Structure and organization of the chicken H2B histone gene family

Characterization and expression of the mouse endonuclease G gene

Endonuclease G (Endo G) is a nuclease of prokaryotic lineage found in the mitochondria of vertebrates that has been suggested to play a role in mitochondrial DNA (mtDNA) replication. We have isolated and sequenced the entire mouse endo G gene, determined the limits of the mRNA, and mapped the promoter region. The coding sequence of the single copy gene is interrupted by two introns and analysis of the transcripts does not support a model by which more than one Endo G isoform could be produced by alternative splicing. We have also characterized a full-length human Endo G cDNA and comparison at the protein level of the human, bovine, and murine nucleases indicates a high degree of conservation except in the respective mitochondrial targeting signals. Endo G is ubiquitously expressed and the steady-state levels of its mRNA vary by a factor greater than seven between different tissues. The relationship between the mtDNA copy number and Endo G mRNA levels is not strictly proportional but tissues richer in mtDNA have higher amounts of the mRNA and vice versa.

Characterization of the mouse histone gene cluster on chromosome 13: 45 histone genes in three patches spread over 1Mb

The histone gene cluster on mouse chromosome 13 has been isolated and characterized. Using overlapping YAC clones containing histone genes from chromosome 13, a contig of approximately 2 Mb has been defined. It contains 45 histone genes, organized in three patches containing tightly clustered genes. An 80-kb patch (patch III) containing 12 histone genes is near one end of the contig, and a similar-sized patch (patch I) containing 15 histone genes is near the other end of the contig, located at least 500 kb from the central patch (patch II) of histone genes. The entire cluster contains six histone H1 genes, including the testis-specific histone H1t gene that maps to the middle of the cluster. All nine histone H3 genes in this cluster have been sequenced, and their level of expression determined. Each histone H3 gene is distinct, with five genes encoding the H3.2 protein subtype and four genes encoding the H3.1 protein. They are all expressed, with each histone H3 gene accounting for a small proportion of the total histone H3 mRNA.

Characterization of the 55-kb mouse histone gene cluster on chromosome 3

The histone gene cluster on mouse chromosome 3 has been isolated as a series of overlapping P1 clones, covering 110-120 kb, by probing with the histone H3-614 gene that had been mapped previously to mouse chromosome 3. There are genes for 10 core histone proteins present in a 55-kb cluster within this contig. There are three histone H3 genes, two of which are identical; four histone H2a genes, two of which are identical, one histone H4 gene; and two histone H2b genes. These histone H3 and H2a genes encode approximately 40% of the total H3 and H2a mRNA, whereas the histone H4 and histone H2b genes encode < 10% of the total H4 and H2b mRNA. There are no histone H1 genes present in this cluster. All of the histone H2a genes encode histone H2a.2 proteins (or variants of H2a.2), and account for all the H2a.2 genes in the mouse genome. All three histone H3 genes encode the histone H3.2 protein. A 21-kb region containing the adjacent H3-614 and H2a-614 genes has been duplicated and is present in an inverted repeat separated by 4.5 kb. The other two H2a genes are adjacent, with the 3' ends of their mRNAs separated by only 49 nucleotides in the DNA and the U7 snRNP binding sites separated by only 20 nucleotides. One of the histone H2b genes has lost the stem-loop sequence characteristic of the replication-dependent histone mRNAs and encodes only polyadenylated mRNAs.

Structure of a cluster of mouse histone genes

The structure of a 25 kilobase region of mouse DNA containing 6 functional histone genes and an H2a pseudogene has been determined. The sequences and levels of expression of the H3 and H2b gene as well as the sequence of the H2a pseudogene have been determined.

Targeted disruption of H2B-V encoding a particular H2B histone variant causes changes in protein patterns on two-dimensional polyacrylamide gel electrophoresis in the DT40 chicken B cell line

The chicken H2B gene family comprises eight members (H2B-I to H2B-VIII), which are all located in two major histone gene clusters. All of them have been shown to encode four different protein variants (classes I to IV). In the DT40 chicken B cell line, the H2B-V gene, encoding the class III H2B variant, constituted about 10% of the total intracellular mRNA from all the H2B genes. To study the nature of this particular variant in vivo, we generated heterozygous (H2B-V, +/-) and homozygous (H2B-V, -/-) DT40 mutants by targeted integration. The remaining H2B genes were shown to be expressed more in these mutants than in the wild-type cell lines. The growth rate of DT40 cells was unchanged in the absence of the H2B-V gene. Two-dimensional polyacrylamide gel electrophoresis showed that the protein patterns were, on the whole, similar between the wild-type and homozygous cell lines. However, within this constant background, some cellular proteins disappeared or decreased quantitatively in the homozygous mutants, and several other proteins increased or newly appeared. These results suggest that the class III H2B variant participates negatively or positively in regulation of the expression of particular genes that encode the proteins that vary in DT40 cells. This type of regulation is possibly mediated through alterations in nucleosome structure over the restricted regions involving the putative genes of the DT40 genome.

