Nucleotide sequences of H1 histone genes from Xenopus laevis. A recently diverged pair of H1 genes and an unusual H1 pseudogene

Birth-and-Death Evolution with Strong Purifying Selection in the Histone H1 Multigene Family and the Origin of orphon H1 Genes

Histones are small basic nuclear proteins with critical structural and functional roles in eukaryotic genomes. The H1 multigene family constitutes a very interesting histone class gathering the greatest number of isoforms, with many different arrangements in the genome, including clustered and solitary genes, and showing replication-dependent (RD) or replication-independent (RI) expression patterns. The evolution of H1 histones has been classically explained by concerted evolution through a rapid process of interlocus recombination or gene conversion. Given such intriguing features, we have analyzed the long-term evolutionary pattern of the H1 multigene family through the evaluation of the relative importance of gene conversion, point mutation, and selection in generating and maintaining the different H1 subtypes. We have found the presence of an extensive silent nucleotide divergence, both within and between species, which is always significantly greater than the nonsilent variation, indicating that purifying selection is the major factor maintaining H1 protein homogeneity. The results obtained from phylogenetic analysis reveal that different H1 subtypes are no more closely related within than between species, as they cluster by type in the topologies, and that both RD and RI H1 variants follow the same evolutionary pattern. These findings suggest that H1 histones have not been subject to any significant effect of interlocus recombination or concerted evolution. However, the diversification of the H1 isoforms seems to be enhanced primarily by mutation and selection, where genes are subject to birth-and-death evolution with strong purifying selection at the protein level. This model is able to explain not only the generation and diversification of RD H1 isoforms but also the origin and long-term persistence of orphon RI H1 subtypes in the genome, something that is still unclear, assuming concerted evolution.

Purifying selection and birth-and-death evolution in the histone H4 gene family

Histones are small basic proteins encoded by a multigene family and are responsible for the nucleosomal organization of chromatin in eukaryotes. Because of the high degree of protein sequence conservation, it is generally believed that histone genes are subject to concerted evolution. However, purifying selection can also generate a high degree of sequence homogeneity. In this study, we examined the long-term evolution of histone H4 genes to determine whether concerted evolution or purifying selection was the major factor for maintaining sequence homogeneity. We analyzed the proportion (p(S)) of synonymous nucleotide differences between the H4 genes from 59 species of fungi, plants, animals, and protists and found that p(S) is generally very high and often close to the saturation level (p(S) ranging from 0.3 to 0.6) even though protein sequences are virtually identical for all H4 genes. A small proportion of genes showed a low level of p(S) values, but this appeared to be caused by recent gene duplication. Our findings suggest that the members of this gene family evolve according to the birth-and-death model of evolution under strong purifying selection. Using histone-like genes in archaebacteria as outgroups, we also showed that H1, H2A, H2B, H3, and H4 histone genes in eukaryotes form separate clusters and that these classes of genes diverged nearly at the same time, before the eukaryotic kingdoms diverged.

Deletion of the unique gene encoding a typical histone H1 has no apparent phenotype in Aspergillus nidulans

We have cloned the H1 histone gene (hhoA) of Aspergillus nidulans. This single-copy gene codes for a typical linker histone with one central globular domain. The open reading frame is interrupted by six introns. The position of the first intron is identical to that of introns found in some plant histones. An H1-GFP fusion shows exclusive nuclear localization, whereas chromosomal localization can be observed during condensation at mitosis. Surprisingly, the deletion of hhoA results in no obvious phenotype. The nucleosomal repeat length and susceptibility to micrococcal nuclease digestion of A. nidulans chromatin are unchanged in the deleted strain. The nucleosomal organization of a number of promoters, including in particular the strictly regulated niiA-niaD bidirectional promoter is not affected.

