A high-resolution map of the brown (b, Tyrp1) deletion complex of mouse chromosome 4

An essential gene mutagenesis screen across the highly conserved piebald deletion region of mouse chromosome 14

The piebald deletion complex is a set of overlapping chromosomal deficiencies on distal mouse chromosome 14. We surveyed the functional genetic content of the piebald deletion region in an essential gene mutagenesis screen of 952 genomes to recover seven lethal mutants. The ENU-induced mutations were mapped to define genetic intervals using the piebald deletion panel. Lethal mutations included loci required for establishment of the left-right embryonic axis and a loss-of-function allele of Phr1 resulting in respiratory distress at birth. A functional map of the piebald region integrates experimental genetic data from the deletion panel, mutagenesis screen, and the targeted disruption of specific genes. A comparison of several genomic intervals targeted in regional mutagenesis screens suggests that the piebald region is characterized by a low gene density and high essential gene density with a distinct genomic content and organization that supports complex regulatory interactions and promotes evolutionary stability.

New insights into the active site structure and catalytic mechanism of tyrosinase and its related proteins

Tyrosinases are widely distributed in nature. They are copper-containing oxidases belonging to the type 3 copper protein family, together with catechol oxidases and haemocyanins. Tyrosinases are essential enzymes in melanin biosynthesis and therefore responsible for pigmentation of skin and hair in mammals, where two more enzymes, the tyrosinase-related proteins (Tyrps), participate in the pathway. The structure and catalytic mechanism of mammalian tyrosinases have been extensively studied but they are not completely understood because of the lack of information on the tertiary structure. The availability of crystallographic data of one plant catechol oxidase and one bacterial tyrosinase has improved the model of the three-dimensional structure of the active site of the enzyme. Furthermore, sequence comparison of tyrosinase and the Tyrps reveals that the three orthologue proteins share many key structural features, because of their common origin from an ancestral gene, although the specific residues responsible for their different catalytic capabilities have not been identified yet. This review summarizes our current knowledge of tyrosinase and Tyrps structure and function and describes the catalytic mechanism of tyrosinase and Dct/Tyrp2, which are better characterized.

A conserved transcriptional enhancer that specifies Tyrp1 expression to melanocytes

Pigment cells of mammals originate from two different lineages: melanocytes arise from the neural crest, whereas cells of the retinal pigment epithelium (RPE) originate from the optic cup of the developing forebrain. Previous studies have suggested that pigmentation genes are controlled by different regulatory networks in melanocytes and RPE. The promoter of the tyrosinase-related family gene Tyrp1 has been shown to drive detectable transgene expression only to the RPE, even though the gene is also expressed in melanocytes as evident from Tyrp1-mutant mice. This indicates that the regulatory elements responsible for Tyrp1 gene expression in the RPE are not sufficient for expression in melanocytes. We thus searched for a putative melanocyte-specific regulatory sequence and demonstrate that a bacterial artificial chromosome (BAC) containing the Tyrp1 gene and surrounding sequences is able to target transgenic expression to melanocytes and to rescue the Tyrp1b (brown) phenotype. This BAC contains several highly conserved non-coding sequences that might represent novel regulatory elements. We further focused on a sequence located at -15 kb, which we identified as a melanocyte-specific enhancer as shown by cell culture and transgenic mice experiments. In addition, we show that the transcription factor Sox10 can activate this conserved enhancer. The presence of a distal Tyrp1 regulatory element, which specifies melanocyte-specific expression, supports the idea that separate regulatory sequences can mediate differential gene expression in melanocytes and RPE.

Oncogenic function for the Dlg1 mammalian homolog of the Drosophila discs-large tumor suppressor

The fact that several different human virus oncoproteins, including adenovirus type 9 E4-ORF1, evolved to target the Dlg1 mammalian homolog of the membrane-associated Drosophila discs-large tumor suppressor has implicated this cellular factor in human cancer. Despite a general belief that such interactions function solely to inactivate this suspected human tumor suppressor protein, we demonstrate here that E4-ORF1 specifically requires endogenous Dlg1 to provoke oncogenic activation of phosphatidylinositol 3-kinase (PI3K) in cells. Based on our results, we propose a model wherein E4-ORF1 binding to Dlg1 triggers the resulting complex to translocate to the plasma membrane and, at this site, to promote Ras-mediated PI3K activation. These findings establish the first known function for Dlg1 in virus-mediated cellular transformation and also surprisingly expose a previously unrecognized oncogenic activity encoded by this suspected cellular tumor suppressor gene.

