YAC/P1 contigs defining the location of 56 microsatellite markers and several genes across a 3.4-cM interval on mouse chromosome 11

A three-megabase yeast artificial chromosome contig spanning the C57BL mouse Igh locus

The mouse Ig H chain (Igh) complex locus is composed of >100 gene segments encoding the variable, diversity, joining, and constant portions of the Ab H chain protein. To advance the characterization of this locus and to identify all the V(H) genes, we have isolated the entire region from C57BL/6 and C57BL/10 as a yeast artificial chromosome contig. The mouse Igh locus extends approximately three megabases and contains at least 134 V(H) genes classified in 15 partially interspersed families. Two non-Igh pseudogenes (Odc-rs8 and Rpl32-rs14) were localized in the distal part of the locus. This physical yeast artificial chromosome map will provide important structure and guidance for the sequencing of this large, complex, and highly repetitive locus.

Analysis of mitotic microtubule-associated proteins using mass spectrometry identifies astrin, a spindle-associated protein

We purified microtubules from a mammalian mitotic extract and obtained an amino acid sequence from each microtubule-associated protein by using mass spectrometry. Most of these proteins are known spindle-associated components with essential functional roles in spindle organization. We generated antibodies against a protein identified in this collection and refer to it as astrin because of its association with astral microtubule arrays assembled in vitro. Astrin is approximately 134 kDa, and except for a large predicted coiled-coil domain in its C-terminal region it lacks any known functional motifs. Astrin associates with spindle microtubules as early as prophase where it concentrates at spindle poles. It localizes throughout the spindle in metaphase and anaphase and associates with midzone microtubules in anaphase and telophase. Astrin also localizes to kinetochores but only on those chromosomes that have congressed. Deletion analysis indicates that astrin's primary spindle-targeting domain is at the C terminus, although a secondary domain in the N terminus can target some of the protein to spindle poles. Thus, we have generated a comprehensive list of major mitotic microtubule-associated proteins, among which is astrin, a nonmotor spindle protein.

Abnormal bone marrow stroma in mice deficient for nemo-like kinase, Nlk

The stromal compartment of the bone marrow is composed of various cell types that provide trophic and instructive signals for hematopoiesis. The mesenchymal stem cell is believed to give rise to all major cellular components of the bone marrow microenvironment. Nemo-like kinase, Nlk, is a serine-threonine kinase that connects MAP kinase and Wnt signaling pathways; its in vivo function in mouse is unknown. We have generated mice with a targeted disruption of Nlk and find that the complex phenotype significantly varies with the genetic background. Whereas C57BL/6 mice lacking Nlk die during the third trimester of pregnancy, the 129/Sv background supports survival into adolescence; such mice are growth retarded and suffer from various neurological abnormalities. We show here that the Nlk deficiency syndrome includes aberrant differentiation of bone marrow stromal cells. Varying degrees of morphological abnormality, such as increased numbers of adipocytes, large blood sinuses and absence of bone-lining cells are observed in the bone marrow of mutant mice. Nlk deficient mice thus provide a novel model to study the genetic requirements for bone marrow stromal differentiation.

Only one nemo-like kinase gene homologue in invertebrate and mammalian genomes

The nemo-like kinase (Nlk) connects the MAP kinase and Wnt signalling pathways. We have found that invertebrate (Caenorhabditis elegans, Drosophila melanogaster) and mammalian genomes (Mus musculus and Homo sapiens) each contain only a single functional Nlk gene. The mouse genome also harbours a transcriptionally silent processed Nlk pseudogene residing on chromosome 2. Thus, while genes encoding upstream (such as Wnts and frizzelds) and downstream (such as TCF/LEF) components of the Wnt signalling pathway have been extensively diversified during evolution, genes encoding components of the common core of the connecting signalling structure (such as beta-catenin, GSK beta and Nlk) have been maintained in single copies.