Organization and expression of H1 histone and H1 replacement histone genes

The H1 family is the most divergent subgroup of the highly conserved class of histone proteins [Cole: Int J Pept Protein Res 30:433-449, 1987]. In several vertebrate species, the H1 complement comprises five or more subtypes, and tissue specific patterns of H1 histones have been described. The diversity of the H1 histone family raises questions about the functions of different H1 subtypes and about the differential control of expression of their genes. The expression of main type H1 genes is coordinated with DNA replication, whereas the regulation of synthesis of replacement H1 subtypes, such as H1 zero and H5, and the testis specific H1t appears to be more complex. The differential control of H1 gene expression is reflected in the chromosomal organization of the genes and in different promoter structures. This review concentrates on a comparison of the chromosomal organization of main type and replacement H1 histone genes and on the differential regulation of their expression. General structural and functional data, which apply to both H1 and core histone genes and which are covered by recent reviews, will not be discussed in detail.

The chicken histone gene family

1. Most of the chicken 43 core and H1 histone genes belong to two major histone gene clusters. 2. Each of six H1 genes encodes a different H1 protein sequence. 3. The known core histone genes, four H2A, seven H2B, and seven H3 genes, respectively, encode two, three and three different protein variants, whereas the four known H4 genes encode the same amino acid sequence. 4. The core histone genes have particular transcription regulatory elements within the 5'-flanking regions and the regulations of their expressions are distinct, even though they are members of the same core histone gene family. 5. There are some undefined differences in the DNA structures of the particular core histone genes in various chicken tissues and these structural variations probably result in differences in their transcriptional regulation.

Analysis of the core histone gene cluster of the annelid Platynereis dumerilii

The arrangement of the polychaete annelid Platynereis dumerilii core histone gene cluster and nucleotide sequence has been reported (D. Sellos, S. A. Krawetz and G. H. Dixon, 1990). The H2B and H3 mRNAs are transcribed from one DNA strand, while the H2A and H4 histone mRNAs are transcribed from the other. The H1 gene is not contained as a member of this cluster. Computer assisted sequence analysis of this region was undertaken to define the organization and representation of the various sequence motifs embedded within this region. The analysis revealed that two large regions on opposite strands of the cluster were similar to one another. This organization is reminiscent of an ancient gene duplication event from which the various members independently evolved.

The Xenopus U7 snRNA-encoding gene has an unusually compact structure

A subclone containing a single Xenopus borealis U7 snRNA-encoding gene has been microinjected into X. laevis oocyte nuclei to examine its expression using [32P]GTP as an in vivo label. Only two U7 snRNA bands were detected after incubation, and subsequent fractionation of the oocyte showed that only the larger transcript is present in the nucleus. The sequence of this functional U7 gene shows that, in addition to the coding region, it contains, in the appropriate locations, the 3'-box and proximal sequence element (PSE) which are typical of Pol II-transcribed snRNA genes. Surprisingly, the Xenopus U7 gene contains two adjacent octamer-binding motifs located only 12 and 24 bp upstream from the PSE, instead of the usual location around 150-200 bp upstream. No other cis-acting elements appear to be present. A 5' deletion analysis shows that the transcription level of this U7 gene remains constant if sequences upstream of the two octamer motifs are removed, yet is undetectable when an additional 34 bp containing both octamers and the PSE are removed. This confirms that the Xenopus U7 gene is the most compact snRNA-encoding gene isolated to date. A comparison of U7 sequences shows there is a much greater conservation in the 5' half of the molecule, which contains sequences that base-pair with target pre-mRNA, than in the 3' half which can form a single stem-loop structure that varies in size.

The C-domain in the H1 histone is structurally conserved

The C-domain of H1 is conserved in composition and not in sequence. The following regularities have been identified: the distribution of lysine, alanine and proline is non-random; alanine occurs in doublets and at intervals of 4-6 significantly more often than expected for random sequences of equal composition; and lysine also deviates from random distribution in that doublets are under-represented and intervals of 2-7 are over-represented. Lysine preferentially occurs in singlets and alanine in doublets rather than triplets or quadruplets. This discourages the formation of helices without neutralization of lysine charges. When lysine residues are paired with DNA phosphate residues, helices are highly probable. Interproline spacing promotes short helical segments. The regularities arising from the conservation of composition and non-random residue distribution suggests that C-domains adopt similar structures and in fact are structurally conserved.

