Comparative sequence analysis of the human and pufferfish Huntington's disease genes

Crystal structure of a dimeric chymotrypsin inhibitor 2 mutant containing an inserted glutamine repeat

We have constructed mutants of chymotrypsin inhibitor 2 with short glutamine repeats inserted into its inhibitory loop. These mutants oligomerize when expressed in Escherichia coli. The dimer of a mutant with four glutamines now has been crystallized, and its structure has been solved by molecular replacement by using the wild-type monomer as a search model. The structure of each half of the dimer is found to be the same as that of the wild-type monomer, except around the glutamine insertion. It was proposed that the components of the oligomers are held together by hydrogen bonds between the main-chain and side-chain amides of the glutamine repeats. Instead, they appear to form by swapping domains on folding in E. coli, and the glutamine repeats connecting the components of the dimers are disordered.

Pathogenesis of neurodegenerative diseases associated with expanded glutamine repeats: new answers, new questions

Eight diseases are now known to be caused by an expansion mutation of the trinucleotide repeat CAG encoding glutamine. Each disease is caused by a CAG expansion in a different gene, and the genes bear no similarity to each other except for the presence of the repeat. Nonetheless, the essential feature of all of these disorders is neurodegeneration in a set of overlapping cortical and subcortical regions. Disease age of onset, and in some cases severity, is correlated with repeat length. These and other observations have led to the hypothesis that CAG expansion causes disease by a toxic gain-of-function of the encoded stretch of polyglutamine residues. Expansion-induced abnormalities of cytoskeletal function or neuronal signalling processes may contribute to the pathogenic process. In addition, theoretical and experimental analysis of the chemistry of uninterrupted stretches of glutamine residues suggest that polyglutamine-containing proteins or protein fragments may aggregate, via a "polar zipper", into beta pleated sheets. Recent findings have now established the presence of such aggregates in selected regions of brain from affected individuals, in transgenic mice expressing expanded repeats, and in isolated cells transfected with expanded repeats. The aggregates are most prominently manifest as neuronal intranuclear inclusion bodies. As the investigation of the link between these inclusions and cell dysfunction and death continues, it is possible that new avenues for therapeutic intervention will emerge.

Characterization of the transcription factor MTF-1 from the Japanese pufferfish (Fugu rubripes) reveals evolutionary conservation of heavy metal stress response

The pufferfish Fugu rubripes was recently introduced as a new model organism for genomic studies, since it contains a full set of vertebrate genes but only 13% as much DNA as a mammal. Fugu genes tend to be smaller and densely spaced due to shortening of introns and intergenic spacers. We isolated the Fugu gene for the metal-responsive transcription factor MTF-1 (MTF1), a mediator of heavy metal regulation and oxidative stress response previously characterized in mammals. In addition, most of the cDNA sequence was also determined. The 780 amino acid MTF-1 protein of Fugu is very similar to that of mouse and human, with 90% amino acid identity in the DNA binding zinc finger domain and 57% overall identity. Expression of the pufferfish cDNA in mammalian cells shows that Fugu MTF-1 has the same DNA binding specificity as its mammalian counterpart and also induces transcription in response to zinc and cadmium. The protein-coding part of the Fugu MTF-1 gene spans 6.4 kb and consists of 11 exons. Upstream region and first exon constitute a CpG island. The distance between stop codon and polyadenylation motifs is >2 kb, suggesting a very long 3' untranslated mRNA region, followed by another CpG island which may represent the promoter of the next gene downstream. Part of the MTF-1 genomic structure was also determined in the mouse, and some striking similarities were found: for example, the upstream adjacent gene in both species is INPP5P, encoding a phosphatase. The mouse MTF-1 promoter is also embedded in a CpG island, which however shares no sequence similarity to the one of Fugu. The Fugu CpG island is shorter than the one of the mouse and has no elevated [G+C] content; these and other data indicate that CpG islands of fish may represent a primordial stage of CpG island evolution.

Structures, sequence characteristics, and synteny relationships of the transcription factor E4TF1, the splicing factor U2AF35 and the cystathionine beta synthetase genes from Fugu rubripes

A cosmid containing the beta-amyloid precursor protein (APP) from Fugu rubripes has been completely sequenced. In addition to APP, the cosmid contains the E4TF1-60 transcription factor, the U2AF35 pre-mRNA splicing factor, and the cystathionine beta synthetase (CBS) gene. The human homologues of all four genes map to human chromosome 21 but are not clustered; APP and E4TF1-60 map within 21q21, whereas U2AF35 and CBS map approximately 20Mb distal in 21q22. 3. The protein sequences of the Fugu genes vary in their overall level of similarity to their mammalian homologues, but several regions of functional importance are almost identical. As expected, the intron/exon structures of the homologous pairs of genes are highly conserved, but there are significant differences in the compaction ratios. The introns of APP and E4TF1-60 are 49- and 24-fold smaller in Fugu than in human, and the intergenic distance is compressed at least 100-fold. For U2AF35 and CBS, the introns are compressed only five- to eightfold. These size differences were compared with those for a number of previously reported Fugu genes; in general, levels of compaction of Fugu genes are consistent with the isochore locations of the human homologues.

Triplet repeat variability in the signal peptide sequence of the Xmrk receptor tyrosine kinase gene in Xiphophorus fish

Trinucleotide repeats in several human genes have been found to undergo spontaneous variation in repeat numbers in succeeding generations. Expansion of the repeat beyond a certain length causes specific pathological disorders. So far, a naturally occurring triplet repeat instability of transcribed sequences has been reported only from humans. However, the signal peptide encoding region of the receptor tyrosine kinase gene Xmrk from fish of the genus Xiphophorus contains a CTG repeat that differs in length even between closely related individuals. The consequence of this variability is signal peptides with shorter or longer hydrophobic core regions reaching, in some individuals, the critical maximum length for functional protein export or even exceeding it. In one stock, animals that are homozygous for such an allele were extremely rare, indicating that the triplet repeat length variability of the Xmrk gene of Xiphophorus may indeed have an influence on the function of the gene product and, under certain conditions, may affect the fitness of the individual.