Possible involvement of a ubiquitous and several distinct elements in the transcription regulation of the chicken H3 histone gene family

We have studied possible modes of transcription regulation of four members (H3-II, H3-III, H3-IV and H3-V) of the twelve chicken H3 genes. Results of transient CAT assays using 5'-truncated mutants of H3-IV, together with those reported previously for H3-II and H3-III, indicated that all these four H3 genes possessed a ubiquitous element, the CCAAT sequence, in addition to several distinct elements. Transient CAT assays using the 5'-extended mutants of these four H3 genes showed that the promoter activities decreased with increasing lengths of the 5'-extended fragments, and that the effects were strong for H3-IV and H3-V, but only moderate for H3-II and H3-III.

Effects of histone acetylation, ubiquitination and variants on nucleosome stability

The properties of the nucleosomes of a salt-soluble, transcriptionally active gene-enriched fraction of chicken erythrocyte chromatin were evaluated by hydroxyapatite dissociation chromatography. We have demonstrated previously that the salt-soluble, transcriptionally active gene-enriched polynucleosomes are enriched in dynamically acetylated and ubiquitinated histones, and in an atypical U-shaped nucleosome that possessed about 20% less protein than a typical nucleosome. Further, newly synthesized histones H2A and H2B exchange preferentially with the nucleosomal histones H2A and H2B of this salt-soluble chromatin fraction. Analysis of the histones eluting from the hydroxyapatite-bound chromatin demonstrated that hyperacetylated and ubiquitinated (u), including multi-ubiquitinated, H2A-H2B.1 dimers dissociated at lower concentrations of NaCl than unmodified dimers or dimers with histone variants H2A.Z and/or H2B.2. Cross-linking studies revealed that at least 50% of uH2B.1 was paired with uH2A. uH2A-uH2B.1 dimers dissociated at lower NaCl concentrations than H2A-uH2B.1 dimers. Hyperacetylated histone (H3-H4)2 tetramers also eluted at lower concentrations of NaCl than unmodified tetramers. Our results support the idea that acetylation and ubiquitination of histones H2A and H2B.1 increase the lability of H2A-H2B.1 dimers in transcriptionally active nucleosomes. In contrast, our observations suggest that histone variants H2A.Z and H2B.2. stabilize the association of the H2A-H2B dimer in nucleosomes. The elevated lability of the H2A-H2B dimer may facilitate processes such as the exchange of these dimers with newly synthesized histones, the elongation process of transcription and transcription factor binding.

Presence of particular transcription regulatory elements in the 5'-intergenic region shared by the chicken H2A-III and H2B-V pair

The two chicken histone gene families, H2A and H2B, contain nine and eight members, respectively, within two major histone gene clusters. Six genes each from families H2A and H2B have been found to be closely associated in inverted directions as H2A/H2B gene pairs. Two previously sequenced H2A members (H2A-I and H2A-II) encode the same amino acid (aa) sequence (class I), whereas seven sequenced H2B genes encode three different variants (classes I, II and III). In this study, we first sequenced H2A-III, a member of the H2A family, which is located in inverted orientation and 350 bp upstream from H2B-V, encoding the class-III H2B protein. The protein encoded by H2A-III differs from the class-I H2A protein in a single aa (Ala70-->Pro; class II). As a step toward elucidation of the transcriptional regulation of the H2A and H2B families, we fused this 5'-intergenic region to the cat gene in inverted orientations to generate two chimeric plasmids, pH2A-III-350 and pH2B-V-350. Transient CAT assays using these constructs indicated that the promoter of H2B-V is more active than that of H2A-III. CAT assays with 5'-deletion mutants of H2A-III and H2B-V showed that they each possess particular transcriptional motifs which are located relatively close to, or apart from, their own coding regions. These findings, together with those reported previously on the H2A-V/H2B-II pair, suggest distinct manners of transcription regulation of different members of the chicken histone gene families, H2A and H2B.

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.