SPXX, a frequent sequence motif in gene regulatory proteins

A new DNA-binding unit, composed of four amino acid residues and common in gene regulatory proteins, is proposed. The occurrences of the sequences Ser-Pro-X-X (SPXX) and Thr-Pro-X-X (TPXX) in gene regulatory proteins are compared with those in general proteins. These sequences are found more frequently in gene regulatory proteins including homoeotic gene products, segmentation gene products, steroid hormone receptors and certain oncogene products, than they are in DNA-binding proteins that are not directly involved in gene regulation, such as the core histones, or in general proteins. It is therefore suggested that these sequences contribute to DNA-binding in a manner important for gene regulation. Amino acid residues characteristic of the types of proteins are found as the variable residues X: basic residues, Lys and Arg, in histones, H1 and sea urchin spermatogenous H2B; Tyr in RNA polymerase II; and Ser, Thr, Ala, Leu and Pro in other gene regulatory proteins S(T)PXX sequences are located on either side of other DNA-recognizing units such as Zn fingers, helix-turn-helices, and cores of histones. The structure of a S(T)PXX sequence is presumed to be a beta-turn I stabilized by two hydrogen bonds, and its potential mode of DNA-binding is discussed.

The phosphorylation site of Ca(2+)-dependent protein kinase from alfalfa

A 50 kDa, calcium-dependent protein kinase (CDPK) was purified about 1000-fold from cultured cells of alfalfa (Medicago varia) on the basis of its histone H1 phosphorylation activity. The major polypeptide from bovine histone H1 phosphorylated by either animal protein kinase C (PK-C) or by the alfalfa CDPK gave an identical phosphopeptide pattern. The phosphoamino acid determination showed phosphorylation of serine residues in histone H1 by the plant enzyme. Histone-related oligopeptides known to be substrates for animal histone kinases also served as substrates for the alfalfa kinase. Both of the studied peptides (GKKRKRSRKA; AAASFKAKK) inhibited phosphorylation of H1 histones by bovine and alfalfa kinases. The results of competition studies with the nonapeptide (AAASFKAKK), which is a PK-C specific substrate, suggest common features in target recognition between the plant Ca(2+)-dependent kinase and animal protein kinase C. We also propose that synthetic peptides like AAASFKAKK can be used as a tool to study substrates of plant kinases in crude cell extracts.

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.

Use of Xenopus oocytes to study the expression of cloned genes and translation of mRNA

One of the most active areas of research in the field of molecular biology is the examination of the mechanisms associated with the regulation of gene expression. Our understanding of the events in eukaryotic transcription has been aided by the ability to test the expression of various genomic DNA constructs after their microinjection into the germinal vesicle of Xenopus oocytes. This in vivo transcription system has permitted the analysis of the involvement of cis-acting DNA sequences and the examination of the effect of co-injected trans-acting factors on gene expression. Furthermore, the Xenopus oocyte has been employed widely as an in vivo translation system. Not only is the Xenopus oocyte system a sensitive assay for the translation of rare mRNAs but it also has the ability to post-translationally modify and compartmentalize numerous types of proteins. Finally, the Xenopus oocyte has proven useful in the procedures associated with the cloning and screening of cDNAs.

A novel method for generating a nested set of unidirectional deletion mutants using mixed oligodeoxynucleotides

A novel method that allows introduction of unidirectional deletions into cloned DNA is described. This method is based on the use of a mixture of oligodeoxynucleotide primers that have fixed 5' ends defining the end point of the deletion and variable 3' ends composed of mixtures of all four nucleotides at six positions. The 5' ends of the oligodeoxynucleotides are hybridized to a fixed location of the M13K11RX templates and the 3' ends are hybridized randomly to the DNA to be analyzed. Such oligodeoxynucleotide primers when extended with DNA polymerase can direct deletions of intervening parts of the single-stranded DNA that by design contains multiple EcoK sites; the deletion products are selected on a host strain with the EcoK restriction system (e.g., using JM101 cells). This method is an efficient way of generating a nested set of deletion mutants useful for dideoxy-sequencing. It can be used for creating a set of deletion mutants with a particular codon at the 5' or 3' end point.