Counting on comparative maps

Comparative maps record the history of chromosome rearrangements that have occurred during the evolution of plants and animals. Effective use of these maps in genetic and evolutionary studies relies on quantitative analyses of the patterns of segment conservation. We review the analytical methods that have been developed for characterizing these maps and evaluate their application to existing comparative maps mainly for plants and animals.

Genomic characterization of the Neurofibromatosis Type 1 gene of Fugu rubripes

The genomic structure of the Neurofibromatosis Type1 (NF1) gene of Fugu rubripes was investigated by sequence analysis of two overlapping cosmids. The Fugu NF1 gene spans 27 kb and is 13 times smaller than the human counterpart owing primarily to reduced intron size. The predicted amino acid sequence is highly related to that of human neurofibromin, exhibiting an overall similarity of 91.5%. Nearly all exons described for the human NF1 gene could be identified, except exon 12b and the alternatively spliced exons 9br and 48a. With the exception of the splice acceptor site in front of exon 16, all splice sites are in identical positions to those found in the human gene. Intron 1, which is 100-140 kb long in humans, spans 2575 bp in the Fugu NF1 gene. Another large intron of the human NF1 gene, intron 27b (45-50 kb), is 3942 bp of size in Fugu. Sequences related to the OMgp gene (Oligodendrocyte-Myelin-glycoprotein) or the EVI2A gene (ecotropic viral integration site), which are inserted into human NF1 intron 27b, were not detected in the corresponding Fugu intron. However, a single exon gene with similarity to the human EVI2B gene has been found on the reverse strand of Fugu intron 27b. This suggests that the human EVI2B gene and the Fugu gene in intron 27b have a common ancestor. We found the expression of this inserted gene in liver and kidney, but not in brain tissue of Fugu rubripes.

Characterization of the Huntington's disease (HD) gene homologue in the zebrafish Danio rerio

The Huntington's disease (HD) gene contains a trinucleotide repeat that is expanded and unstable in patients with the disease (HDCRG, 1993). As the first step toward investigating a potential role for this gene in early vertebrate development, we isolated the homolog of the Huntington's disease (ZHD) cDNA in zebrafish. This cDNA encodes a predicted protein product of 3121 amino acids with 70% identity to human huntingtin. The first exon is predicted to encode four glutamines, followed by only one proline, demonstrating that the polymorphic polyproline stretch found in mammalian HD sequences is absent in the fish. We sequenced approximately 900bp upstream from the predicted start codon and found that it lacks a TATA box, CCAAT box, or Sp1 binding sites. Western blot analysis revealed that the protein is expressed at a high level in late embryonic development and at moderate levels in the adult head.

Identification of an evolutionarily conserved 110 base-pair cis-acting regulatory sequence that governs Wnt-1 expression in the murine neural plate

The generation of anterior-posterior polarity in the vertebrate brain requires the establishment of regional domains of gene expression at early somite stages. Wnt-1 encodes a signal that is expressed in the developing midbrain and is essential for midbrain and anterior hindbrain development. Previous work identified a 5.5 kilobase region located downstream of the Wnt-1 coding sequence which is necessary and sufficient for Wnt-1 expression in vivo. Using a transgenic mouse reporter assay, we have now identified a 110 base pair regulatory sequence within the 5.5 kilobase enhancer, which is sufficient for expression of a lacZ reporter in the approximate Wnt-1 pattern at neural plate stages. Multimers of this element driving Wnt-1 expression can partially rescue the midbrain-hindbrain phenotype of Wnt-1(−/−) embryos. The possibility that this region represents an evolutionarily conserved regulatory module is suggested by the identification of a highly homologous region located downstream of the wnt-1 gene in the pufferfish (Fugu rubripes). These sequences are capable of appropriate temporal and spatial activation of a reporter gene in the embryonic mouse midbrain; although, later aspects of the Wnt-1 expression pattern are absent. Genetic evidence has implicated Pax transcription factors in the regulation of Wnt-1. Although Pax-2 binds to the 110 base pair murine regulatory element in vitro, the location of the binding sites could not be precisely established and mutation of two putative low affinity sites did not abolish activation of a Wnt-1 reporter transgene in vivo. Thus, it is unlikely that Pax proteins regulate Wnt-1 by direct interactions with this cis-acting regulatory region. Our analysis of the 110 base pair minimal regulatory element suggests that Wnt-1 regulation is complex, involving different regulatory interactions for activation and the later maintenance of transgene expression in the dorsal midbrain and ventral diencephalon, and at the midbrain-hindbrain junction.

Huntingtin: a single bait hooks many species

Cloning of the Huntington's disease gene uncovered huntingtin, which is remarkable for its lack of similarity with known proteins despite its large size, approximately 350 kDa. Subsequent experiments established that huntingtin has an as yet unknown function, crucial for embryonic development and neurogenesis. Recent protein trapping to identify huntingtin interactors now reveals that many different prey fall victim to huntingtin bait.

