNA gene for DNA replication in five kinds of enteric bacteria and two kinds of plasmids. The model which was first proposed for regulation of transcription in simian virus 40 was based on the following observations: a stem-loop structure of low free energy was located 3' downstream from the transcriptional initiation site; sequences homologous to the loop were located at the symmetrical site with the stem-loop at the center; and the loop encountered any of these homologous sequences after one rotation of superhelix depending on the superhelical density. If the loop interacted with the complementary sequences in the opposite strand, DNA formed a specific cruciform or T-shaped structure. The superhelical model proposed that transcription was regulated by the conversion of the template DNA in the regular, the cruciform, and the T-shaped structures. The model was applicable to all the structural genes and the primer RNA genes tested so far, except histone genes. In eukaryotes, only one stem-loop structure which conformed to the superhelical model was constructed in most of the genes except the growth hormone genes, the globin genes of human, and the human interferon gamma gene. An average length of the stem-loop was 46 bases, and the 5' end of the stem loop was located at the 30th base downstream from the transcriptional initiation site on the average in eukaryotes. In some genes, a consensus sequence was detected in the loops of the same kind of gene in different species or of different kind of gene in the same species.

Organization and nucleotide sequence of rainbow trout histone H2A and H3 genes

A 2.56-kbp fragment containing genes coding for histones H2A and H3 that forms a portion of the 10.2-kbp cluster containing all five histone genes isolated from a lambda-Charon 4A library of rainbow trout genomic DNA has been characterized in detail and its complete nucleotide sequence determined. The genes are arranged in tandem, being encoded on the same DNA strand. They are separated by 380 bp of intergenic spacer DNA that contains an alternating purine-pyrimidine stretch of 20 bp and a 46-bp stretch that has the potential of forming a triple cruciform structure. The histone genes contain no introns, have the RNA polymerase II promoter-associated signals known as CAAT and TATA boxes in their 5' flanking regions and contain a conserved inverted repeat sequence, similar to that found in histone genes of other species, capable of forming a hairpin structure at the 3' end of the transcription unit.

Genomic organization of the genes coding for the six main histones of the chicken: complete sequence of the H5 gene

The organization of the genes coding for histones in the chicken has been examined, with special reference to that coding for the tissue-specific, developmentally regulated histone H5. Two recombinant phages containing sequences complementary to cloned H5 cDNA have been isolated from a genomic chicken library. The clones have been characterized by heteroduplex formation, restriction nuclease analysis, hybridization to cloned homologous histone gene probes, and DNA sequencing. Hybridization to genomic DNA has shown that there is only one copy of the H5 gene per haploid genome, whereas there are six to 11 copies of the genes for the other histones. Examination of 29 X 10(3) base-pairs of DNA sequences flanking the H5 gene has revealed the absence of any other histone genes which, although not tandemly reiterated, for the most part appear to reside in loosely organized clusters. The complete DNA sequence of the H5 gene and flanking regions, as well as the mapping of the 5'-end of its messenger RNA by primer extension with AMV reverse transcriptase, has shown that the gene has no introns and little homology to other histone genes, including those for H1.

Variation in the DNA methylation pattern of expressed and nonexpressed genes in chicken

Using methyl-sensitive and -insensitive restriction enzymes, Hpa II and Msp I, the methylation status of various chicken genes was examined in different tissues and developmental stages. Tissue-specific differences in methylation were found for the delta-crystallin, beta-tubulin, G3PDH, rDNA, and actin genes but not for the histone genes. Developmental decreases in methylation were noted for the delta-crystallin and actin genes in chicken kidney between embryo and adult. Since most of the sequences examined were housekeeping genes, transcriptional differences are apparently not a necessary accompaniment to changes in DNA methylation at the CpG sites examined. The only exception is sperm DNA where the delta-crystallin, beta-tubulin, and actin genes are highly methylated and almost certainly not transcribed. However the G3PDH genes are no more highly methylated in sperm than in other somatic tissues. Many sequences homologous to the rDNA and histone probes used are unmethylated in all tissues examined including sperm, but a methylated rDNA subfraction is more heavily methylated in sperm than in other tissues. We speculate as to the significance of these differences in sperm DNA methylation in the light of possible requirements for early gene activation and the probable deleterious mutagenic effects of heavy methylation within coding sequences.