Nucleotide sequence of the rat gamma-crystallin gene region and comparison with an orthologous human region

Molecular diversity and genomic organisation of the alpha, beta and gamma eye lens crystallins from the Antarctic toothfish Dissostichus mawsoni

The eye lens of the Antarctic toothfish living in the -2 degrees C Southern Ocean is cold-stable. To investigate the molecular basis of this cold stability, we isolated, cloned and sequenced 22 full length crystallin cDNAs. We found two alpha crystallins (alphaA, alphaB), six beta crystallins (betaA1, betaA2, betaA4, betaB1, betaB2, betaB3) and 14 gamma crystallins (gammaN, gammaS1, gammaS2, gammaM1, gammaM3, gammaM4, gammaM5, gammaM7, gammaM8a, gammaM8b, gammaM8c, gammaM8d, gammaM8e, and gammaM9). Alignments of alpha, beta and gamma with other known crystallin sequences indicate that toothfish alpha and beta crystallins are relatively conserved orthologues of their vertebrate counterparts, but the toothfish and other fish gammaM crystallins form a distinct group that are not orthologous to mammalian gamma crystallins. A preliminary Fingerprinted Contig analysis of clones containing crystallin genes screened from a toothfish BAC library indicated alpha crystallin genes occurred in a single genomic region of ~266 kbp, beta crystallin genes in ~273 kbp, while the gamma crystallin gene family occurred in two separate regions of ~180 and ~296 kbp. In phylogenetic analysis, the gammaM isoforms of the ectothermic toothfish displayed a diversity not seen with endothermic mammalian gamma crystallins. Similar to other fishes, several toothfish gamma crystallins are methionine-rich (gammaM isoforms) which may have predisposed the toothfish lens to biochemically attenuate gamma crystallin hydrophobicity allowing for cold adaptation. In addition to high methionine content, conservation of alphabeta crystallins both in sequence and abundance suggests greater functional constraints relative to gamma crystallins. Conversely, reduced constraints upon gamma crystallins could have allowed for greater evolutionary plasticity resulting in increased polydispersity of gamma crystallins contributing to the cold-stability of the Antarctic toothfish lens.

Isolation of a single-stranded DNA-binding protein from the methylotrophic yeast, Pichia pastoris and its identification as zeta crystallin

A single-stranded DNA (ssDNA)-binding protein (SSB) that binds to specific upstream sequences of alcohol oxidase (AOX1) promoter of the methylotrophic yeast Pichia pastoris has been isolated and identified as zeta crystallin (ZTA1). The cDNA encoding P.pastoris ZTA1 (PpZTA1) was cloned into an Escherichia coli expression vector, the recombinant PpZTA1 was expressed and purified from E.coli cell lysates. The DNA-binding properties of recombinant PpZTA1 are identical to those of the SSB present in P.pastoris cell lysates. PpZTA1 binds to ssDNA sequences >24 nt and its DNA-binding activity is abolished by NADPH. This is the first report on the characterization of DNA-binding properties of a yeast ZTA1.

Crystallins, genes and cataract

Far from being a physical entity, assembled of inanimate structural proteins, the ocular lens epitomizes the biological ingenuity that sustains an essential and near-perfect physical system of immaculate optics. Crystallins (alpha, beta, and gamma) provide transparency by dint of their high concentration, but it is debatable whether proteins that provide transparency are any different, biologically or structurally, from those that are present in non-transparent structures or tissues. It is becoming increasingly clear that crystallins may have a plethora of metabolic and regulatory functions, both within the lens as well as outside of it. Alpha-crystallins are members of a small heat shock family of proteins and beta/gamma-crystallins belong to the family of epidermis-specific differentiation proteins. Crystallin gene expression has been studied from the perspective of the lens specificity of their promoters. Mutations in alpha-, beta-, and gamma-crystallins are linked with the phenotype of the loss of transparency. Understanding catalytic, non-structural properties of crystallins may be critical for understanding the malfunction in molecular cascades that lead to cataractogenesis and its eventual therapeutic amelioration.