Isolation and expression of cDNA clones coding for two sequence variants of Xenopus laevis histone H5

We have cloned and characterized cDNAs coding for two variants of Xenopus laevis H5 histone protein (previously called H1s). cDNA was synthesized from RNA of immature erythrocytes in a single reaction using a modification of the method of Gubler and Hoffman [Gene 25 (1983) 263-269], and blunt-end ligated into the HincII site of the phage vector M13mp9. Immunological screening with a polyclonal antibody yielded two clones expressing H5 peptide. Sequence characterization revealed that both clones contained partial cDNA inserts and that the smaller 340-bp clone initiated reverse transcription within the coding region, at a site rich in adenine. Rescreening of the cDNA bank by nucleic acid hybridization produced eleven additional H5 clones, one of which coded for a second variant of H5. These two variants, called XLH5A and XLH5B, are very similar in sequence and code for proteins of 195 and 193 amino acids, respectively, which may be the H1D and H1E variants observed previously. XLH5, avian H5 and human H1O share identity at both nucleotide and amino-acid sequence levels. Further, the XLH5-coding mRNA is likely polyadenylated and lacks the highly conserved, 23-nucleotide dyad symmetry element found within the 3' untranslated regions of most histone-coding mRNAs.

Expression of a histone H1-like protein is restricted to early Xenopus development

Genes whose expression is restricted to oogenesis and early development may have important functions in these processes. Northern analysis showed that Xenopus B4 mRNA is expressed in oogenesis and embryogenesis through to the neurula stage. Immunocytochemistry with anti-B4 antibodies showed that B4 protein is only detectable in preneurula stages; it is localized to nuclei and is associated with metaphase chromosomes. Immunoblotting revealed approximately constant levels of B4 protein per embryo for the first 2 days of development. Thus, as the number of nuclei increases during early development, the amount of B4 protein per nucleus is diluted out. Sequencing of two B4 cDNA clones revealed that the predicted B4 translation product is a 29-kD protein with 29% identity with histone H1, distributed over the entire length of its sequence. The B4 protein also has certain other H1 protein characteristics--a tripartite structure consisting of a mainly hydrophobic central domain flanked by an amino-terminal segment and a long hydrophilic carboxyterminal tail containing a tandemly repeated amino acid motif. However, in contrast to histone H1 mRNA, B4 mRNA has a classic polyadenylation signal, is polyadenylated, and lacks the histone H1 3' noncoding consensus sequence involved in RNA processing.

Monoclonal autoantibodies recognizing histone variants

Balb/c mice were immunized with affinity purified Ro(SS-A) from human origin in order to allow the preparation of monoclonal anti-Ro(SS-A) antibodies. After fusion of mouse myeloma cells (line Sp2/0 A914) with spleen cells from one of these mice, anti-Ro(SS-A) monoclonals were not obtained, but, instead, two IgM producing hybridomas reactive with histone H1 and one with histone H2B. The specificity of the anti-H1 monoclonals was investigated by means of immunoblotting of very lysine-rich histone variants from mouse which were separated by two-dimensional gelelectrophoresis. One of them (CLB-ANA 105) has H1(0) specificity with respect to the histone variants of mouse and man, but recognizes H5 as well as H1 from Xenopus laevis. Another monoclonal (CLB-ANA 108) reacts with the variant H1c from mouse, exclusively. From the way these monoclonals were produced, we postulate that they were not the result of immunization, but comprise specificities of naturally occurring autoantibodies.