The identification and characterization of microsatellites in the compact genome of the Japanese pufferfish, Fugu rubripes: perspectives in functional and comparative genomic analyses

Fugu rubripes (Fugu) has one of the smallest recorded vertebrate genomes and is an economic tool for comparative DNA sequence analysis. Initial characterization of 128 kb of Fugu DNA attributed the compactness of this genome, in part, to a sparseness of repetitive DNA sequence compared with mammalian genomic sequences. This paper describes a new and comprehensive analysis in which 501 theoretically possible microsatellites with a repeat unit of one to six bases were used to query two orders of magnitude more Fugu DNA (i.e. 11.338 Mb). A total of 6042 microsatellites were identified and categorized. In decreasing order, the 20 most frequently occurring microsatellites are AC, A, C, AGG, AG, AGC, AAT, AAAT, ACAG, ACGC, ATCC, AAC, ATC, AGGG, AAAG, AAG, AAAC, AT, CCG and TTAGGG. The 20 most frequently occurring microsatellites represent 81.79% of all microsatellites identified. Our results indicate that one microsatellite occurs every 1.876 kb of DNA in Fugu, 11.55% of the microsatellites are detected in open reading frames that are predicted protein coding regions. With respect to the proportion of microsatellites present in open reading frames and the total abundance (bp) of all microsatellites, the genome of Fugu is similar to the genome of many other vertebrate species. Previous estimates performed indicate that approximately 1% of many vertebrate genomes are comprized of microsatellite sequences. However, many differences prevail in the abundance and frequency of the individual microsatellite classes. Many of the frequently occurring microsatellites in Fugu are known to code in other species for regions in proteins such as transcription factors, whilst others are associated with known functions, such as transcription factor binding sites and form part of promoter regions in DNA sequences of genes. Therefore, it is likely that such repeats in genomes have a role in the evolution of genes, regulation of gene expression and consequently the evolution of species.

Analysis of pufferfish homologues of the AT-rich human APP gene

Mutations in the beta-amyloid precursor protein (APP) gene are associated with some forms of Familial Alzheimer's Disease. The human APP gene is large, the 19 exons span approximately 300 kb, and AT-rich, at 40% GC. We have examined the genomic structure and cDNA sequence of the APP gene in the pufferfish Fugu rubripes and Tetraodon fluviatilis, respectively. In contrast to human, the Fugu APP gene spans less than 10 kb of DNA, with the introns compacted 48-fold on average. Two axons, alternatively processed in humans, are absent in both pufferfish. APP is the largest, most AT-rich gene examined in Fugu and is also the most highly compressed. The genomic sequences spanning the human and the Fugu APP genes were analysed with a set of exon and gene prediction programs. Results show that these are highly reliable for the Fugu gene with lower false positive and false negative rates than are seen in the analysis of the human gene. Comparative analysis of Fugu sequences homologous to very AT-rich regions in the human genome may, therefore, be advantageous in gene-finding efforts, both for their highly reduced sizes and their reliable gene predictions.

Isolation and genomic characterization of the TUPLE1/HIRA gene of the pufferfish Fugu rubripes

In an effort to obtain a small genomic construct for the generation of a HIRA transgenic mouse, we have isolated and sequenced the Fugu TUPLE1/HIRA gene. We have compared the gene organization and the proteins encoded in pufferfish and human and also searched for conserved DNA sequences that might be important in gene regulation. The pufferfish gene spans approx. 9 kb, which is approx. 11 times smaller than the human gene, owing to the reduced size of the introns. Like its human counterpart, it is organized into 25 exons. The majority of the splice sites are in identical positions to those found in the human gene, however, for three internal exons the positions of the splice sites are not directly comparable. The coding regions are almost identical in size and show a high degree of similarity, especially at the amino and carboxy termini. Comparisons of 5' and 3' sequences failed to detect similarities or sequences involved in regulation.

The neural cell adhesion molecule L1: genomic organisation and differential splicing is conserved between man and the pufferfish Fugu

The human gene for the neural cell adhesion molecule L1 is located on Xq28 between the ALD and MeCP2 loci. Mutations in the L1 gene are associated with four related neurological disorders, X-linked hydrocephalus, spastic paraplegia (SPG1), MASA syndrome, and X-linked corpus callosum agenesis. The clinical relevance of L1 has led us to sequence the L1 gene in human and to investigate its conservation in the vertebrate model genome of the pufferfish, Fugu rubripes (Fugu), a species with a compact genome of around 40Mb. For this purpose we have sequenced a human and a Fugu cosmid clone containing the corresponding L1 genes. For comparison, we have also amplified and sequenced the complete Fugu L1 cDNA. We find that the genomic structure of L1 is conserved. The human and Fugu L1 gene both have 28 exons of nearly identical size. Differential splicing of exons 2 and 27 is conserved over 430 million years, the evolutionary time span between the teleost Fugu and the human L1 gene. In contrast to previously published Fugu genes, many introns are larger in the Fugu L1 gene, making it slightly larger in size despite the compact nature of the Fugu genome. Homology at the amino acid and the nucleotide level with 40% and 51%, respectively, is lower than that of any previously reported Fugu gene. At the level of protein structure, both human and Fugu L1 molecules are composed of six immunoglobulin (Ig)-like domains and five fibronectin (Fn) type III domains, followed by a transmembrane domain and a short cytoplasmic domain. Only the transmembrane and the cytoplasmic domains are significantly conserved in Fugu, supporting their proposed function in intracellular signalling and interaction with cytoskeletal elements in the process of neurite outgrowth and fascicle formation. Our results show that the cytoplasmic domain can be further subdivided into a conserved and a variable region, which may correspond to different functions. Most pathological missense mutations in human L1 affect conserved residues. Fifteen out of 22 reported missense mutations alter amino acids that are identical in both species.