Gene co-option in physiological and morphological evolution

Co-option occurs when natural selection finds new uses for existing traits, including genes, organs, and other body structures. Genes can be co-opted to generate developmental and physiological novelties by changing their patterns of regulation, by changing the functions of the proteins they encode, or both. This often involves gene duplication followed by specialization of the resulting paralogous genes into particular functions. A major role for gene co-option in the evolution of development has long been assumed, and many recent comparative developmental and genomic studies have lent support to this idea. Although there is relatively less known about the molecular basis of co-option events involving developmental pathways, much can be drawn from well-studied examples of the co-option of structural proteins. Here, we summarize several case studies of both structural gene and developmental genetic circuit co-option and discuss how co-option may underlie major episodes of adaptive change in multicellular organisms. We also examine the phenomenon of intraspecific variability in gene expression patterns, which we propose to be one form of material for the co-option process. We integrate this information with recent models of gene family evolution to provide a framework for understanding the origin of co-optive evolution and the mechanisms by which natural selection promotes evolutionary novelty by inventing new uses for the genetic toolkit.

Complex regulatory element within the gammaE- and gammaF-crystallin enhancers mediates Pax6 regulation and is required for induction by retinoic acid

The paired domain, DNA-binding domain of Pax6 and other Pax transcription factors, is composed of two subdomains (PAI and RED), each recognizing distinct half-sites of the bipartite binding site in adjacent major grooves of the DNA helix. The alternatively spliced Pax6(5a) isoform containing 14 extra amino acids within the PAI domain recognizes the 5aCON sequence consisting of four interdigitated 5' half-sites of the bipartite consensus sequence. A genome database search for similar tetrameric Pax6(A) recognition sequences led to the identification of a Pax6-binding site in the lens-specific enhancer of the mouse E- and F-crystallin genes. This binding site combines the properties of bipartite and tetrameric recognition sequences and, by mutational analysis, is shown to mediate Pax6-dependent regulation of the E- and F-crystallin promoter constructs both in primary chicken lens cells and in chicken embryo fibroblasts. The Pax6-binding site is adjacent to a previously identified retinoic acid response element and is itself required for retinoic acid induction of the F- and E-crystallin genes, suggesting that Pax proteins and retinoic acid receptors cooperate in transcriptional regulation. In summary, our protein-DNA binding and transactivation studies suggest that -crystallin genes are under the control of a multifunctional enhancer element that mediates Pax6 regulation as well as retinoic acid-mediated induction.

Antagonistic action of Six3 and Prox1 at the gamma-crystallin promoter

Gamma-crystallin genes are specifically expressed in the eye lens. Their promoters constitute excellent models to analyse tissue-specific gene expression. We investigated murine CRYGE/f promoters of different length in lens epithelial cell lines. The most active fragment extends from position -219 to +37. Computer analysis predicts homeodomain and paired-domain binding sites for all rodent CRYGD/e/f core promoters. As examples, we analysed the effects of Prox1 and Six3, which are considered important transcription factors involved in lens development. Because of endogenous Prox1 expression in N/N1003A cells, a weak stimulation of CRYGE/f promoter activity was found for PROX1. In contrast, PROX1 stimulated the CRYGF promoter 10-fold in CD5A cells without endogenous PROX1. In both cell lines Six3 repressed the CRYGF promoter to 10% of its basal activity. Our cell transfection experiments indicated that CRYG expression increases as Six3 expression decreases. Prox1 and Six3 act antagonistically on regulation of the CRYGD/e/f promoters. Functional assays using randomly mutated gammaF-crystallin promoter fragments define a Six3-responsive element between -101 and -123 and a Prox1-responsive element between -151 and -174. Since Prox1 and Six3 are present at the beginning of lens development, expression of CRYGD/e/f is predicted to remain low at this time. It increases as Six3 expression decreases during ongoing lens development.

