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PubMed1986

Sequences of four mouse histone H3 genes: implications for evolution of mouse histone genes.

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.

Amino Acid Sequence↗
PubMed1990

The two macronuclear histone H4 genes of the hypotrichous ciliate Stylonychia lemnae.

Macronuclear DNA of hypotrichous ciliates is organized in short gene-sized molecules, each containing all regulatory sequences for autonomous replication and expression. In these organisms the histone genes are not clustered but dispersed on different molecules of various sizes. Two histone H4 genes containing fragments, one of 1.7 kb and one of 2.8 kb, were found in the macronucleus of Stylonychia lemnae. Restriction and sequence data reveal that the two genes-sized pieces are derived from different micronuclear precursors. Both histone H4 genes code for the same protein of 103 aminoacids but differ greatly in their 5'-and 3'-regions.

Amino Acid Sequence↗
PubMed1988

Early increase in histone H1(0) mRNA during differentiation of F9 cells to parietal endoderm.

We have isolated and characterized cDNA clones coding for the H1 histone subtype H1(0) in mouse teratocarcinoma cells. The mRNA is 2100 nt long and contains a coding sequence which is highly related to that of the human H1(0) gene. Using this cDNA as a probe, we have shown that, in comparison to undifferentiated F9 cells, differentiated F9 teratocarcinoma cells contain large amounts of H1(0) mRNA. This increase takes place very early during differentiation and does not correlate with changes in the rate of cell division. This indicates that the accumulation of H1(0) mRNA is not the result of reduced proliferation. Most likely on the contrary, the increase in the amount of H1(0) and the resulting effects on the formation of high order chromatin structures are parts of the differentiation program induced in F9 cells.

Amino Acid Sequence↗
PubMed1986

Codon usage in histone gene families of higher eukaryotes reflects functional rather than phylogenetic relationships.

The nucleic acid sequences coding for 23 H3 histone genes from a variety of species have been analyzed using a computer assisted alignment and analysis program. Although these histones are highly conserved within and between highly divergent species, they represent various classes of histones whose patterns of expression are distinctively regulated. Surprisingly, in dendrograms derived from these comparisons, H3 sequences cluster according to their modes of regulation rather than phylogenetically. These clusters are generated from highly distinctive patterns of codon usage within the functional gene classes. We suggest that one factor involved in specifying the differing codon usage patterns between functional classes is a difference in requirements for rapid translation of mRNA. In addition, the data presented here, together with structural and sequence information, suggest a heterodox evolutionary model in which genes related to the intron-bearing, basally expressed H3.3 vertebrate genes are the ancestors of the intronless H3.1 class of genes of higher eukaryotes. The H3.1 class must have arisen, therefore, following duplication of a primitive H3.3 gene, but prior to the plant-animal divergence. Implications of the data presented are discussed with regard to functional and evolutionary relationships.

Amino Acid Sequence↗
PubMed1987

Translation is required for regulation of histone mRNA degradation.

When DNA synthesis is inhibited, the mRNAs coding for the replication-dependent histone proteins are selectively destabilized. The histone genes have been altered and reintroduced into tk- mouse L cells by cotransfection with the herpesvirus thymidine kinase gene. Two features of the mRNA are necessary for regulation of degradation: first, the hairpin loop must be present at the 3' end of the histone mRNA; and second, the histone mRNA must be capable of being translated to within 300 nucleotides of the 3' end of the RNA. Polyadenylated histone mRNAs are stable, as are histone mRNAs that contain in-frame termination codons early in the coding region or 500 nucleotide 3' untranslated regions with a normal hairpin loop at the 3' end.

Amino Acid Sequence↗
PubMed1987

Mouse histone H2A and H2B genes: four functional genes and a pseudogene undergoing gene conversion with a closely linked functional gene.