A 2-Mb YAC/BAC-based physical map of the ovum mutant (Om) locus region on mouse chromosome 11

The embryonic lethal phenotype observed when DDK females are crossed with males from other strains results from a deleterious interaction between the egg cytoplasm and the paternal pronucleus soon after fertilization. We have previously mapped the Om locus responsible for this phenotype, called the DDK syndrome, to an approximately 2-cM region of chromosome 11. Here, we report the generation of a physical map of 28 yeast and bacterial artificial chromosome clones encompassing the entire genetic interval containing the Om locus. This contig, spanning approximately 2 Mb, was used to map precisely genes and genetic markers of the region. We determined the maximum physical interval for Om to be 1400 kb. In addition, 11 members of the Scya gene family were found to be organized into two clusters at the borders of the Om region. Two other genes (Rad51l3 and Schlafen 2) and one EST (D11Wsu78e) were also mapped in the Om region. This integrated map provides support for the identification of additional candidate genes for the DDK syndrome.

Locus of dominant hairless gene (Ht) causing abnormal hair and keratinization maps to rat chromosome 10

The rat dominant hairless gene (Ht) of the WBN/Ila-Ht rat causes atrichosis in Ht/Ht and hypotrichosis in Ht/+. Furthermore the Ht/Ht shows signs of abnormal keratinization and almost all of the Ht/Ht die in an immature stage before weaning in the conventional environment. Ht/+ was affected by dermatitis caused by Staphylococcus aureus, suggesting that the gene Ht might involve defense mechanisms against infection. In this study, we performed the linkage analysis of the gene Ht by outcross with the Brown Norway rat in the SPF environment. Ninety-six backcross progeny of (BN x WBN/Ila-Ht/Ht) F1 x WBN/Ila-Ht/Ht were typed with microsatellite markers and the gene Ht was mapped on chromosome 10 between Asgr1 and Nos2 within the map distance of 6.2 cM.

Predetermined chromosomal deletion encompassing the Nf-1 gene

Complex chromosomal rearrangements (deletions, inversions, translocations) are a hallmark of human tumour cells. Yet, the generation of animal models for gross chromosomal abnormalities still presents a formidable challenge. Here, we describe a versatile procedure for chromosomal engineering that was used to generate an ES cell line with a megabase deletion encompassing the tumour suppressor gene neurofibromatosis-1 (Nf-1) on mouse chromosome 11, which is often deleted in tumours of neural crest origin. Homologous recombination into sites flanking Nf-1 was used to introduce artificial sequences (triple-helix, loxP, vector backbone) that can be employed for in vitro recovery of intervening sequences or the generation of in vivo deletions. This strategy may be developed into a scheme by which large chromosomal regions with precisely defined end points may be excised from mammalian cells and reintroduced after suitable in vitro modification.

Campomelic dysplasia translocation breakpoints are scattered over 1 Mb proximal to SOX9: evidence for an extended control region

Campomelic dysplasia (CD), a skeletal malformation syndrome with or without XY sex reversal, is usually caused by mutations within the SOX9 gene on distal 17q. Several CD translocation and inversion cases have been described with breakpoints outside the coding region, mapping to locations >130 kb proximal to SOX9. Such cases are generally less severely affected than cases with SOX9 coding-region mutations, as is borne out by three new translocation cases that we present. We have cloned the region extending 1.2 Mb upstream of the SOX9 gene in overlapping bacterial-artificial-chromosome and P1-artificial-chromosome clones and have established a restriction map with rare-cutter enzymes. With sequence-tagged-site-content mapping in somatic-cell hybrids, as well as with FISH, we have precisely mapped the breakpoints of the three new and of three previously described CD cases. The six CD breakpoints map to an interval that is 140-950 kb proximal to the SOX9 gene. With exon trapping, we could isolate five potential exons from the YAC 946E12 that spans the region, four of which could be placed in the contig in the vicinity of the breakpoints. They show the same transcriptional orientation, but only two have an open reading frame (ORF). We failed to detect expression of these fragments in several human and mouse cDNA libraries, as well as on northern blots. Genomic sequence totaling 1,063 kb from the SOX9 5'-flanking region was determined and was analyzed by the gene-prediction program GENSCAN and by a search of dbEST and other databases. No genes or transcripts could be identified. Together, these data suggest that the chromosomal rearrangements most likely remove one or more cis-regulatory elements from an extended SOX9 control region.