Gene expression of receptors and enzymes involved in GABAergic and glutamatergic neurotransmission in the CNS of rats behaviourally dependent on ethanol

The steady state levels of the messenger RNA (mRNA) of eight GABA(A) receptor subunits, five glutamate receptor subunits and seven enzymes involved in the synthesis of glutamate and GABA were measured in eight regions of rat brain in a recently developed animal model of 'behavioural dependence' on ethanol. 'Behavioural dependence' including loss of control was induced by offering the rats the choice between ethanol and water over a 9-month period (Group A). This group was compared with a group given the choice between ethanol and water for only 2 months (not yet 'behaviourally dependent', Group B), a group forced to consume ethanol as sole fluid over a 9-month period (also not 'behaviourally dependent', Group C) and ethanol-naive control rats (Group D). All groups were sacrificed 1 month after the ethanol was withdrawn. The mRNA concentrations of all eight GABA receptor subunits, four out of the five subunits of different glutamate receptors and those of seven enzymes involved in GABA and glutamate production were reduced almost exclusively in the parieto-occipital cortex in Groups A and B, but not Group C. These data suggest that the synthesis of glutamate and GABA and the activities of their respective neurons are selectively impaired in the parieto-occipital cortex in the groups having consumed ethanol in a free-choice design, in which its rewarding properties can better take effect than after forced administration. As the parieto-occipital cortex is believed to contain emotional memory structures, it may be hypothesized that the glutamatergic and GABAergic neuronal systems in this area are involved in the development of memory for reward from ethanol. However, they are not specifically associated with 'behavioural dependence'.

Chromosomal location effects on gene sequence evolution in mammals

BACKGROUND

Nucleotide substitution rates and G + C content vary considerably among mammalian genes. It has been proposed that the mammalian genome comprises a mosaic of regions - termed isochores - with differing G + C content. The regional variation in gene G + C content might therefore be a reflection of the isochore structure of chromosomes, but the factors influencing the variation of nucleotide substitution rate are still open to question.

RESULTS

To examine whether nucleotide substitution rates and gene G + C content are influenced by the chromosomal location of genes, we compared human and murid (mouse or rat) orthologues known to belong to one of the chromosomal (autosomal) segments conserved between these species. Multiple members of gene families were excluded from the dataset. Sets of neighbouring genes were defined as those lying within 1 centiMorgan (cM) of each other on the mouse genetic map. For both synonymous substitution rates and G + C content at silent sites, neighbouring genes were found to be significantly more similar to each other than sets of genes randomly drawn from the dataset. Moreover, we demonstrated that the regional similarities in G + C content (isochores) and synonymous substitution rate were independent of each other.

CONCLUSIONS

Our results provide the first substantial statistical evidence for the existence of a regional variation in the synonymous substitution rate within the mammalian genome, indicating that different chromosomal regions evolve at different rates. This regional phenomenon which shapes gene evolution could reflect the existence of 'evolutionary rate units' along the chromosome.

lir-2, lir-1 and lin-26 encode a new class of zinc-finger proteins and are organized in two overlapping operons both in Caenorhabditis elegans and in Caenorhabditis briggsae

lin-26, which encodes a unique Zn-finger protein, is required for differentiation of nonneuronal ectodermal cells in Caenorhabditis elegans. Here, we show that the two genes located immediately upstream of lin-26 encode LIN-26-like Zn-finger proteins; hence their names are lir-1 and lir-2 (lin-26 related). lir-2, lir-1, and lin-26 generate several isoforms by alternative splicing and/or trans-splicing at different positions. On the basis of their trans-splicing pattern, their intergenic distances, and their expression, we suggest that lir-2, lir-1, and lin-26 form two overlapping transcriptional operons. The first operon, which is expressed in virtually all cells, includes lir-2 and long lir-1 isoforms. The second operon, which is expressed in the nonneuronal ectoderm, includes short lir-1 isoforms, starting at exon 2 and lin-26. This unusual genomic organization has been conserved in C. briggsae, as shown by cloning the C. briggsae lir-2, lir-1, and lin-26 homologs. Particularly striking is the sequence conservation throughout the first lir-1 intron, which is very long in both species. Structural conservation is functionally meaningful as C. briggsae lin-26 is also expressed in the nonneuronal ectoderm and can complement a C. elegans lin-26 null mutation.