Genomic anatomy of the Tyrp1 (brown) deletion complex

Chromosome deletions in the mouse have proven invaluable in the dissection of gene function. The brown deletion complex comprises >28 independent genome rearrangements, which have been used to identify several functional loci on chromosome 4 required for normal embryonic and postnatal development. We have constructed a 172-bacterial artificial chromosome contig that spans this 22-megabase (Mb) interval and have produced a contiguous, finished, and manually annotated sequence from these clones. The deletion complex is strikingly gene-poor, containing only 52 protein-coding genes (of which only 39 are supported by human homologues) and has several further notable genomic features, including several segments of >1 Mb, apparently devoid of a coding sequence. We have used sequence polymorphisms to finely map the deletion breakpoints and identify strong candidate genes for the known phenotypes that map to this region, including three lethal loci (l4Rn1, l4Rn2, and l4Rn3) and the fitness mutant brown-associated fitness (baf). We have also characterized misexpression of the basonuclin homologue, Bnc2, associated with the inversion-mediated coat color mutant white-based brown (B(w)). This study provides a molecular insight into the basis of several characterized mouse mutants, which will allow further dissection of this region by targeted or chemical mutagenesis.

X-ray-induced deletion complexes in embryonic stem cells on mouse chromosome 15

Chromosomal deletions have long been used as genetic tools in dissecting the functions of complex genomes, and new methodologies are still being developed to achieve the maximum coverage. In the mouse, where the chromosomal deletion coverage is far less extensive than that in Drosophila, substantial coverage of the genome with deletions is strongly desirable. This article reports the generation of three deletion complexes in the distal part of mouse Chromosome (Chr) 15. Chromosomal deletions were efficiently induced by X rays in embryonic stem (ES) cells around the Otoconin 90 (Oc 90), SRY-box-containing gene 10 (Sox 10), and carnitine palmitoyltransferase 1b (Cpt 1 b) loci. Deletions encompassing the Oc 90 and Sox 10 loci were transmitted to the offspring of the chimeric mice that were generated from deletion-bearing ES cells. Whereas deletion complexes encompassing the Sox 10 and the Cpt 1 b loci overlap each other, no overlap of the Oc 90 complex with the Sox 10 complex was found, possibly indicating the existence of a haploinsufficient gene located between Oc 90 and Sox 10. Deletion frequency and size induced by X rays depend on the selective locus, possibly reflecting the existence of haplolethal genes in the vicinity of these loci that yield fewer and smaller deletions. Deletions induced in ES cells by X rays vary in size and location of breakpoints, which makes them desirable for mapping and for functional genomics studies.

Effects of Male Germ-Cell Stage on the Frequency, Nature, and Spectrum of Induced Specific-Locus Mutations in the Mouse

By means of the mouse specific-locus test (SLT) with visible markers, which is capable of detecting intragenic mutations as well as larger lesions, about 20 mutagens have been studied comparatively across arrays of male germ-cell stages. In addition, a very large historical control, accumulated over decades, provides data on spontaneous mutations in males. Each mutagen has a characteristic germ-cell-stage sensitivity pattern. Although most chemicals yield their maximum numbers of mutations following exposure of spermatozoa and late spermatids, mutagens have now been identified that peak in each of the major stages of spermatogenesis and spermiogenesis, including those in which effects on recombination can also be induced. Stem-cell spermatogonia have yielded positive results with only five of 15 mutagenic chemicals. In postspermatogonial stages, all chemicals, as well as radiations, induce primarily large lesions (LL). By contrast, in spermatogonia (either stem-cell or differentiating) all chemicals except one (bleomycin) produce very few such lesions. The spectrum of relative mutation frequencies at the seven loci of the SLT is characteristic for treated germ-cell stage and mutagen. Treatments that induce primarily LL are characterized by a great preponderance of s (Ednrb)-locus mutations (possibly due to a paucity of haplo-insufficient genes in the surrounding region); and those that induce very few, if any, LL by a great preponderance of p-locus mutations. Spontaneous locus-spectra differ from both types of treatment-induced spectra; moreover, there are two distinct types of spontaneous spectra, depending on whether mutations occurred in mitotic cells or during the perigametic interval.

TYRP1 is associated with dun coat colour in Dexter cattle or how now brown cow?