Structure and chromosomal mapping of the TNF-alpha inducible endothelial protein 1 (Edp1) gene in the mouse

EDP1 was identified as a human gene activated transcriptionally by tumour necrosis factor alpha in endothelial cells. Here we have characterised the mouse Edp1 gene. We show that the gene encodes a highly conserved protein and describe its intron/exon structure. The presence of related genes in the sequence databases suggests that Edp1 is part of a gene family. Fine mapping of the gene in the mouse genome indicates that, as expected from its location on human chromosome 17, the mouse Edp1 gene maps to mouse chromosome 11. However, surprisingly, the gene does not map to the expected region of mouse chromosome 11 suggesting that a change in the order of genes has occurred within a conserved linkage group.

Quantitative trait loci affecting body weight and fatness from a mouse line selected for extreme high growth

Quantitative trait loci (QTL) influencing body weight were mapped by linkage analysis in crosses between a high body weight selected line (DU6) and a control line (DUKs). The two mouse lines differ in body weight by 106% and in abdominal fat weight by 100% at 42 days. They were generated from the same base population and maintained as outbred colonies. Determination of line-specific allele frequencies at microsatellite markers spanning the genome indicated significant changes between the lines on 15 autosomes and the X chromosome. To confirm these effects, a QTL analysis was performed using structured F2 pedigrees derived from crosses of a single male from DU6 with a female from DUKs. QTL significant at the genome-wide level were mapped for body weight on chromosome 11; for abdominal fat weight on chromosomes 4, 11, and 13; for abdominal fat percentage on chromosomes 3 and 4; and for the weights of liver on chromosomes 4 and 11, of kidney on chromosomes 2 and 9, and of spleen on chromosome 11. The strong effect on body weight of the QTL on chromosome 11 was confirmed in three independent pedigrees. The effect was additive and independent of sex, accounting for 21-35% of the phenotypic variance of body weight within the corresponding F2 populations. The test for multiple QTL on chromosome 11 with combined data from all pedigrees indicated the segregation of two loci separated by 36 cM influencing body weight.

Vector-hexamer PCR isolation of all insert ends from a YAC contig of the mouse Igh locus

We have developed a simple PCR strategy, termed vector-hexamer PCR, that is unique in its ability to easily recover every insert end from large insert clones in YAC and BAC vectors. We used this method to amplify and isolate all insert ends from a YAC contig covering the mouse Igh locus. Seventy-seven ends were amplified and sequenced from 36 YAC clones from four libraries in the pYAC4 vector. Unexpectedly, 40% of the insert ends of these YACs were LINE1 repeats. Nonrepetitive ends were suitable for use as probes on Southern blots of digested YACs to identify overlaps and construct a contig. The same strategy was used successfully to amplify insert ends from YACs in the pRML vector from the Whitehead Institute/MIT-820 mouse YAC library and from BACs in pBeloBAC11. The simplicity of this technique and its ability to isolate every end from large insert clones are of great utility in genomic investigation. [The nucleotide sequence data reported in this paper are accessible in GenBank under accession nos. B07512-B07598.]

Positional cloning and gene identification

After genetic mapping and physical representation of a particular genomic region containing the gene underlying a particular Mendelian trait, a successful positional cloning strategy depends on the efficient detection and analysis of genes in the critical interval. Several gene detection strategies are presently available to compile an inventory of genes from large genomic regions. Here, the principle of these methods is briefly reviewed and their relative value for positional cloning projects compared.

A mammalian homolog of the bacterial monomeric sarcosine oxidases maps to mouse chromosome 11, close to Cryba1

We have cloned a cDNA from a mouse gene, Pso (peroxisomal sarcosine oxidase). Pso appears to encode a homolog of the single-subunit (40 kDa) bacterial sarcosine oxidases. The mouse Pso gene product would contain a peroxisomal localization sequence, like that of the recently reported rabbit enzyme, Mouse Pso lies between 20 and 50 kb upstream of the promoter of the Sez6 gene, close to Crybal on chromosome 11. Pso is expressed very strongly and specifically in liver and kidney. The gene appears to be present widely in eutherian mammals.