Cataract mutations and lens development

The lens plays an essential role for proper eye development. Mouse mutants affecting lens development are excellent models for corresponding human disorders. Moreover, using mutations in particular genes the process of eye and lens development can be dissected into distinct steps. Therefore, three mouse mutants will be described in detail and discussed affecting three essential stages: formation of the lens vesicle, initiation of secondary lens fiber cell formation, and terminal differentiation of the secondary fiber cells. The mutant aphakia (ak) has been characterized by bilaterally apakic eyes [Varnum and Stevens (1968) J. Hered. 59, 147-150], and the corresponding gene was mapped to chromosome 19 [Varnum and Stevens (1975) Mouse News Letters 53, 35]. Recent investigations in our laboratory refined the linkage 0.6 +/- 0.3 N cm proximal to the microsatellite marker D19Mit10. The linked gene Pax2, responsible for proper development of the posterior part of the eye and the optic nerve, was excluded as candidate gene by sequence analysis. Histological analysis of the homozygous ak mutants revealed a persisting lens stalk and subsequently the formation of lens rudiments. The lens defects led to irregular iris development and retinal folding. Congenital aphakia is known as a rare human anomaly. Besides a corneal dystrophy (CDTB), no corresponding disease is localized at the homologous region of human chromosome 10q23. The Cat3 mutations are characterized by vacuolated lenses caused by alterations in the beginning of secondary lens fiber cell differentiation at embryonic day 12.5. Secondary malformations develop at the cornea and the iris, but the retina remains unaffected. Two mutant alleles of the Cat3 locus have been mapped to mouse chromosome 10 very close to the microsatellite markers D10Mit41 and D10Mit95 (less than 0.3 cM). Since Cat3 is mapped to a position, which is homologous to human chromosome 12q21-24, the disorder cornea plana congenita can be considered as a candidate disease. The series of Cat2 mutations have been mapped close to the locus encoding the gamma-crystallin gene cluster Cryg [Löster et al. (1994) Genomics 23, 240-242]. The Cat2nop mutation is characterized by a deletion of 11 bp and an insertion of 4 bp in the 3rd exon of Crygh leading to a truncated gamma B-crystallin. The defect in the Crygh gene is causative for the stop of lens fiber cell differentiation from embryonic day 15.5 onward. Besides the lens, no further ocular tissue is affected. The Cat2 mouse mutants are interesting models for human cataracts caused by mutations in the gamma-crystallin genes at human chromosome 2q32-35. The ak, Cat3 and Cat2 mutants are discussed in the context of other mutants affecting early eye and lens development. Additionally, human congenital cataracts are discussed, which have been characterized similar to the mouse models. The overview of the three types of mutants demonstrates that genes, which affect the early eye development, e.g. at the lens vesicle stage, have consequences for the development of the whole eye. In contrast, if the mutation influences later steps of lens differentiation, the consequences are restricted to the lens only. These data indicate a decreasing effect of the lens for the regulation of eye development during embryogenesis.