The organisation and expression of histone genes from Xenopus borealis

We have isolated genomic clones from Xenopus borealis representing 3 different types of histone gene cluster. We show that the major type (H1, H2B, H2A, H4, H3), present at about 60-70 copies per haploid genome (1), is tandemly reiterated with a repeat length of 15 kb. In situ hybridization to mitotic chromosomes shows that the majority of histone genes in Xenopus borealis are at one locus. This locus is on the long arm of one of the small sub-metacentric chromosomes. A minor cluster type with the gene order H1, H3, H4, H2A is present at about 10-15 copies. The genome also contains rare or unique cluster types present at less than 5 copies having other types of organisation. An isolate of this type had the gene order H1, H4, H2B, H2A, H1 (no H3 cloned). Microinjection of all of the clones into Xenopus laevis oocyte nuclei shows that most of the genes present are functional or potentially functional and a number of variant histone proteins have been observed. S1 mapping experiments confirm that the genes of the major cluster are expressed in all tissues and at all developmental stages examined.

RNA 3' cleavage and polyadenylation in oocytes and unfertilized eggs of Xenopus laevis

Xenopus laevis histone H4 and H1 genes were transcribed in vitro to generate artificial precursor mRNAs (pre-mRNAs). These pre-mRNAs were microinjected into oocytes, matured oocytes, and unfertilized eggs of Xenopus laevis and their 3' cleavage and polyadenylation were investigated. In the oocyte nucleus both H4 and H1 pre-mRNAs were 3' cleaved but were not detectably polyadenylated. In the oocyte cytoplasm there was neither 3' cleavage nor polyadenylation of these histone pre-mRNAs. When injected into either matured oocytes or unfertilized eggs, the pre-mRNAs underwent 3' cleavage but this was inefficient when compared to the oocyte nucleus. In addition approximately 50% of the remaining uncleaved pre-mRNA was subject to a polyadenylation activity which added A tails of approximately 70 A residues. In contrast, artificial mouse beta-globin pre-mRNAs were not detectably 3' cleaved or polyadenylated in either microinjected oocytes or unfertilized eggs.

Immunological relationships among vertebrate lysine-rich histones

1. The relationship between sequence homology and immunological cross-reaction was investigated by enzyme-linked immunosorbent assay and immunoblotting using polyclonal antisera against lysine-rich histones (LRH) of known sequence, chicken H1 and H5, trout Hl and Xenopus H1s. 2. The order of immunological relatedness was consistent with known homologies among these LRH and goose H5, but quantitative correlations reflected varied locations of antigenic determinants. 3. When immunoblotting was extended to LRH from eight more vertebrates, it was evident that avian H5, mammalian H1o and anuran H1s form a sub-class, to which turtle H1s may belong, that urodele erythrocytes contain no H5-like histone and that fish "H5" is more like H1 than the H5/H1s/H1o subclass.

The inability of the Psammechinus miliaris H3 RNA to be processed in the Xenopus oocyte is associated with sequences distinct from those highly conserved amongst sea urchin histone RNAs

3' processing of precursors of the H3 RNA of the sea urchin Psammechinus miliaris in Xenopus oocytes is dependent upon sea urchin U7 snRNA. Sequences necessary for this interaction are highly conserved in all sea urchin histone precursor RNAs (including the Psammechinus H3) which, in contrast, are efficiently processed in the Xenopus oocyte without the addition of the homologous U7 snRNA. We resolve this seeming paradox by demonstrating here that the inability of the sea urchin Psammechinus miliaris H3 histone RNA to be processed in the Xenopus oocyte is associated with nucleotides immediately 3' to the conserved downstream sea urchin histone sequence element. Thus, a sequence-specific element (or lack of it) is responsible for the poor recognition of the Psammechinus H3 precursor RNA by the Xenopus processing machinery.