The sequence of five mouse histone genes, two H2a and three H2b genes on chromosome 13 has been determined. The three H2b genes all code for different proteins, each differing in two amino acids from the others. The H2b specific elements present 5' to H2b genes from other species are present in all three mouse H2b genes. All three H2b genes are expressed in the same relative amounts in three different mouse cell lines and fetal mice. The H2b gene with the H2b specific sequence closest to the TATAA sequence is expressed in the highest amount. One of the H2a genes lacks the first 9 amino acids, the promoter region, the last 3 amino acids and contains an altered 3' end sequence. Despite these multiple defects, there is only one nucleotide change between the two H2a genes from codon 9 to 126. This indicates that a recent gene conversion has occurred between these two genes. The similarity of the nucleotide sequences in the coding regions of mouse histone genes is probably due to gene conversion events targeted precisely at the coding region.

Animals↗
PubMed1988

Persistence of a micrococcal nuclease sensitive region spanning the promoter-coding region junction of a cell cycle regulated human H4 histone gene throughout the cell cycle.

We have examined the chromatin structure of the cell cycle regulated human H4 histone gene FO108A at various times during the cell cycle, by treating nuclei isolated from synchronized HeLa S3 cells with micrococcal nuclease. Purified DNA was fractionated electrophoretically, transferred to nitrocellulose, and hybridized to small (150-250 nucleotides) radiolabeled probes from various portions of the promoter and coding regions of the gene. Our results indicate the existence of a micrococcal nuclease sensitive region located between positions -60 and +90 base pairs (bp) from the start codon of the gene, which includes the TATA box. This nuclease-sensitive region persists at all the cell cycle times analyzed. Hybridization with a 250-bp probe containing only coding region sequences reveals a disrupted nucleosomal ladder during early S phase, when this H4 histone gene replicates and exhibits an enhanced level of transcription. By mid-S phase, the regular nucleosomal structure of the coding region is restored and persists during subsequent phases of the cell cycle. The disruption of a normal nucleosomal organization in the promoter and mRNA coding regions of this H4 histone gene is also supported by the sensitivity of these sequences to S1 nuclease.

Chromatin↗
PubMed1988

Cell-cycle regulation as a mechanism for targeting proteins to specific DNA sequences in Tetrahymena thermophila.

Transcriptionally active macronuclei and transcriptionally inert micronuclei of the ciliated protozoan Tetrahymena thermophila contain similar DNA sequences but have very different histones associated with the linker regions of chromatin. In situ hybridization showed that a gene coding for micronuclear linker histone is expressed only in association with micronuclear DNA replication, whereas the gene for macronuclear H1 histone is expressed during macronuclear (but not during micronuclear) S phase. These results indicate that cell-cycle regulation plays an important role in directing proteins to the appropriate nucleus in Tetrahymena and that the replication-expression model [Gottesfeld, J. & Bloomer, L. S. (1982) Cell 28, 781-791; Wormington, W. M., Schlissel, M. & Brown, D. D. (1983) Cold Spring Harbor Symp. Quant. Biol. 47, 879-884] for establishing appropriate transcriptionally active or repressed chromatin complexes during DNA replication is generally applicable.

Animals↗
PubMed1978

Genes and spacers of cloned sea urchin histone DNA analyzed by sequencing.

A cloned histone gene cluster of the highly reiterated type from the sea urchin Psammechinus miliaris was analyzed by DNA sequencing. More than half of the 6 kb repeat was sequenced, including coding regions of all five histones, some prelude and trailing sequences lying adjacent to the structural gense, and segments of the AT-rich spacer DNA. The gene cluster does not code for gonad-specific histone variants but may instead be active in early sea urchin development, as indicated by comparison to reference histones. The encoded histones seem not to be derived from longer precursor proteins, not is there any evidence for insert sequences within the coding regions. Sequence similarities exist among the putative ribosome-binding sites adjacent to the initiator codons of individual genes. The AT-rich spacer segments between the genes differ from each other, are made up from relatively simple nucleotide arrangements, but are not repetitious, and apparently do not code for additional large proteins.