Three murine cataract mutants (Cat2) are defective in different gamma-crystallin genes

A number of murine cataract mutations have been localized to chromosome 1 close to the gamma-crystallin gene cluster (Cryg) (Everett et al., 1994, Genomics 20: 429-434; Löster et al., 1994, Genomics 23: 240-242). Based on the size of the mapping or allelism tests they have not been shown to be genetically distinct and have been assigned to locus symbol Cat2. Here we assign three mutations to the respective gamma-crystallin gene. Using a systematic candidate gene approach to analyze the entire Cryg cluster, an A-->G transition was found in exon 2 of Cryga for the ENU-436 mutation and is designated Cryga1Neu. The mutant allele Crygbnop (formerly Cat2(nop)) is caused by a replacement of 11 bp by 4 bp in the third exon of Crygb, while a C-->G transversion in exon 3 of Cryge has been found for the Cryget (formerly Cat2(t)) mutation. For the mutation Cryga1Neu, an Asp-->Gly exchange is deduced, whereas the mutations Crygbnop and Cryget lead to the formation of in-frame stop codons and give rise to truncated proteins of 144 and 143 amino acids, respectively. The effects of the mutations upon gamma-crystallin structure are likely to be quite different. The Cryga1Neu mutation is expected to affect the link between Greek-key motifs 2 and 3, whereas both Crygbnop and Cryget mutations are supposed to truncate the fourth Greek-key motif. All three mutations are predicted to alter protein folding of the gamma-crystallins and result in lens cataract, but the phenotype for each is quite distinctive.

Junk DNA and sectorial gene repression

Transcriptional repression in eukaryotes often involves tens or hundreds of kilobase pairs, two to three orders of magnitude more than the bacterial operator/repressor model does. Classical repression, represented by this model, was maintained over the whole span of evolution under different guises, and consists of repressor factors interacting primarily with promoters and, in later evolution, also with enhancers. The use of much larger amounts of DNA in the other mode of repression, here called the sectorial mode ('superrepression'), results in the conceptual transfer of so-called junk DNA to the domain of functional DNA. This contribution to the solution of the c-value paradox involves perhaps 15% of genomic 'junk,' and encompasses the bulk of the introns, thought to fill a stabilizing role in sectorially repressed chromatin structures. In the case of developmental genes, such structures appear to be heterochromatoid in character. However, solid clues regarding general structural features of superrepressed terminal differentiation genes remain elusive. The competition among superrepressible DNA sectors for sectorially binding factors offers, in principle, a molecular mechanism for developmental switches. Position effect variegation may be considered an abnormal manifestation of normal processes that underly development and involve heterochromatoid sectorial repression, which is apparently required for local elimination or modulation of morphological features (morpholysis). Sectorial repression of genes participating either in development or in terminal differentiation is considered instrumental in establishing stable cell types, and provides a basis for the distinction between determination and cell type specification. The gamut of possible stable cell types may have been broadened by the appearance in evolution of heavy isochores. Additional types of relatively frequent GC-rich cis-acting DNA motifs may offer reiterated binding sites to factors endowed with a selective (though not individually strong) affinity for these motifs. The majority of sequence motifs thought to be used in superrepression need not be individually maintained by natural selection. It is re-emphasized that the dispensability of sequences is not an indicator of their nonfunctionality and that in many cases, along noncoding sequences, nucleotides tend to fill functions collectively, rather than individually.