A highly conserved sequence in H1 histone genes as an oligonucleotide hybridization probe: isolation and sequence of a duck H1 gene

A 3.5-kb HindIII fragment of a histone gene cluster was isolated from a recombinant phage out of a duck genomic library. This DNA contains a duck H1 gene and its flanking sequences. The hybridization probe, which was used to screen for the H1 gene, had been designed on the basis of a comparative analysis of available H1 gene and protein data. Most H1 histones contain repeated motifs in their C-terminal domain, and these form part of an octapeptide (ser pro lys lys ala lys lys pro) that is highly conserved in many H1 histone proteins. A comparison of the duck H1 described here with two different published chicken H1 histone sequences reveals conservative amino acid exchanges at 22 (of 217 and 218, respectively) positions. The homology is maintained at the flanking sequences, and includes the putative H1 histone gene-specific signal structures and the established 3' stem and loop structures and the CAAGA box. The duck H1 gene and its flanking sequence have been found in identical arrangements in two recombinant bacteriophages, but minor sequence variations and genomic Southern blotting after HindIII digestion suggest that we have either isolated alleles of this genome segment or that the gene described may occur twice per haploid duck genome.

Molecular cloning of a pea H1 histone cDNA

A pea (Pisum sativum, var. Little Marvel) H1 histone cDNA has been isolated from a lambda gt11 expression vector library. This cDNA has been sequenced and shown to represent the entire protein-coding region of the mRNA. The deduced protein sequence is 265 amino acids long (28018 Da) and contains 70 lysines and 3 arginines. The structure of the encoded protein is comparable to animal lysine-rich histones. The central region, which has an amino acid composition similar to that found in the globular domains of animal lysine-rich histones, is flanked by an amino-terminal region rich in lysine, glutamic acid and proline and by a carboxyl-terminal region rich in lysine, alanine, valine and proline. Despite the structural similarities, the protein has little sequence homology with animal lysine-rich histones. This H1 protein is unusual because 12 of the first 40 amino acids are glutamic acid.

An intervening sequence in an unusual histone H1 gene of Tetrahymena thermophila

An intervening sequence of 254 base pairs interrupts the coding region of the single gene for macronuclear histone H1 of the ciliated protozoan, Tetrahymena thermophila. The intervening sequence has splice junctions similar to those found in RNA polymerase II genes of other organisms. No obvious similarities are observed between this intron and the self-splicing intervening sequence of the Tetrahymena ribosomal gene. The derived amino acid sequence describes a small extremely basic H1 protein missing most of the central hydrophobic domain that is conserved in all other H1 proteins. Macronuclei divide amitotically, without chromosome condensation, suggesting the conserved globular domain of H1 plays a role in higher-order chromatin structure.

Compensatory mutations suggest that base-pairing with a small nuclear RNA is required to form the 3' end of H3 messenger RNA

Processing of the 3' end of sea urchin H3 histone pre-mRNA requires conserved sequence elements and the presence of U7 snRNA. A mutation in the conserved CAAGAAGA sequence of the H3 pre-mRNA that renders 3' processing of this precursor defective is shown to be suppressed by a compensatory change in the U7 snRNA, restoring the base-pairing potential of the two RNAs. RNA-RNA contacts between these two molecules appear to be an essential feature of the 3' processing reaction.

Chromosomal organization of chicken histone genes: preferred associations and inverted duplications

We present a detailed picture of the disposition of core and H1 histone genes in the chicken genome. Forty-two genes were located within four nonoverlapping regions totalling approximately 175 kilobases and covered by three cosmid clones and a number of lambda clones. The genes for the tissue-specific H5 histone and other variant histones were not found in these regions. The longest continuous region mapped was 67 kilobases and contained 21 histone genes in five dissimilar clusters. No long-range repeat was evident, but there were preferred associations, such as H1 genes with paired, divergently transcribed H2A-H2B genes and H3-H4 associations. However, there were exceptions, and even when associations such as H1-H2A-H2B we maintained, the order of those genes within a cluster may not have been. Another feature was the presence of three (unrelated) clusters in which genes were symmetrically ordered around central H3 genes; in one such cluster, the boundaries of a duplicated H2A-H4 gene pair contained related repeat sequences. Despite the dispersed nature of chicken histone genes, the number of each type was approximately equal, being represented as follows: 6 H1, 10 H2A, 8 H2B, 10 H3, and 8 H4.