Histones and histone genes in higher plants: structure and genomic organization

The primary structure of the plant histone genes has been deduced from the comparison of the nucleotide sequences of 23 genes and 14 cDNAs from eight different species. These data confirmed the extreme conservation of histones H3 and H4 in plant and animal kingdoms. Histone H2B is more variable than H2A and the histone H1 is the less conserved histone. Some interesting observations concerning the non-conserved regions of H2A and H2B in their extended C- and N-terminal regions are reported. Only three plant histone genes were found to possess intervening sequences: one H1 gene and two H3.3 like genes. The most striking differences found between the two kingdoms are the absence from plant histone genes of the palindromic structure existing downstream of the animal genes and the fact that plant histone mRNAs are polyadenylated. This suggests that the post-transcriptional regulation of expression of histone genes is different in the two kingdoms. In plants the multiple copies of the histone genes are organized into multigenic families. In the complex genome of maize the multiple copies of the genes are highly dispersed on the genome.

Subfamilies of histone H3 and H4 genes are located on most, possibly all of the chromosomes in maize

It has been previously shown that in the genome of maize the multiple copies of the histone H3 and H4 multigenic families are organized into eight to ten subfamilies each containing a variable number of copies. Each subfamily is characterized by a specific proximal environment and thus can be revealed by blot-hybridization with its specific 5' probe. Restriction fragment length polymorphism (RFLP) combined with monosomic analysis was used to localize several H3 and H4 subfamilies on maize chromosomes. H3 and H4 genes were found to be located on most, possibly all of the chromosomes, revealing a remarkably dispersed organization of these multigenic families.

Presence of distinct transcriptional regulatory elements in the 5'-flanking region shared by the chicken H3 histone gene homopair

The chicken H3 histone gene family contains nine members belonging to two major histone gene clusters. Six of these genes have been sequenced and shown to encode two different H3 protein variants. Five H3 genes (H3-I, -II, -IV, -V, and -VI) encode the same amino acid sequence (class I) and another H3 gene (H3-III) differs from class I in a single amino acid (IIe113-Met) (class II). H3-II and H3-III have inverted orientations and share a 5' intergenic region of about 900 bp. To understand the regulation of expression of these two genes, we fused the 5'-flanking region to the CAT gene in inverted orientations to generate two chimeric plasmids, pH3-II-900 and pH3-III-900. Transient CAT assays using these constructs indicated that the promoter of H3-III is more active than that of H3-II. CAT assays with deletion mutants showed that H3-II and H3-III each possess a particular transcription regulatory sequence 5' adjacent to their coding sequence. In addition, the functional sequences of H3-II have no effect on expression of H3-III and vice versa. These results suggest that the regulations of expression of the two H3 genes are distinct.

Evidence for possible structural changes of particular H3 and H2B histone genes in different chicken tissues (cells)

The two chicken histone gene families H3 and H2B contain nine and eight members, respectively. To clarify whether the structures of these genes differ in different tissues (and cells), we analyzed DNAs from chicken lung, kidney, oviduct, and sperm. An H3-specific probe (probe 1.3SS) hybridized with a 10 kb EcoRI fragment carrying two H3 genes (H3-II and H3-III) from the lung, kidney, and oviduct with intensities of about one quarter of that of the fragment from the sperm. On the other hand, the intensities of hybridization of the H2B-specific probes (probes H2B-Ia, H2B-IIb, and H2B-III) with a 12 kb EcoRI fragment carrying two H2B genes (H2B-IV and H2B-V) from the oviduct, lung, and sperm were about a quarter of the intensity of hybridization with this fragment from the kidney. These findings, together with those reported previously, suggest that these particular histone genes H3 and H2B possess inherent abilities to form either a tight or loose structure, and that they exist in a loose form in the sperm and kidney but in a tight form in the other tissues tested.

Structural change of a particular H2B histone gene possibly results in differences in its transcriptional regulation in different chicken tissues

The chicken H2B histone gene family consists of eight highly homologous members (H2B-I to H2B-VIII) belonging to two major histone gene clusters. Seven of these genes have been sequenced and shown to encode three different H2B protein variants. Northern analysis with a probe, which mainly consists of the 5'-flanking region containing the sequence for the mRNA leader of H2B-V encoding a particular H2B protein variant, revealed that the mRNA level transcribed from this particular gene was higher in the kidney than in the oviduct and lung. To elucidate whether the structure of the H2B gene differs in the three different tissues, we analyzed DNAs from the oviduct, lung, and kidney. On Southern analysis, various H2B gene-specific probes hybridized with two particular H2B genes (H2B-IV and H2B-V), which are located in close proximity within a 12 kb EcoRI fragment, from the oviduct and lung with an intensity of about one quarter of that from the kidney. These findings suggest that some difference of DNA structure of the H2B-V gene may result in its relatively higher expression in the kidney.