The pufferfish SLP-1 gene, a new member of the SCL/TAL-1 family of transcription factors

The SCL/TAL-1 gene encodes a basic helix-loop-helix (bHLH) transcription factor essential for the development of all hemopoietic lineages and also acts as a T-cell oncogene. Four related genes have been described in mammals (LYL-1, TAL-2, NSCL1, and NSCL2), all of which exhibit a high degree of sequence similarity to SCL/TAL-1 in the bHLH domain and two of which (LYL-1 and TAL-2) have also been implicated in the pathogenesis of T-cell acute lymphoblastic leukemia. In this study we describe the identification and characterization of a pufferfish gene termed SLP-1, which represents a new member of this gene family. The genomic structure and sequence of SLP-1 suggests that it forms a subfamily with SCL/TAL-1 and LYL-1 and is most closely related to SCL/TAL-1. However, unlike SCL/TAL-1, SLP-1 is widely expressed. Sequence analysis of a whole cosmid containing SLP-1 shows that SLP-1 is flanked upstream by a zinc finger gene and a fork-head-domain gene and downstream by a heme-oxygenase and a RING finger gene.

Round-spotted pufferfish (Tetraodon fluviatilis) snf5 gene is oriented in a tail-to-tail manner with the set gene which encodes an inhibitor of protein phosphatase 2A

The round-spotted pufferfish Tetraodon fluviatilis has a genome size of 380 Mb which is slightly smaller than that of another pufferfish Fugu rubripes rubripes (Fugu). Due to its compact genome and small introns, Fugu has been introduced as a model for genome studies. Recently, the round-spotted pufferfish has also been proposed as a new model for genome studies because of the ease in obtaining material and high-sequence homology to that of Fugu. In this study, we have cloned and characterized the snf5 and set genes from the round-spotted pufferfish. The snf5 gene is composed of 9 exons spanning about 2.9 kb whereas the set gene consists of 8 exons spanning about 2.7 kb. They are linked in a tail-to-tail manner with an intergenic region of about 6.5 kb. So far, the genomic structures of human snf5 and set genes are unknown. Based on our data, the pufferfish SNF5 and SET display high amino acid sequence identity (>90%) with the respective human genes. By primer extension and sequence analysis, we found that putative promoter region of the snf5 gene contains a typical TATA box and numerous potential binding sites for transcription factors including AP1, AP2, AP3, c-Myb, HNF-5, and NF-IL6. As for the set gene, its promoter region does not have any TATA or CCAAT motif and contains a few potential binding sites for transcriptional factors such as c-Myb and gamma-IRE. When these promoter regions were placed upstream of the CAT reporter gene and transfected into a carp CF cell line, the 5'-upstream 1.6-kb DNA fragment of the snf5 gene displayed stronger promoter activity, approximately three-fold higher than that of the 5'-upstream 1.3 kb DNA fragment of the set gene. By transient expression and immunofluorescent staining, we also showed that the pufferfish SNF5 and SET are nuclear proteins, consistent with their postulated roles as transcriptional factors.

Clonability and gene distribution on human chromosome 21: reflections of junk DNA content?

Data from transcriptional mapping of human chromosome 21 have been compiled from a number of sources. Regardless of the gene identification technique used, a consistent picture has developed: the centromere proximal half of 21q, which contains 50% of the DNA (20 Mb), harbors only 10% of the expressed sequences. Because of the variety of gene isolation techniques used, this result is unlikely to arise simply from methodological artefacts, biases in clonability or tissue specificity of expression. This region is known to be AT-rich and to contain APP, the largest gene (spanning 300 kb) currently analyzed on 21q. Interesting preliminary data from analysis of the Fugu rubripes homolog of APP has shown an unusually high, 50-fold, compaction of intron size, raising the intriguing possibility that >90% of the DNA in the human gene may be functionless. Thus, data from a variety of approaches suggest that a large part of 21q very likely has neither coding capacity nor associated regulatory function. By these criteria, it is a good candidate for a repository of junk DNA.

The comparative genomic structure and sequence of the surfeit gene homologs in the puffer fish Fugu rubripes and their association with CpG-rich islands

The puffer fish Fugu rubripes (Fugu) has a compact genome approximately one-seventh the size of man, mainly owing to small intron size and the presence of few dispersed repetitive DNA elements, which greatly facilitates the study of its genes at the genomic level. It has been shown previously that, whereas the Surfeit genes are tightly clustered at a single locus in mammals and birds, the genes are found at three separate loci in the Fugu genome. Here, Fugu gene homologs of all six Surfeit genes (Surf-1 to Surf-6) have been cloned and sequenced, and their gene structure has been compared with that of their mammalian and avian homologs. The predicted protein products of each gene are well conserved between vertebrate species, and in most cases their gene structures are identical to their mammalian and avian homologs except for the Fugu Surf-6 gene, which was found to lack an intron present in the mouse gene. In addition, we have identified conserved regulatory elements at the 5' and 3' ends of the Surf-3/rpL7a gene by comparison with the mammalian and chicken Surf-3/rpL7a gene homologs, including the presence of a polypyrimidine tract at the extreme 5' end of this ribosomal protein gene. The Fugu Surfeit gene homologs appear to be associated with CpG-rich islands, like the Surfeit genes in higher vertebrates, but these Fugu CpG islands are similar to the nonclassical islands characteristic of other fish species. Our observations support the use of the Fugu genome to study vertebrate gene structure, to predict the structure of mammalian genes, and to identify vertebrate regulatory elements. [The sequence data described in this paper have been submitted to the data library under accession nos. Y15170 (Surf-2, Surf-4), Y15171 (Surf-3, Surf-1, Surf-6), and Y15172 (Surf-5.)]