Animals↗
PubMed1979

Isolation of a genomal clone containing chicken histone genes.

We have used enriched chicken histone cDNA to select genomal clones from a chicken library. Because the cDNA probe also contained other sequences, a further screening of positive plagues with negative probes eliminated most non-histone gene clones. One 'positively-selected' genomal clone, lambda CH-01, hybridised with cloned sea-urchin histone genes and also detected histone genes in EcoRI-digested genomal sea-urchin DNA. Limited DNA sequencing of HaeIII fragments identified two sequences within the coding region of chicken histone H2A. A third fragment predicted an amino acid sequence with strong homology to an H1 histone sequence.

Amino Acid Sequence↗
PubMed1990

Coding and noncoding sequences at the 3' end of yeast histone H2B mRNA confer cell cycle regulation.

Yeast (Saccharomyces cerevisiae) histone mRNA synthesis is tightly regulated to the S phase of the cell division cycle as a result of both transcriptional and posttranscriptional regulation. We focused on the role of posttranscriptional control in histone H2B1 gene (HTB1) regulation and studied a portion of the HTB1 message required for cell-cycle-specific accumulation. The 3' end of the HTB1 gene containing a 17-amino-acid coding sequence and entire noncoding sequence was fused to the bacterial neomycin phosphotransferase II gene (neo) under control of the GAL1 promoter. The expression of the endogenous and chimeric HTB1 genes was analyzed during the yeast cell cycle. As yeast cells entered a synchronous cell cycle following release from alpha-factor arrest, the level of GAL1-promoter-controlled neo-HTB1 message increased approximately 12-fold during S phase and dropped to basal level when the cells left S phase. This indicates that the 3' end of the HTB1 mRNA is capable of conferring cycle-specific regulation on a heterologous message. Deletion analysis of the 3' end showed that the signal for cell cycle control of HTB1 mRNA includes contiguous coding and noncoding sequences surrounding the stop codon. This differs from the situation in mammalian cells, whose posttranscriptional regulation of histone genes is mediated through a short sequence containing a stem-loop structure near the very terminus of the untranslated 3' end.

Base Sequence↗
PubMed1990

A cytotoxic monoclonal anti-leukemia antibody binds to histone H1.

Monoclonal antibody (MAb) AP64 is a mouse IgM MAb raised against human acute non-lymphocytic leukemia (ANLL) cells. It has been shown to bind to a wide variety of cell lines and is capable of initiating complement (C) dependent cytotoxicity. Other studies indicated that MAb AP64 can effect long term cure in a leukemia minimal residual disease model. By using various techniques we have determined the identity of a protein which is bound by this MAb. Immunofluorescent studies have shown that MAb AP64 stains the nuclei of fixed cells as well as metaphase chromosomes, indicating that this MAb binds to a component of chromatin. Biochemical characterization revealed that MAb AP64 western blots a 31 and 32 kilodalton doublet from NP-40 extracts from both rat and human leukemia cells. The mobility of this doublet is identical under reducing and non-reducing conditions. Further studies have shown that the bands detected by western blot analysis using MAb AP64 as a probe have a similar migration to those of bovine histone H1. Also, 1 nanogram of bovine histone H1 can be detected by MAb AP64 when spotted onto nitrocellulose. These data demonstrate that MAb AP64 binds to a conserved epitope present on molecules coded for by the histone H1 gene family.

Antibodies, Monoclonal↗
PubMedDate not supplied

Non-coding DNA in macronuclear chromosomes of hypotrichous ciliates.