Nucleotide sequences of two members of the chicken H4 histone-encoding gene family

The nucleotide sequences of two genes (H4-III and H4-IV) from the chicken H4 histone-encoding gene family have been determined. The four H4 genes, including the previously sequenced H4-I and H4-II genes, encode the same amino acid sequence and possess several copies of the possible Sp1-binding sequences on the coding and noncoding strands within the 5'-flanking regions.

Nucleotide sequences of two members of the chicken H3 histone-encoding gene family

The nucleotide sequences of two genes (H3-II and H3-III) from the chicken H3 histone-encoding gene family have been determined. H3-II and H3-III, respectively, possess possible AP-1- and Sp1-binding sequence elements of the forms 5'-CGAGTCAG and 5'-GGGCGGG, whereas all three H3 genes, including the previously sequenced H3-I gene, encode the same amino acid sequence.

Nucleotide sequence of a member of the chicken H2B histone-encoding gene family

The nucleotide sequence of a gene from the chicken H2B histone-encoding gene family has been determined. Our findings, together with those in a previous paper [Grandy and Dodgson, Nucleic Acids Res. 15 (1987) 1063-1080], show that the seven H2B genes encode three different histone variants.

Cloning of the cDNA and gene for a human D2 dopamine receptor

A clone encoding a human D2 dopamine receptor was isolated from a pituitary cDNA library and sequenced. The deduced protein sequence is 96% identical with that of the cloned rat receptor with one major difference: the human receptor contains an additional 29 amino acids in its putative third cytoplasmic loop. Southern blotting demonstrated the presence of only one human D2 receptor gene. Two overlapping phage containing the gene were isolated and characterized. DNA sequence analysis of these clones showed that the coding sequence is interrupted by six introns and that the additional amino acids present in the human pituitary receptor are encoded by a single exon of 87 base pairs. The involvement of this sequence in alternative splicing and its biological significance are discussed.

Expression of replication-dependent histone genes in avian spermatids involves an alternate pathway of mRNA 3'-end formation

In somatic cells the expression of replication-dependent histone genes is coupled to the S phase of the cell cycle. However, we have found a number of novel H2a, H2b, and H3 poly(A)+ RNA species in avian haploid round spermatids. The spermatid-specific H2a and H2b 0.8-kilobase RNAs are transcribed from a subset of the replication-dependent H2a and H2b gene families. Two cDNAs derived from the spermatid-specific H2b transcripts were isolated and sequenced. The structures of these cDNAs reveal that the spermatid-specific RNAs are identical to the 0.5-kilobase poly(A)- H2b mRNAs expressed in proliferating somatic cells, except for the addition of poly(A) at the 3' ends. The site of poly(A) addition in the spermatid-specific RNAs is located 26 to 28 nucleotides 3' of the poly(A)- H2b mRNA terminus. Thus, the hairpin structures and purine-rich elements required for the U7 small nuclear ribonucleoprotein-mediated cleavage reaction that generates the 3' ends of poly(A)- H2b mRNAs are not utilized in spermatids and are retained in the poly(A)+ H2b RNAs.

Selection for B cells with productive IgL gene rearrangements occurs in the bursa of Fabricius during chicken embryonic development

The vast majority of immunoglobulin-expressing mature chicken B lymphocytes contain one functionally rearranged and one unrearranged allele of the immunoglobulin light chain (IgL) gene. Therefore, nearly all IgL V-J rearrangements present in mature chickens are in-frame. In contrast, the Ig genes of mature mammalian B cells contain a high proportion of out-of-frame V-J joints. To investigate the basis for this difference, gene rearrangement at the chicken IgL locus was characterized during embryonic development and in mature B-cell lines. Joining of the single functional variable (VL) segment with the single joining (JL) segment occurs in cells in multiple tissues during a transient period of chicken embryogenesis. Only one-third of the V-J joints cloned from days 10-12 of development are in-frame. An increasing proportion of in-frame V-J joints is observed within the bursa of Fabricius at successively later stages of development. Our data suggest that the bursa of Fabricius serves during embryonic development as a site of selective amplification of cells that have undergone productive V-J joining, such that nearly all V-J joints present in postembryonic B cells are in-frame. The high frequency of rearranged alleles joined in-frame that is found in posthatching bursal cells and mature B-cell lines appears to result from a low frequency with which cells undergo IgL rearrangement at both alleles, rather than from an increase in the precision of V-J joining in avian species.