Alu sequences

Alu sequences are frequently encountered during study of human genomic nucleic acid and form a major component of repetitive DNA. This review describes the origin of Alu sequences and their subsequent amplification and evolution into distinct subfamilies. In recent years a number of different functional roles for Alu sequences have been described. The multiple influences of Alu sequences on RNA polymerase II-mediated gene expression and the presence of Alu sequences in RNA polymerase III-generated transcripts are discussed.

Aberrant processing of the Fugu HD (FrHD) mRNA in mouse cells and in transgenic mice

The puffer fish ( Fugu rubripes ) has a compact genome of 400 Mbp which is approximately 7.5-fold smaller than the human genome. It contains a similar number of genes but is deficient in intergenic, intronic and dispersed repetitive sequences. Fugu is becoming established as the model vertebrate genome for the identification and characterisation of novel human genes and conserved regulatory sequences. It has also been proposed that Fugu genes may provide natural mini-genes for the production of transgenic mice. We have used the Fugu homologue of the Huntington's disease (HD) gene to test this possibility. The human and Fugu HD genes cover 170 kb and 23 kb respectively and have previously been sequenced in their entirety. In Fugu tissue, the Fugu HD gene was found to be expressed as predicted from the gene sequence but three differentially spliced forms were also detected. Despite the absence of conserved promoter sequences, the Fugu promoter was found to be functional in mouse cells. We have generated mice transgenic for the Fugu HD gene and conducted a detailed expression analysis across the entire 10 kb transcript. This revealed the presence of many aberrant splice forms which would be incompatible with the production of the Fugu huntingtin protein. The Fugu HD gene is incorrectly processed in mouse cells both in vitro and in vivo which sheds doubt on the usefulness of Fugu genes for transgenesis.

Cloning and sequencing of complement component C9 and its linkage to DOC-2 in the pufferfish Fugu rubripes

The Japanese pufferfish Fugu rubripes has a 400 Mb genome with high gene density and minimal non-coding complexity, and is therefore an ideal vertebrate model for sequence comparison. The identification of regions of conserved synteny between Fugu and humans would greatly accelerate the mapping and ordering of genes. Fugu C9 was cloned and sequenced as a first step in an attempt to characterize the region in Fugu homologous to human chromosome 5p13. The 11 exons of the Fugu C9 gene share 33% identity with human C9 and span 2.9 kb of genomic DNA. By comparison, human C9 spans 90 kb, representing a 30-fold difference in size. We have also determined by cosmid sequence scanning that DOC-2, a tumour suppresser gene which also maps to human 5p13, lies 6-7 kb from C9 in a head-to-head or 5' to 5' orientation. These results demonstrate that the Fugu C9/DOC-2 locus is a region of conserved synteny. Sequence scanning of overlapping cosmids has identified two other genes, GAS-1 and FBP, both of which map to human chromosome 9q22, and lie adjacent to the Fugu C9/DOC-2 locus, indicating the boundary between two syntenic regions.

Towards a reconciliation of the introns early or late views: triosephosphate isomerase genes from insects

The gene encoding the glycolytic enzyme, triosephosphate isomerase (TPI; EC 5.3.1.1), is a favourite model for molecular evolutionists who either subscribe to the theory that introns co-evolved with the ancestral gene, the introns early view, or alternatively, that introns are more recent immigrants. The discovery of an intron in the TPI gene of Culex mosquitoes at a site which was predicted by proponents of the intron early school supported that theory. More recently, the discovery of additional intron sites in several eukaryotes was presented as evidence supporting the introns late school. We have found the 'Culex intron' in two closely related mosquitoes, but not in two more evolutionary primitive Dipterans, suggesting that, if it is an 'ancient intron', loss may be more frequent than that supposed by the intron late school. In addition, we have found that three introns punctuating the TPI gene from the Lepidopteran, Heliothis, appear to be ancestrally related and may be the result of transposable element insertion, 50-90 million years ago. It is argued that both opposing schools in the intron debate be reconciled -- some introns may have been early and certainly others have arrived subsequent to the appearance of the TPI gene.

Sequence of the human immunoglobulin diversity (D) segment locus: a systematic analysis provides no evidence for the use of DIR segments, inverted D segments, "minor" D segments or D-D recombination

We have determined the complete nucleotide sequence of the human immunoglobulin D segment locus on chromosome 14q32.3 and identified a total of 27 D segments, of which nine are new. Comparison with a database of rearranged heavy chain sequences indicates that the human antibody repertoire is created by VDJ recombination involving 25 of these 27 D segments, extensive processing at the V-D and D-J junctions and use of multiple reading frames. We could find no evidence for the proposed use of DIR segments, inverted D segments, "minor" D segments or D-D recombination. Conventional VDJ recombination, which obeys the 12/23 rule, is therefore sufficient to explain the wealth of lengths and sequences for the third hypervariable loop of human heavy chains.

Computational gene discovery and human disease

Bioinformatics is now an essential tool in many aspects of human molecular genetics research. Methods for the prediction of gene structure are essential components in genomic sequencing projects and provide the key to deriving protein sequence and locating intron/exon junctions. Sequence comparison and database searching are the pre-eminent approaches for predicting the likely biochemical function of new genes, although sequence profiles derived from families of aligned sequences have advantages in the detection of remote sequence relationships. The use of sequence database analysis for large-scale comparative analysis of genome sequence data from model organisms is emerging as the most important recent development in the application of bioinformatics methods for characterizing candidate disease genes.