Genetic aspects of embryonic eye development in vertebrates

The vertebrate eye comprises tissues from different embryonic origins, e.g., iris and ciliary body are derived from the wall of the diencephalon via optic vesicle and optic cup. Lens and cornea, on the other hand, come from the overlying surface ectoderm. The timely action of transcription factors and inductive signals ensure the correct development of the different eye components. Establishing the genetic basis of eye defects has been an important tool for the detailed analysis of this complex process. One of the main control genes for eye development was discovered by the analysis of the allelic series of the Small eye mouse mutants and characterized as Pax6. It is involved in the interaction between the optic cup and the overlaying ectoderm. The central role for Pax6 in eye development is conserved throughout the animal kingdom as the murine Pax6 gene induces ectopic eyes in transgenic Drosophila despite the obvious diverse organization of the eye in the fruit fly compared to vertebrates. In human, mutations in the PAX6 gene are responsible for aniridia and Peter's anomaly. In addition to Pax6, other mutations affecting the interaction of the optic cup and the lens placode have been documented in the mouse. For the differentiation of the retina from the optic cup several genes are responsible: Mi leads to microphthalmia, if mutated, and encodes for a transcription factor, which is expressed in the melanocytes of the pigmented layer of the retina. In addition, further genes are implicated in the correct development of the retina, e.g., Chx10, Dlx1, GH6, Msx1 and -2, Otx1 and -2, or Wnt7b. Mutations within the retinoblastoma gene (RB1) are responsible for retinal tumors. Knock-out mutants of RB1 exhibit a block of lens differentiation prior to the retinal defect. Besides the influence of Rb1, the lens differentiates under the influence of growth factors (e.g., FGF, IGF, PDGF, TGF), and specific genes become activated encoding cytoskeletal proteins (e.g., filensin, phakinin, vimentin), structural proteins (e.g., crystallins) or membrane proteins (e.g., Mip). The optic nerve originates from the neural retina; ganglion cells grow to the optic stalk, forming the optic nerve. Its retrograde walk to the brain through the rudiment of the optic stalk depends on the correct Pax2 expression.

Molecular cloning of a chick cochlea cDNA encoding a subunit of DNA replication factor C/activator 1

A chick cochlea cDNA library was constructed to clone molecules involved in peripheral auditory transduction and in the maintenance and regeneration of the sensory neuroepithelium following damage. Characterization of the library showed it to be of high complexity, to contain a high proportion of full-length cDNA inserts, and to contain a representative proportion of clones derived from hair cell transcripts. A cDNA clone encoding the chick homolog of the 40-kD subunit of the human replication factor C (also called activator 1) was isolated and the complete cDNA sequence determined. The predicted amino acid sequence is about 90% identical to that of the human homolog. Expression of the message for this replication factor was detected in brain and liver as well as in the cochlea. Expression levels in the brain are relatively high and are similar in developing and adult chicken nervous tissue. This suggests that replication factor C message expression, unlike that for the functionally associated factor proliferating cell nuclear antigen (PCNA), may be constitutive rather than cell cycle dependent. Although likely to be involved in DNA replication within the receptor neuroepithelium, expression of this replication factor message is not likely to constitute a marker for proliferation.

Striking sequence similarity over almost 100 kilobases of human and mouse T-cell receptor DNA

We report here the comparative DNA sequence analysis of nearly 100 kilobases of contiguous DNA in the C delta to C alpha region of the alpha/delta T cell receptor loci (TCRAC/TCRDC) of mouse and man. This analysis--the largest genomic sequence comparison so far--provides new insights into the functions of the T cell receptor genes as well as the surrounding chromosome structure through the identification of actively conserved DNA sequences. In this comparison we have identified a very high level of organizational and noncoding sequence similarity (approximately 71%) in contrast to previous findings in the beta-globin gene cluster. This observation begins to question the notion that much of the chromosomal non-coding sequence is junk.

Genomic sequences of murine gamma B- and gamma C-crystallin-encoding genes: promoter analysis and complete evolutionary pattern of mouse, rat and human gamma-crystallins

The murine genes, gamma B-cry and gamma C-cry, encoding the gamma B- and gamma C-crystallins, were isolated from a genomic DNA library. The complete nucleotide (nt) sequences of both genes were determined from 661 and 711 bp, respectively, upstream from the first exon to the corresponding polyadenylation sites, comprising more than 2650 and 2890 bp, respectively. The new sequences were compared to the partial cDNA sequences available for the murine gamma B-cry and gamma C-cry, as well as to the corresponding genomic sequences from rat and man, at both the nt and predicted amino acid (aa) sequence levels. In the gamma B-cry promoter region, a canonical CCAAT-box, a TATA-box, putative NF-I and C/EBP sites were detected. An R-repeat is inserted 366 bp upstream from the transcription start point. In contrast, the gamma C-cry promoter does not contain a CCAAT-box, but some other putative binding sites for transcription factors (AP-2, UBP-1, LBP-1) were located by computer analysis. The promoter regions of all six gamma-cry from mouse, rat and human, except human psi gamma F-cry, were analyzed for common sequence elements. A complex sequence element of about 70-80 bp was found in the proximal promoter, which contains a gamma-cry-specific and almost invariant sequence (crygpel) of 14 nt, and ends with the also invariant TATA-box. Within the complex sequence element, a minimum of three further features specific for the gamma A-, gamma B- and gamma D/E/F-cry genes can be defined, at least two of which were recently shown to be functional. In addition to these four sequence elements, a subtype-specific structure of inverted repeats with different-sized spacers can be deduced from the multiple sequence alignment. A phylogenetic analysis based on the promoter region, as well as the complete exon 3 of all gamma-cry from mouse, rat and man, suggests separation of only five gamma-cry subtypes (gamma A-, gamma B-, gamma C-, gamma D- and gamma E/F-cry) prior to species separation.