Expression of replication-dependent histone genes in avian spermatids involves an alternate pathway of mRNA 3'-end formation

In somatic cells the expression of replication-dependent histone genes is coupled to the S phase of the cell cycle. However, we have found a number of novel H2a, H2b, and H3 poly(A)+ RNA species in avian haploid round spermatids. The spermatid-specific H2a and H2b 0.8-kilobase RNAs are transcribed from a subset of the replication-dependent H2a and H2b gene families. Two cDNAs derived from the spermatid-specific H2b transcripts were isolated and sequenced. The structures of these cDNAs reveal that the spermatid-specific RNAs are identical to the 0.5-kilobase poly(A)- H2b mRNAs expressed in proliferating somatic cells, except for the addition of poly(A) at the 3' ends. The site of poly(A) addition in the spermatid-specific RNAs is located 26 to 28 nucleotides 3' of the poly(A)- H2b mRNA terminus. Thus, the hairpin structures and purine-rich elements required for the U7 small nuclear ribonucleoprotein-mediated cleavage reaction that generates the 3' ends of poly(A)- H2b mRNAs are not utilized in spermatids and are retained in the poly(A)+ H2b RNAs.

Conservation of histone H2A/H2B intergene regions: a role for the H2B specific element in divergent transcription

The organization and function of potential regulatory elements associated with the promoters of chicken H2A and H2B genes pairs have been examined. The intergene regions of six dispersed and divergently-transcribed H2A/H2B gene pairs contain several extremely well conserved and spaced blocks of sequence homology. Adjacent coding regions are on average 342 base-pairs apart. Respective TATA boxes are separated by 180 base-pairs and within this confined region there are four CCAAT boxes and a previously identified 13 base-pair H2B-specific element (H2B-box) which has homology to the octamer motif present in a number of gene promoter/enhancer elements. Transcription of H2A and H2B genes from wild-type and mutant constructs was measured in transient assays by transfection into HeLa cells, and in permanently transformed clonal cell lines. In vitro separation of the two genes at a unique intergenic site significantly decreased transcription of each gene. This suggested that the H2A/H2B gene pairs contained overlapping promoters. Deletion or point mutagenesis of the H2B-specific element decreased the levels of H2B and the H2A transcripts indicating that this sequence is a common regulatory element of both genes in the divergent-pair configeration.

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.

Chicken chromosomal protein HMG-14 and HMG-17 cDNA clones: isolation, characterization and sequence comparison

A cDNA clone coding for the chicken high-mobility group 14 (HMG-14) mRNA has been isolated from a chicken-liver cDNA library by screening with two synthetic oligodeoxynucleotide pools whose sequences were derived from the partial amino acid sequence of the HMG-14 protein. A chicken HMG-17 cDNA clone was also isolated in a similar fashion. Comparison of the two chicken HMG cDNA clones to the corresponding human cDNA sequences shows that chicken and human HMG-14 mRNAs and polypeptides are considerably less similar than are the corresponding HMG-17 sequences. In fact, the chicken HMG-14 is almost as similar to the chicken HMG-17 in amino acid sequence as it is to mammalian HMG-14 polypeptides. HMG-14 and HMG-17 mRNAs seem to contain a conserved sequence element in their 3'-untranslated regions whose function is at present unknown. The chicken HMG-14 and HMG-17 genes, in contrast to their mammalian counterparts, appear to exist as single-copy sequences in the chicken genome, although there appear to exist one or more additional sequences which partially hybridize to HMG-14 cDNA. Chicken HMG-14 mRNA, about 950 nucleotides in length, was detected in chicken liver RNA but was below our detection limits in reticulocyte RNA.

Nuclear protein(s) binding to the conserved DNA hexameric sequence postulated to regulate transcription of wheat histone genes

Nuclear protein(s) that specifically bind(s) to the upstream hexamer motif, ACGTCA, of wheat histone H3 and H4 genes has (have) been identified. Sequences homologous to this hexamer are found to be conserved in the upstream region of not only wheat histone genes but also other plant and animal histone genes. This suggests a possible role(s) for the hexamer and the nuclear protein(s) in the transcriptional regulation of the wheat histone genes. This hexamer is homologous to the upstream core sequence, TGACGTCA, which is highly conserved in some animal genes whose expression is regulated by cAMP.