Expression and distribution of the dentatorubral-pallidoluysian atrophy gene product (atrophin-1/drplap) in neuronal and non-neuronal tissues

Utilizing an affinity-purified antiserum directed against the carboxyl terminal region of atrophin-1/drplap (residues 1170-1185), we have examined the expression and distribution of the protein in a variety of neuronal and non-neuronal tissues. Immunohistochemical analyses of gelatin-embedded sections of monkey brain demonstrated a wide-spread distribution of the protein throughout the cerebrum and cerebellum. Labeling was primarily cytoplasmic within neuronal cell bodies and dendrites. Prominently staining regions included layers II, III, V, and VI of cerebral cortex, CA1-4 of the hippocampus, caudate nucleus, putamen, globus pallidus, amygdala, thalamus, red nucleus, pons, Purkinje cells, and deep cerebellar nuclei. Immunoblot analysis of extracts of frontal cortex from a wide variety of mammalian species (human, monkey, rabbit, rat, mouse, and bovine) detected a 190 kDa band in each extract. No cross-reactive material of similar molecular weight was detected in an extract of avian (chicken) central nervous system (CNS) tissue. Furthermore, in the rat, expression of the protein was predominantly neuronal in origin as immunoblot analyses of non-neuronal tissue extracts detected little or no 190 kDa protein. Collectively these investigations suggest a ubiquitous expression of atrophin-1/drplap in mammalian CNS tissue and provide initial immunochemical data for the study of the neuroanatomic and perhaps, phylogenetic relationships between mammalian and non-mammalian forms of the protein.

G protein alpha subunit multigene family in the Japanese puffer fish Fugu rubripes: PCR from a compact vertebrate genome

We compare the complexity and organization of the G protein alpha subunit multigene family in the vertebrate genomes of mammals and the Japanese puffer fish Fugu rubripes. Fourteen Fugu G alpha genes were identified of the 16 genes characterized previously in mammals, including Fugu genes from the four classes of alpha subunits Gs, Gi, Gq, and G12. Fugu and mammalian G alpha coding sequences are highly homologous, and the intron/exon structure of the fish and mammalian orthologs is identical throughout the coding regions. A novel G alpha gene, G alpha p1, was also identified in Fugu rubripes and two other species of puffer fish. The complete sequence of Gnaz and the tandemly duplicated genes Gnai2 and Gnat1 were obtained from a Fugu genomic cosmid library. Introns in the puffer fish G alpha genes lacked repeat DNA sequences, other than simple sequence length repeats, and most introns were significantly shorter in Fugu than in mammalian orthologs. The compact genome of puffer fish provides a unique vertebrate model for characterizing multigene families and identifying novel genes directly from genomic DNA by PCR amplification with degenerate primers. The fact that Fugu encodes most, if not all, of the G protein alpha subunits identified in mammals strongly supports Fugu as a model organism for vertebrate genome research.

Glutamine repeats and inherited neurodegenerative diseases: molecular aspects

Several dominantly inherited, late onset, neurodegenerative diseases are due to expansion of CAG repeats, leading to expansion of glutamine repeats in the affected proteins. These proteins are of very different sizes and, with one exception, show no sequence homology to known proteins or to each other; their functions are unknown. In some, the glutamine repeat starts near the N-terminus, in another near the middle and in another near the C-terminus, but regardless of these differences, no disease has been observed in individuals with fewer than 37 repeats, and absence of disease has never been found in those with more than 41 repeats. Protein constructs with more than 41 repeats are toxic to E. coli and to CHO cells in culture, and they elicit ataxia in transgenic mice. These observations argue in favour of a distinct change of structure associated with elongation beyond 37-41 glutamine repeats. The review describes experiments designed to find out what these structures might be and how they could influence the properties of the proteins of which they form part. Poly-L-glutamines form pleated sheets of beta-strands held together by hydrogen bonds between their amides. Incorporation of glutamine repeats into a small protein of known structure made it associate irreversibly into oligomers. That association took place during the folding of the protein molecules and led to their becoming firmly interlocked by either strand- or domain-swapping. Thermodynamic considerations suggest that elongation of glutamine repeats beyond a certain length may lead to a phase change from random coils to hydrogen-bonded hairpins. Possible mechanisms of expansion of CAG repeats are discussed in the light of looped DNA model structures.

Fugu intron oversize reveals the presence of U15 snoRNA coding sequences in some introns of the ribosomal protein S3 gene

We present here the analysis of the genomic organization of the Fugu gene coding for ribosomal protein S3 and its intron encoded U15 RNA, and compare it with the homologous human and Xenopus genes. Only two of the six Fugu S3 gene introns do not contain the U15 sequence and are in fact shorter than 100 nucleotides, as most Fugu introns. The other four introns are somewhat longer and contain sequences homologous to U15 RNA; two of these represent functional copies, as shown by microinjections of Fugu transcripts into Xenopus oocytes, whereas the other two appear to be nonfunctional pseudocopies. Thus Fugu turns out to be ideal for the study of intron encoded snoRNAs, partly because of the reduced cloning and sequencing workload, and partly because the intron length per se can be an indication of the presence of a snoRNA coding sequence.

Conserved linkage between the puffer fish (Fugu rubripes) and human genes for platelet-derived growth factor receptor and macrophage colony-stimulating factor receptor

We have cloned and sequenced the teleost homologs of the human genes encoding platelet-derived growth factor receptor-beta (PDGFR beta) and macrophage colony-stimulating factor 1 receptor (CSFIR) from the puffer fish Fugu rubripes. The Fugu PDGFR beta and CSFIR genes each consist of 21 coding exons similar to the human CSFI gene, but are considerably smaller than their human counterparts because of the smaller introns. Furthermore, the two Fugu genes are linked tandemly in a head-to-tail array similar to their human homologs with 2.2 kb of intergenic sequence. Amino acid sequences of the Fugu and human PDGFR beta and CSFIR genes show an overall homology of 45% and 39%, respectively, with the kinase domains showing a much higher degree of conservation. Dot-matrix analysis revealed several short stretches of conserved sequences in the 3' untranslated regions of the PDGFR beta genes and the adjacent promoter regions of the CSFIR genes. These conserved sequences may have a role in the regulation of expression of either or both of these closely linked genes.