Tyrosinase related protein 1 (TYRP1), which is involved in the coat colour pathway, was mapped to BTA8 between microsatellites BL1080 and BM4006, using a microsatellite in intron 5 of TYRP1. The complete coding sequence of bovine TYRP1 was determined from cDNA derived from skin biopsies of cattle with various colours. Sequence data from exons 2-8 from cattle with diluted phenotypes was compared with that from non-diluted phenotypes. In addition, full-sib families of beef cattle generated by embryo transfer and half-sib families from traditional matings in which coat colour was segregating were used to correlate TYRP1 sequence variants with dilute coat colours. Two non-conservative amino acid changes were detected in Simmental, Charolais and Galloway cattle but these polymorphisms were not associated with diluted shades of black or red, nor with the dun coat colour of Galloway cattle or the taupe brown colour of Braunvieh and Brown Swiss cattle. However, in Dexter cattle all 25 cattle with a dun brown coat colour were homozygous for a H424Y change. One Dexter that was also homozygous Y434 was red because of an "E+/E+" genotype at MC1R which lead to the production of only phaeomelanin. None of the 70 remaining black or red Dexter cattle were homozygous for Y434. This tyrosine mutation was not found in any of the 121 cattle of other breeds that were examined.

Molecular and functional mapping of the piebald deletion complex on mouse chromosome 14

The piebald deletion complex is a set of overlapping chromosomal deficiencies surrounding the endothelin receptor B locus collected during the Oak Ridge specific-locus-test mutagenesis screen. These chromosomal deletions represent an important resource for genetic studies to dissect the functional content of a genomic region, and several developmental defects have been associated with mice homozygous for distinct piebald deletion alleles. We have used molecular markers to order the breakpoints for 20 deletion alleles that span a 15.7-18-cM region of distal mouse chromosome 14. Large deletions covering as much as 11 cM have been identified that will be useful for regionally directed mutagenesis screens to reveal recessive mutations that disrupt development. Deletions identified as having breakpoints positioned within previously described critical regions have been used in complementation studies to further define the functional intervals associated with the developmental defects. This has focused our efforts to isolate genes required for newborn respiration and survival, skeletal patterning and morphogenesis, and central nervous system development.

Genes, receptors, signals and responses to lipopolysaccharide endotoxin

C3H/HeJ inbred mice have been very useful for identifying genetic elements responsible for endotoxin mediated responses. Depending on the type of assays employed, Tlr-2, Tlr-4 and Lps/Ran have been shown to be important in lipopolysaccharide (LPS)-mediated responses. The concept of a single LPS gene being responsible for the genetic defect found in C3H/HeJ mice should therefore be re-examined more closely. Given the most recent discoveries, it is probable that more than one signal transduction pathway is involved. One is a CD14-dependent pathway, the other a CD14-independent pathway. Identification of the genetic elements involved in these pathways will be beneficial in designing therapeutic strategies for treating patients with endotoxic or septic shock.

The mouse Cer1 (Cerberus related or homologue) gene is not required for anterior pattern formation

Cer1 is the mouse homologue of the Xenopus Cerberus gene whose product is able to induce development of head structures during embryonic development. The Cer1 protein is a member of the cysteine knot superfamily and is expressed in anterior regions of the mouse gastrula. A segmental pattern of expression with nascent and newly formed somites is also seen. This suggests an additional role in development of the axial skeleton, musculature, or peripheral nervous system. Xenopus animal cap assays and mouse germ-layer explant recombination experiments indicate that the mouse protein can act as a patterning molecule for anterior development in Xenopus, including induction of Otx2 expression, and suggest it may have a similar role in mouse development. However, we present here genetic data that demonstrate that Cer1 is not necessary for anterior patterning, Otx2 expression, somite formation, or even normal mouse morphogenesis.

Mechanisms of mutation induction in germ cells of the mouse as assessed by the specific locus test

Mouse germ cell specific locus mutagenesis data and a molecular characterization of mutant alleles have been reviewed to arrive at an understanding of the mechanism of mutation induction in mammals. (a) The spermatogenic stage specificity for the sensitivity to mutation induction by 20 chemical mutagens is considered. (b) The effects of a saturable repair process and its recovery over time are examined for the mutagenic efficiency of ethylnitrosourea. (c) The mutagenic events following methylnitrosourea and chlorambucil are shown to be mainly deletions. In contrast the mutations recovered after ethylnitrosourea treatment are almost exclusively base pair substitutions. (d) It is emphasized that to date very few specific locus experiments have been designed to test for mutagenic events outside the interval stem cell spermatogonia-mature spermatozoa. A specific locus mutation has recently been shown to be due to loss of heterozygosity via mitotic recombination in an early zygote stage and suggests a broader range of possible mechanisms of mutation when these stages are considered. (e) With the cloning of all 7 marker loci mutation analysis at the molecular level will allow a more direct assessment of the mutation process in future studies.