Structure and lens expression of the gene encoding chicken beta A3/A1-crystallin

The beta A1- and beta A3-crystallins are major polypeptides in the lenses of vertebrates. We present evidence that a single beta A3/A1 gene encodes these two proteins in the chicken. The beta A3/A1 gene has been sequenced and its functional promoter identified in transfection experiments. The chicken beta A3/A1 gene has the same structure as the human orthologue: six exons with standard splice sites and two alternative start codons from which the protein products are apparently translated. Northern analysis revealed an abundant 0.9-kb transcript in the lenses of 1-2-day-old chickens and no detectable transcripts in the rest of the eye, brain, heart, kidney, liver or skeletal muscle. The 5'-flanking sequence of the chicken beta A3/A1 gene is very similar to that of the human and mouse genes, suggesting conservation of important putative regulatory sequences in addition to the TATA box. A thymidine-rich element (bp -218 to -163) and a potential AP-1-binding site (bp -264 to -258) are present within the chicken 5'-flanking region. A DNA fragment from -382 to +22 of the chicken beta A3/A1 gene is sufficient to promote expression of the bacterial cat gene in transfected chicken primary lens epithelial cells, but not in transfected dermal fibroblasts.(ABSTRACT TRUNCATED AT 250 WORDS)

Medium reiteration frequency repetitive sequences in the human genome

Fourteen novel medium reiteration frequency (MER) families were found, in the human genome, by using two different methods. Repetition frequencies per haploid human genome were estimated for each of these families as well as for six previously described MER DNA families. By these measurements, the families were found to contain variable numbers of elements, ranging from 200 to 10,000 copies per haploid human genome.

The Chinese hamster HPRT gene: restriction map, sequence analysis, and multiplex PCR deletion screen

The fine structure of the Chinese hamster hypoxanthine guanine phosphoribosyltransferase (HPRT) gene has been determined; the gene has nine exons and is dispersed over 36 kb DNA. Exons 2-9 are contained within overlapping lambda bacteriophage clones and exon 1 was obtained by an inverse polymerase chain reaction (PCR). All the exons have been sequenced, together with their immediate flanking regions, and these sequences compared to those of the mouse and human HPRT genes. Sequences immediately flanking all exons but the first show considerable homology between the different species but the region around exon 1 is less conserved, apart from the preserved location of putative functional elements. Oligonucleotide primers derived from sequences flanking the HPRT gene exons were used to amplify simultaneously seven exon-containing fragments in a multiplex PCR. This simple procedure was used to identify total and partial gene deletions among Chinese hamster HPRT-deficient mutants. The multiplex PCR is quicker to perform than Southern analysis, traditionally used to study such mutants, and also provides specific exon-containing fragments for further analysis. The Chinese hamster HPRT gene is often used as a target for mutation studies in vitro because of the ease of selection of forward and reverse mutants; the information presented here will enhance the means of investigating molecular defects within this gene.