Huntington's disease: translating a CAG repeat into a pathogenic mechanism

The specific pattern of neuronal cell death in Huntington's disease (HD) is triggered by an abnormal version of the huntingtin protein, which is produced by translation of the HD gene defect, an expanded CAG repeat in a novel 4p16.3 gene. The extended amino-terminal polyglutamine segment may act via the protein's inherent activity, increasing it or decreasing it in a graded fashion, or, alternatively, it may confer the ability to interact with a completely different set of cellular pathways, focusing attention on the HD protein's normal and abnormal physiological functions.

The conserved role of Krox-20 in directing Hox gene expression during vertebrate hindbrain segmentation

Transient segmentation in the hindbrain is a fundamental morphogenetic phenomenon in the vertebrate embryo, and the restricted expression of subsets of Hox genes in the developing rhombomeric units and their derivatives is linked with regional specification. Here we show that patterning of the vertebrate hindbrain involves the direct upregulation of the chicken and pufferfish group 2 paralogous genes, Hoxb-2 and Hoxa-2, in rhombomeres 3 and 5 (r3 and r5) by the zinc finger gene Krox-20. We identified evolutionarily conserved r3/r5 enhancers that contain high affinity Krox-20. binding sites capable of mediating transactivation by Krox-20. In addition to conservation of binding sites critical for Krox-20 activity in the chicken Hoxa-2 and pufferfish Hoxb-2 genes, the r3/r5 enhancers are also characterized by the presence of a number of identical motifs likely to be involved in cooperative interactions with Krox-20 during the process of hindbrain patterning in vertebrates.

Quality not quantity: the pufferfish genome

The genome of the pufferfish, Fugu rubripes (Fugu) is compact. With a similar gene complement to mammals and a genome size of just 400 Mb, gene density is high averaging one every 6-7 kb. Initial characterization of this genome has shown that although genes are much smaller and more densely spaced, their intron/exon structure is conserved with the resulting introns being small. There is little repetitive DNA in the genome and this greatly facilitates comparative genomic studies. The coding content of genes is highly conserved as are critical regulatory elements of some genes. Other DNA is not, however, and this allows the identification of homologous coding sequence between Fugu and mammalian genes. Although the genome of Fugu is 7.5 times smaller than the human genome, not all genes are reduced proportionately. Some regions of the genome show conserved synteny with mammalian genomes, although at the present time only short physical distances have been examined. The structure of the genome is also being studied. Initial data suggest that this may be different to that found in mammals. It is not clear that the same kind of isochore structure is present in this early vertebrate genome. Patterns of methylation may be different resulting in a different distribution of CpG islands. An attempt is being made to centralize both resources and data from the genome of Fugu so that everything may be integrated into a single, publicly accessible database which in turn, may be integrated with databases from other organisms.

A functional role for some Fugu introns larger than the typical short ones: the example of the gene coding for ribosomal protein S7 and snoRNA U17

The compact genome of Fugu rubripes, with its very small introns, appears to be particularly suitable to study intron-encoded functions. We have analyzed the Fugu gene for ribosomal protein S7 (formerly S8, see Note), whose Xenopus homolog contains in its introns the coding sequences for the small nucleolar RNA U17. Except for intron length, the organization of the Fugu S7 gene is very similar to that of the Xenopus counterpart. The total length of the Fugu S7 gene is 3930 bp, compared with 12691 bp for Xenopus. This length difference is uniquely due to smaller introns. Although short, the six introns are longer than the approximately 100 bp size of most Fugu introns, as they host U17 RNA coding sequences. While four of the six U17 sequences are 'canonical', the remaining two represent diverged U17 pseudocopies. In fact, microinjection in Xenopus oocytes of in vitro synthesized Fugu transcripts containing the 'canonical' U17f sequence results in efficient production of mature U17 RNA, while injection of a transcript containing the U17 psi b sequence does not.

Translocation events in the evolution of aminoacyl-tRNA synthetases

We have characterized hisS, the gene encoding the histidyl-tRNA synthetase (HisRS) from the tetraodontoid fish Fugu rubripes. The hisS gene is about 3.5 kbp long and contains 13 exons and 12 introns of 172 bp, on average. The Fugu hisS gene encodes a putative protein of 519 amino acids with the three motifs identified as signatures of class 2 aminoacyl-tRNA synthetases. A model for the shifting of intron 8 between Fugu and hamster is proposed based on the successive appearance of a cryptic splicing site followed by an insertion mutation that created a new acceptor site. In addition, sequence comparisons suggest that the hisS gene has undergone a translocation through the first intron. As a result, the Fugu HisRS has an N-terminal sequence markedly different from that in the human and hamster enzymes. We propose that similar events have been responsible for variations at the N-terminal end of other aminoacyl-tRNA synthetases. Our analysis suggests that this involves exchanges through introns of two exons encoding an ancestral 32-amino acid motif.

Human lipoprotein lipase last exon is not translated, in contrast to lower vertebrates

We have sequenced the first fish (zebrafish, Brachydanio rerio) lipoprotein lipase (LPL) cDNA clone. Similarities were found in mammalian LPL cDNA, but the codon spanning the last two exons (which is thus split by the last intron) is AGA (Arg) as opposed to TGA in mammals. Exon 10 is thus partially translated. These results were confirmed with rainbow trout (Oncorhynchus mykiss). We also investigated whether mammal TGA coded for selenocystein (SeCys), the 21st amino acid, but found that this was not the case: TGA does not encode SeCys but is a stop codon. It thus appears that the sense codon AGA (fish) has been transformed into a stop codon TGA (human) during the course of evolution. It remains to be determined if the "loss" of the C-terminal end of mammalian LPL protein has conferred an advantage in terms of LPL activity or, on the contrary, a disadvantage (e.g., susceptibility to diabetes or atherosclerosis).