Chromosomal organization of chicken histone genes: preferred associations and inverted duplications

We present a detailed picture of the disposition of core and H1 histone genes in the chicken genome. Forty-two genes were located within four nonoverlapping regions totalling approximately 175 kilobases and covered by three cosmid clones and a number of lambda clones. The genes for the tissue-specific H5 histone and other variant histones were not found in these regions. The longest continuous region mapped was 67 kilobases and contained 21 histone genes in five dissimilar clusters. No long-range repeat was evident, but there were preferred associations, such as H1 genes with paired, divergently transcribed H2A-H2B genes and H3-H4 associations. However, there were exceptions, and even when associations such as H1-H2A-H2B we maintained, the order of those genes within a cluster may not have been. Another feature was the presence of three (unrelated) clusters in which genes were symmetrically ordered around central H3 genes; in one such cluster, the boundaries of a duplicated H2A-H4 gene pair contained related repeat sequences. Despite the dispersed nature of chicken histone genes, the number of each type was approximately equal, being represented as follows: 6 H1, 10 H2A, 8 H2B, 10 H3, and 8 H4.

Individual Xenopus histone genes are replication-independent in oocytes and replication-dependent in Xenopus or mouse somatic cells

We have assessed the response of many histone H3 mRNAs and an H1C mRNA in Xenopus tissue culture cells after treatment with the DNA synthesis inhibitor hydroxyurea. The amount of the histone mRNAs falls rapidly in response to the inhibitor. This response is prevented by cycloheximide. Cloned Xenopus histone genes were transfected into mouse cells and a cell line was obtained in which the Xenopus genes were actively expressed giving rise to mRNA with correct 5'-termini. The Xenopus genes were correctly regulated at the level of mRNA amounts in the mouse cell line. Nuclear microinjection experiments with Xenopus oocytes and S1 nuclease analysis of normal ovary RNA showed that the H1C gene, and probably also two H3 genes, which are replication-dependent in somatic cells are expressed in oocytes and are therefore replication-independent in this cell type. The same promoters are used in both replication-dependent and independent expression.

Genomic organization and nucleotide sequence of two distinct histone gene clusters from Xenopus laevis. Identification of novel conserved upstream sequence elements

We have performed a detailed analysis of the genomic organization and the nucleotide sequence of two distinct Xenopus laevis histone gene clusters totaling approximately 23.5 X 10(3) base-pairs. Each cluster contains at least one copy of each of the five histone genes. However, these genes are present in different arrangements within each cluster and different H1A, H2A and H2B proteins (variants) are encoded by the respective genes of each cluster. Southern blot analysis of genomic X. laevis DNA indicates that each cluster is a member of a distinct family of tandemly repeated histone gene clusters. A comparative analysis of the nucleotide sequences flanking the histone genes within these two clusters has revealed the presence of multiple conserved sequence elements that are specific for each histone gene class and located at preferred upstream positions. Several of these elements correspond to sequences that are known to be required for maximal transcription of the corresponding genes. Most of these sequence elements have not been identified previously, although we find that many of them are present at corresponding locations upstream of histone genes from other organisms. We suggest that the conserved upstream sequence elements may play an important role in the expression of histone genes in vivo.

An H1 histone gene from rainbow trout (Salmo gairdnerii)