Massive elimination of sequences occurs in the development of the macronucleus of hypotrichous ciliates. The surviving sequences are presumed to have functions in the macronucleus; what little is known about non-coding macronuclear sequences is reviewed. The 1.7 kbp macronuclear chromosome that carries a histone H4 gene consists primarily of non-coding DNA 5' of the histone gene. This region is shown by sequence comparison to carry several perfectly conserved sequence blocks up to 14 bp long, scattered amongst regions which have evolved greatly since the divergence of Oxytricha nova and Stylonychia lemnae. This result is consistent with the suggestion of Harper and Jahn [Harper, D. S. & Jahn, C. L. 1989. Actin, tubulin and H4 histone genes in three species of hypotrichous ciliated protozoa. Gene, 75:93-107] that this large non-coding 5' region may be involved in the transcriptional regulation of the histone H4 gene carried on the 1.7 kbp chromosome. Very little is known about transcriptional control in hypotrichs; identification of conserved non-coding sequences of orthologous hypotrich genes promises to provide clues to potential cis-acting control signals.

Animals↗
PubMed1987

Unusual structure, evolutionary conservation of non-coding sequences and numerous pseudogenes characterize the human H3.3 histone multigene family.

The genomic organization of the replication-independent, basally expressed, human H3.3 gene is atypical of traditional histone gene organization. The gene contains 3 introns totalling 7.8 kb and unusual direct repeats flank all three intron-exon splice junctions. The transcription initiation site was mapped by S1 nuclease protection analysis and confirms that cDNA clones previously reported were full length. Sequence similarities between regions at the 5' and 3' termini of this human gene and a chicken H3.3 gene lead us to propose that either the previous assignments of termini of the chicken gene are in error, or there are alternative transcription start and polyadenylation sites. The 85% base matching of human and chicken H3.3 3'UTR sequences for 520 bases is unprecedented among homolog 3'UTR segments, especially considering that these species are separated by over 250 Myr of evolution. We also present the sequence of three related processed human H3.3 pseudogenes and provide evidence demonstrating that most of the 20 to 30 copies of the H3.3 gene within the human genome are in fact processed pseudogenes.

Amino Acid Sequence↗
PubMed1989

Human H1 histones: conserved and varied sequence elements in two H1 subtype genes.

The genes coding for two different human H1 histones were isolated, and the primary structures were deduced from the nucleotide sequences. The genes differ from each other and from any other vertebrate H1 structure described until now. The differences occur mainly within the N- and C-terminal H1 domains, whereas the central part of the protein is highly conserved. Within the flanking domains, however, some sequence elements are shared by different H1 subtype genes. An octapeptide, which has been described in C-terminal domains of most H1 histones, is found in both H1 subtypes. The nucleotide sequences of the flanking portions of both H1 genes show conserved motifs at established regulatory sites, but otherwise these 3' and 5' noncoding sequences of both genes differ substantially.

Amino Acid Sequence↗
PubMed1978

Hatching in the sea urchin Lytechinus pictus is accompanied by a shift in histone H4 gene activity.

There is a distinct shift in histone mRNA synthesis at approximately 11--12 hr of sea urchin emhryogenesis, coincident with embryonic hatching. The synthesis of the blastula type (early) histone mRNAs gradually ceases at this stage and a new class of posthatching (late) histone mRNAs is produced. Briefly labeled early and late mRNAs were isolated and identified by means of RNA-DNA hybridization to different cloned histone genes. The late histone HI mRNA is approximately 40 nucleotides longer than the early HI mRNA. The H3, H2A, H2B, and H4 late mRNAs are 15--40 nucleotides shorter than their early counterparts. We present sequence evidence to show that the genes coding for the late H4 mRNA are a separate class from those that code for the early histone H4 message.

Animals↗
PubMed1991

The histone H1-lacZ' fusion protein produced in Escherichia coli binds to the 5'-TTGGCAnnnTGCCAA-3' motif on DNA.

The coding region of the chicken histone H1.03 gene was cloned to a bacterial expression vector, and the 291-amino acid H1-beta-galactosidase fusion protein was isolated after induction with IPTG. The fusion protein recognizes the 5'-TTGGCAnnnTGCCAA-3' motif on DNA. The H1 globular domain was initially shown to be responsible for the sequence-specific binding by functional deletion analysis. This function may be indispensable for the role of H1 as a determinant of nucleosome positioning and as a eukaryotic repressor.

Animals↗