DNA methylation as a regulatory mechanism in rat gamma-crystallin gene expression

We have investigated the methylation state of the rat gamma-crystallin genes in DNA from lens cells at different developmental stages as well as from kidney and heart cells. A clear correlation between the extent of demethylation of the promoter and 5' gene regions and the expression of these genes was observed. No change in the methylation state of the far upstream or 3' regions of the genes was seen. The demethylation of the promoter region was shown to occur during the differentiation from the lens epithelial to the lens fiber cell. The effect of cytosine methylation on gamma-crystallin promoter activity was tested by measuring gamma-crystallin promoter/chloramphenicol acetyltransferase fusion gene expression after in vitro primed repair synthesis of the promoter region in the presence of either dCTP or 5mdCTP. The hemimethylated promoter was no longer capable of promoting high CAT activity after introduction into lens-like cells. Taken together, our data suggest that DNA demethylation may be the determining step in the developmental stage-specific expression of the rat gamma-crystallin genes.

Human gamma-crystallin genes. A gene family on its way to extinction

During hominoid evolution the gamma-crystallins of the lens have decreased in quantity as well as complexity, a change correlated with an increased water content of the lens. To trace the molecular basis for the decrease in gamma-crystallin gene expression, we have characterized the structure and expression of the human gamma-crystallin gene family. We show that the human gamma-crystallin gene family consists of six complete genes (gamma A, gamma B, gamma C, gamma D, psi gamma E and psi gamma F) and one second exon fragment, the gamma G gene. Model experiments showed that, although the gamma G sequence is bordered by consensus splice sites, it is most likely transcriptionally inactive in the lens. In the human embryonic lens the gamma C and gamma D genes accounted for 81% of the gamma-crystallin transcripts, the gamma A gene contributed 14% and the gamma B gene only 5%. The composition of the gamma-crystallin mRNA pool changed only after birth, with the gamma D transcript as the only detectable transcript at ten years of age. The relative activities of the gamma A, gamma C and gamma D promoters in a transient expression system were in agreement with the ratio of their in vivo RNA levels, suggesting that the difference in accumulation of these transcripts is due to differences in the rate of transcription. The gamma B promoter was much more active than expected and had lost its tissue-specificity. Model experiments showed that the low yield of the gamma B transcript is due to post-transcriptional processes, most likely RNa instability mediated by third exon sequences. Together with previous data, our results show that the decrease in expression of the gamma-crystallin genes in the human lens is the consequence of gene loss (gamma G), inactivation of coding sequences (psi gamma E and psi gamma F), decrease in rate of transcription (gamma A), increase in rate of RNA turn-over (gamma B) and a delay in the onset of transcription during development.

Different evolution rates within the lens-specific beta-crystallin gene family

We have determined the sequence of a rat beta A3/A1-crystallin complementary DNA (cDNA) clone and the (partial) sequence of the human beta B3-crystallin gene. Calculation of the ratio of silent to nonsynonymous substitution between orthologous beta A3/A1-, beta B3-, and other beta- and gamma-crystallin sequences revealed that the region encoding the two globular domains of the beta A3/A1-crystallin sequence is the best conserved during evolution, much better than the corresponding region of the beta B1-, beta B3-, or the gamma-crystallin sequences, and even better (at least in the rodent/frog comparison) than the well-conserved alpha A-crystallin sequence. Remarkably, the rate of change of the beta A3/A1-crystallin coding sequence does not differ in the rodent and primate lineages, in contrast with previous findings concerning the evolution rates of the alpha A- or gamma-crystallin sequences in these two lineages. Comparison of the regions that encode the four motifs of the beta-crystallin between orthologous mammalian sequences showed that the extent of nonsynonymous substitution in each of these four homologous motif regions is the same. However, when the orthologous beta-crystallin genes of more distantly related species (mammals vs chicken or frog) are compared, the extent of non-synonymous substitution is higher in the regions encoding the external motifs I and III than in the regions encoding the internal motifs II and IV. This phenomenon is also observed when paralogous members of the beta/gamma-crystallin supergene family are compared.