Identification, sequence, and mapping of the mouse multiple PDZ domain protein gene, Mpdz

The PDZ domain gained its name from the three proteins that were first seen to have homology by virtue of these domains, the mammalian postsynaptic density protein, PSD-95, the Drosophila discs-large septate junction protein, DLG, and the mammalian epithelial tight-junction protein zona occludens, ZO-1. Over 50 PDZ domain-containing genes have been recognized so far from almost any organism subjected to sequencing, including mammals, nematodes, yeast, plants, and bacteria. The domain consists of an approximately 90-amino-acid-residue unit, which is often repeated in the protein. The majority of residues form a conserved spatial structure while a few amino acids in critical positions confer protein binding specificity. A subgroup of PDZ domains have been shown to recognize a short carboxy-terminal amino acid motif, T/SXV (Ser/Thr-X-Val-COO-), where X is any amino acid. We have identified and completely sequenced a gene, Mpdz, that encodes a mouse protein containing 13 such domains. We have also mapped the gene to a series of overlapping deletions on mouse chromosome 4 and can therefore determine that its function is not essential for embryonic development or neonatal survival.

Cutting Edge: Functional Characterization of the Effect of the C3H/HeJ Defect in Mice that Lack an Lps n Gene: In Vivo Evidence for a Dominant Negative Mutation

A point mutation in the Tlr4 gene, which encodes Toll-like receptor 4, has recently been proposed to underlie LPS hyporesponsiveness in C3H/HeJ mice (Lpsd). The data presented herein demonstrate that F1 progeny from crosses between mice that carry a ∼9-cM deletion of chromosome 4 (including deletion of LpsTlr4) and C3H/HeJ mice (i.e., Lps0 × Lpsd F1 mice) exhibit a pattern of LPS sensitivity, measured by TNF activity, that is indistinguishable from that exhibited by Lpsn × Lpsd F1 progeny and whose average response is “intermediate” to parental responses. Thus, these data provide clear functional support for the hypothesis that the C3H/HeJ defect exerts a dominant negative effect on LPS sensitivity; however, expression of a normal Toll-like receptor 4 molecule is apparently not required.

Disruption of retinoid-related orphan receptor beta changes circadian behavior, causes retinal degeneration and leads to vacillans phenotype in mice

The orphan nuclear receptor RORbeta is expressed in areas of the central nervous system which are involved in the processing of sensory information, including spinal cord, thalamus and sensory cerebellar cortices. Additionally, RORbeta localizes to the three principal anatomical components of the mammalian timing system, the suprachiasmatic nuclei, the retina and the pineal gland. RORbeta mRNA levels oscillate in retina and pineal gland with a circadian rhythm that persists in constant darkness. RORbeta-/- mice display a duck-like gait, transient male incapability to sexually reproduce, and a severely disorganized retina that suffers from postnatal degeneration. Consequently, adult RORbeta-/- mice are blind, yet their circadian activity rhythm is still entrained by light-dark cycles. Interestingly, under conditions of constant darkness, RORbeta-/- mice display an extended period of free-running rhythmicity. The overall behavioral phenotype of RORbeta-/- mice, together with the chromosomal localization of the RORbeta gene, suggests a close relationship to the spontaneous mouse mutation vacillans described >40 years ago.

Functional genomics in the mouse: phenotype-based mutagenesis screens

Significant progress has been made in sequencing the genomes of several model organisms, and efforts are now underway to complete the sequencing of the human genome. In parallel with this effort, new approaches are being developed for the elucidation of the functional content of the human genome. The mouse will have an important role in this phase of the genome project as a model system. In this review we discuss and compare classical genetic approaches to gene function-phenotype-based mutagenesis screens aimed at the establishment of a large collection of single gene mutations affecting a wide range of phenotypic traits in the mouse. Whereas large scale genome-wide screens that are directed at the identification of all loci contributing to a specific phenotype may be impractical, region-specific saturation screens that provide mutations within a delimited chromosomal region are a feasible alternative. Region-specific screens in the mouse can be performed in only two generations by combining high-efficiency chemical mutagenesis with deletion complexes generated using embryonic stem (ES) cells. The ability to create and analyze deletion complexes rapidly, as well as to map novel chemically-induced mutations within these complexes, will facilitate systematic functional analysis of the mouse genome and corresponding gene sequences in humans. Furthermore, as the extent of the mouse genome sequencing effort is still uncertain, we underscore a necessity to direct sequencing efforts to those chromosomal regions that are targets for extensive mutagenesis screens.