Simple sequences and the expanding genome

Recent analysis of the contribution of replication slippage to genome evolution shows that it has played a significant role in all species from eubacteria to humans. The overall level of repetition in genomes is related to genome size and to the degree of repetition that can be measured within individual ribosomal RNA genes, suggesting that the entire genome accepts simple sequences in a concerted manner when its size increases. Although coding sequences accept simple sequences much less readily than non-coding sequences, they accept some repeats, particularly (CAG)n, preferentially. This may have consequences for the evolution of the genes involved in trinucleotide expansion diseases and the transcriptional networks of which they may form a part.

Small is beautiful: comparative genomics with the pufferfish (Fugu rubripes)

As the Human Genome Project advances, it is clear that the emphasis will switch from accumulation of data to their interpretation. Comparative genomics provides a powerful way in which to analyse sequence data. Indeed, there is already a long list of 'model' organisms, which allow comparative analyses in a variety of ways. The very small vertebrate genome of the pufferfish provides a simple and economical way of comparing sequence data from mammals and fish, representing a large evolutionary divergence and so permitting the identification of essential elements that are still present in both species. These elements include genes and the associated machinery that controls their expression; elements that, in many cases, have survived the test of time.

Expanded glutamines and neurodegeneration--a gain of insight

Glutamine repeat expansion has been established as the mutation underlying five inherited neurodegenerative diseases. The mechanism by which this apparently universal mutation, in ubiquitously expressed proteins, causes highly selective neurodegeneration is unknown. The proteins containing the glutamine expansions are otherwise unrelated and likely to have different functions. Two recently published papers provide evidence of a conformational change occurring in polyglutamine expansions, which may allow novel interactions and is consistent with a toxic gain-of-function hypothesis. HAP1, a protein that interacts with huntingtin (Huntington's disease protein), has an expression profile that intriguingly mirrors the selective neurodegeneration seen in Huntington's disease.

Conservation of synteny between the genome of the pufferfish (Fugu rubripes) and the region on human chromosome 14 (14q24.3) associated with familial Alzheimer disease (AD3 locus)

The genome of the pufferfish (Fugu rubripes) (400 Mb) is approximately 7.5 times smaller than the human genome, but it has a similar gene repertoire to that of man. If regions of the two genomes exhibited conservation of gene order (i.e., were syntenic), it should be possible to reduce dramatically the effort required for identification of candidate genes in human disease loci by sequencing syntenic regions of the compact Fugu genome. We have demonstrated that three genes (dihydrolipoamide succinyltransferase, S31iii125, and S20i15), which are linked to FOS in the familial Alzheimer disease focus (AD3) on human chromosome 14, have homologues in the Fugu genome adjacent to Fugu cFOS. The relative gene order of cFOS, S31iii125, and S20i15 was the same in both genomes, but in Fugu these three genes lay within a 12.4-kb region, compared to >600 kb in the human AD3 locus. These results demonstrate the conservation of synteny between the genomes of Fugu and man and highlight the utility of this approach for sequence-based identification of genes in human disease loci.

Comparative analysis and genomic structure of the tuberous sclerosis 2 (TSC2) gene in human and pufferfish

Germ-line mutations of the TSC2 tumour suppressor gene have been identified in humans with tuberous sclerosis and in the Eker rat. Tuberin, the human TSC2 gene product, has a small region of homology with rap1GAP and stimulates rap1 GTPase activity in vitro, suggesting that one of its cellular roles is to function as a GTPase activating protein (GAP). We have undertaken a comparative analysis of the TSC2 gene in human and the pufferfish, Fugu rubripes. In addition to the GAP domain, three other regions of the proteins are highly conserved (peptide sequence similarity > 80%). These regions are likely to represent further functional domains. To facilitate analysis of mutations within these domains we have determined the genomic structure of the human TSC2 gene. It comprises 41 exons, including exon 31 which was absent from the originally described spliceoform of the human TSC2 transcript and was identified following exon prediction from Fugu genomic sequence. These findings support the proposal of the Fugu genome as a tool for human gene analysis.

Huntington's disease: CAG genetics expands neurobiology

Huntington's disease, with its progressive uncontrolled movements and characteristic selective neuropathology, has represented a baffling enigma to geneticists and neurobiologists alike. Discovery of the HD gene and its defect has demystified the genetic aspects of the disorder, but has not yet explained its pathogenesis. Attempts to explore this issue suggest that the defect acts as a gain of function, conferring a new deleterious property on the huntingtin protein, and that the gene's normal function may be irrelevant to the disease process.

Pressing ahead with human genome sequencing

While waiting for revolutionary techniques to emerge, conventional approaches have been used to generate more than 40 million bases of DNA sequence from large scale projects involving different organisms. About eight megabases are from the human genome. Does this progress signal the time to move ahead for a massive human genomic sequencing effort, or should we bide our time, waiting for more technical developments? The answer is to move ahead now, choosing carefully those strategies that can be easily adapted to future methodologies.

An update and lessons from whole-genome sequencing projects

A number of prokaryotic and eukaryotic genomes are currently being sequenced. Already, the nucleotide sequences of four yeast chromosomes and of 2.2 Mb from Caenorhabditis elegans have been reported. Human genomic sequences have also been used in comparative studies with both mouse and Fugu rubripes.