A 1.7-kbp DNA region from the 10.2-kb cluster containing the five rainbow trout histone genes has been subcloned in pBR322 and completely sequenced. It contains a trout histone H1 gene together with its 5' and 3' flanking sequences. This H1 gene codes for a H1 variant different from the major trout testis H1 previously sequenced by Macleod et al. (1977). Northern blots of total RNA from trout testis, kidney, and liver indicate that this H1 gene is expressed in all three tissues but that the level of H1 mRNA is much higher in testis than in other tissues. The lack of heterogeneity in the sizes and 5' initiation sites of trout H1 mRNAs is surprising in view of the substantial heterogeneity of H1 variant proteins observed previously. The coding sequence of the H1 gene shows strong evidence of repeated partial duplications of a hexapeptide motif of the form Ala.Ala.Ala.Lys.Lys.Pro and of a pentapeptide phosphorylation-site sequence, Lys.Ser.Pro.Lys.Lys, during its evolution. Comparisons are drawn between this gene and the coding sequences of other vertebrate H1 genes from chicken and Xenopus, and a strong homology is seen in the region of amino acids 22-101, which form the hydrophobic "head" of the H1 molecule. The 5' and 3' regulatory signals in the trout H1 are also compared with those of H1 genes from other sequences.

An H1 histone gene-specific 5' element and evolution of H1 and H5 genes

In previous studies we have shown that the H5 gene is not closely linked to the dispersed clusters of core and H1 histone genes. Here we emphasise features of H1 and H5 genes relevant to their expression in the chicken genome. Of particular note is an H1 gene-specific 5' element, 5' AAACACA 3' found upstream of all H1 genes studied to date. This "H1-box" is not found in the related H5 gene, which is expressed only in erythroid cells. A second aspect relates to generation of histone mRNA 3' termini. The H5 gene is shown to contain a remnant of the dyad symmetry element (as well as other conserved sequences) associated with core and H1-histone gene transcript 3' processing. However, it appears as if H5 has evolved a different mechanism in which the mRNA terminus (which is polyadenylated) is displaced downstream from the dyad element. The two clear differences noted here have the potential to affect transcriptional (H1-box) and post-transcriptional (3' terminus processing) regulation of H1 and H5 gene expression.

Conserved dyad symmetry structures at the 3' end of H5 histone genes. Analysis of the duck H5 gene

The duck H5 histone gene and its flanking DNA have been isolated and sequenced. S1 nuclease mapping reveals that transcription starts 149 nucleotides upstream of the initiation codon and that the site of polyadenylation is located 200 nucleotides downstream of the termination codon. A comparison with the chicken H5 gene demonstrates that the 3' non-translated segment of the polyadenylated H5 mRNA carries two conserved dyad symmetry sequences. The first potential hairpin is located directly after the termination codon of the H5 gene and is highly conserved, whereas the second stem and loop structure maps shortly upstream of the polyadenylation site and shows a homology block at the central part of this inverted DNA repeat.

Clustering of human H1 and core histone genes

An H1 histone gene was isolated from a 15-kilobase human DNA genomic sequence. The presence of H2A, H2B, H3, and H4 genes in this same 15-kilobase fragment indicates that mammalian core and H1 histone genes are clustered.

A transposon-like DNA fragment interrupts a Physarum polycephalum histone H4 gene

A recombinant DNA library was screened for histone H4 genes using a sea urchin probe. One recombinant was analysed by restriction enzyme mapping and Southern blotting. The complete DNA sequence of the H4 histone locus was determined. An 86 base pair interrupting sequence was found within the histone H4 coding sequence. The inserted DNA fragment has some characteristics of a transposable element.

Compilation and analysis of sequences upstream from the translational start site in eukaryotic mRNAs

5-Noncoding sequences have been tabulated for 211 messenger RNAs from higher eukaryotic cells. The 5'-proximal AUG triplet serves as the initiator codon in 95% of the mRNAs examined. The most conspicuous conserved feature is the presence of a purine (most often A) three nucleotides upstream from the AUG initiator codon; only 6 of the mRNAs in the survey have a pyrimidine in that position. There is a predominance of C in positions -1, -2, -4 and -5, just upstream from the initiator codon. The sequence CCAGCCAUG (G) thus emerges as a consensus sequence for eukaryotic initiation sites. The extent to which the ribosome binding site in a given mRNA matches the -1 to -5 consensus sequence varies: more than half of the mRNAs in the tabulation have 3 or 4 nucleotides in common with the CCACC consensus, but only ten mRNAs conform perfectly.