Generation, identification, and recovery of mouse mutations

Mouse mutations can be generated by a variety of techniques including those that rely on inducing agents such as X rays or chemicals and those that involve genetic manipulations such as in transgene insertions and gene knockouts. Each technique has its advantages and disadvantages. Inducing agents are often more efficient when random mutations in as yet unknown genes are desired. In contrast, genetic manipulations are advantageous when the mutagenesis needs to be targeted to certain genes or regions. Once these mutations are produced, they must be systematically identified and characterized to confirm their distinction from other known mutations and environmental influences. Allelism and linkage tests should be performed. Finally, methods for maintaining these mutations should be applied so that studies of them can be pursued in the most efficient manner.

Molecular, genetic and biochemical characterization of lactate dehydrogenase-A enzyme activity mutations in Mus musculus

Four independent heterozygous lactate dehydrogenase (LDH) mutations with approximately 60% of wild-type enzyme activity in whole blood have been recovered. The mutant line Ldh1a2Neu proved to be homozygous lethal, whereas for the three lines Ldh1a7Neu, Ldh1a11Neu, and Ldh1a12Neu homozygous mutants with about 20% residual activity occurred in the progeny of heterozygous inter se matings. However, the number of homozygous mutants was less than expected, suggesting an increased lethality of these animals. Various physicochemical and kinetic properties of LDH are altered. Exons of the Ldh1 gene were PCR amplified and sequenced to determine the molecular lesion in the mutant alleles. Ldh1a2Neu carried an A/T-->G/C transition in codon 112 (in exon 3), resulting in an Asn-->Asp substitution; Asn112 is part of the helix alpha D, which is involved in the coenzyme-binding domain. Ldh1a7Neu contained an A/T-->C/G transversion within the codon for residue 194 in exon 4, causing an Asp-->Ala substitution, which may affect the arrangement of the substrate-binding site. Three base substituions were discovered for the mutation Ldh1a11Neu in exon 7: the transition C/G-->T/A, a silent mutation, and two transversions C/G-->A/T and C/G-->G/C, both missense mutations, which led to the amino acid replacements A1a319-->Glu and Thr321-->Ser, respectively, located in the alpha H helix structure of the COOH tail of LDHA. We suggest that the mutation in the result of a gene conversion event between Ldh1a wild-type gene and the pseudogene Ldhl-ps. The alteration Ile-->Thr of codon 241 in exon 6 caused by the base pair change T/A-->C/G was identified in the mutation Ldh1a12Neu; Ile241 is included in the helix alpha 2G, a structure that is indirectly involved in coenzyme binding. Each of the sequence alterations has a potential impact on the structure of the LDHA protein, which is consistent with the decreased LDH activity and biochemical and physiological alterations.

Complete sequence and polymorphism study of the human TYRP1 gene encoding tyrosinase-related protein 1

The complete 24,667 nucleotide sequence spanning the human TYRP1 gene has been determined from the inserts of two overlapping lambda clones. A LINE-1 repeat element is immediately adjacent to and may demarcate the immediate 5' promoter region of the gene. A search for polymorphism within the seven TYRP1 coding exons has been performed by an RNase mismatch detection procedure. Analysis of the TYRP1 gene in 100 Caucasian individuals of varying hair color has found no amino acid sequence variation nor revealed any hemizygous mutant allele in the hypopigmented phenotype of two 9p- syndrome patients.

Chromosomal deletion complexes in mice by radiation of embryonic stem cells

Chromosomal deletions ("deficiencies') are powerful tools in the genetic analysis of complex genomes. They have been exploited extensively in Drosophila melanogaster, an organism in which deficiencies can be efficiently induced and selected. Spontaneous deletions in humans have facilitated the dissection of phenotypes in contiguous gene syndromes and led to the positional cloning of critical genes. In mice, deletion complexes created by whole animal irradiation experiments have enabled a systematic characterization of functional units along defined chromosomal regions. However, classical mutagenesis in mice is logistically impractical for generating deletion sets on a genome-wide scale. Here, we report a high-throughput method for generating radiation-induced deletion complexes at defined regions in the genome using ES cells. Dozens of deletions of up to several centiMorgans, encompassing a specific locus, can be created in a single experiment and transmitted through the germline. The ability to rapidly create deletion complexes along chromosomes will facilitate systematic functional analyses of the mammalian genome.