Confirmation of maternal transmission ratio distortion at Om and direct evidence that the maternal and paternal "DDK syndrome" genes are linked

The polar, preimplantation-embryo lethal phenotype known as the "DDK syndrome" in the mouse is the result of the complex interaction of genetic factors and a parental-origin effect. We previously observed a modest degree of transmission-ratio distortion in favor of the inheritance of DDK alleles in the Ovum mutant (Om) region of Chromosome (Chr) 11, among offspring of reciprocal F1-hybrid females and C57BL/6 males. In this study, we confirm that a significant excess of offspring inherit DDK alleles from F1 mothers and demonstrate that the preference for the inheritance of DDK alleles is not a specific bias against the C57BL/6 allele or a simple preference for offspring that are heterozygous at Om. Because none of the previous genetic models for the inheritance of the "DDK syndrome" predicted transmission-ratio distortion through F1 females, we reconsidered the possibility that the genes encoding the maternal and paternal components of this phenotype were not linked. We have examined the fertility phenotype of N2 females and demonstrate that the inter-strain fertility of these females is correlated with their genotype in the Om region. This result establishes, directly, that the genes encoding the maternal and paternal components of the DDK syndrome are genetically linked.

The structural integrity of ROR alpha isoforms is mutated in staggerer mice: cerebellar coexpression of ROR alpha1 and ROR alpha4

The recessive mouse mutation staggerer (sg) disturbs the normal development of cerebellar Purkinje cells and affects certain functions of the immune system. To identify the causative gene, we constructed high-resolution genetic and physical maps of the staggerer locus on mouse chromosome 9. The transcription unit of the orphan nuclear receptor ROR alpha was identified in the critical interval. Our mutational analysis confirms a recent report that the sg phenotype may be caused by a genomic deletion in the common coding region of the ROR alpha isoforms. Of the four different isoforms of the ROR alpha gene that are generated by a combination of alternative promoter usage and exon splicing that differ in their DNA-binding properties, isoforms ROR alpha1 and ROR alpha4 are specifically coexpressed in the murine cerebellum and human cerebellum. Thus, at least two isoforms of the murine ROR alpha gene are affected by the genomic deletion associated with the staggerer phenotype. Our finding of cerebellum-specific coregulation suggests that distinct sets of target genes regulated by the ROR alpha1 and ROR alpha4 isoforms are required for Purkinje cell development.

The nude gene encodes a sequence-specific DNA binding protein with homologs in organisms that lack an anticipatory immune system

In the mouse, the product of the nude locus, Whn, is required for the keratinization of the hair shaft and the differentiation of epithelial progenitor cells in the thymus. A bacterially expressed peptide representing the presumptive DNA binding domain of the mouse whn gene in vitro specifically binds to a 11-bp consensus sequence containing the invariant tetranucleotide 5'-ACGC. In transient transfection assays, such binding sites stimulated reporter gene expression about 30- to 40-fold, when positioned upstream of a minimal promotor. Whn homologs from humans, bony fish (Danio rerio), cartilaginous fish (Scyliorhinus caniculus), agnathans (Lampetra planeri), and cephalochordates (Branchiostoma lanceolatum) share at least 80% of amino acids in the DNA binding domain. In agreement with this remarkable structural conservation, the DNA binding domains from zebrafish, which possesses a thymus but no hair, and amphioxus, which possesses neither thymus nor hair, recognize the same target sequence as the mouse DNA binding domain in vitro and in vivo. The genomes of vertebrates and cephalochordates contain only a single whn-like gene, suggesting that the primordial whn gene was not subject to gene-duplication events. Although the role of whn in cephalochordates and agnathans is unknown, its requirement in the development of the thymus gland and the differentiation of skin appendages in the mouse suggests that changes in the transcriptional control regions of whn genes accompanied their functional reassignments during evolution.

SEZ-6: promoter selectivity, genomic structure and localized expression in the brain

AP-1-binding elements from promoter proximal DNA (the small HpaII-digested fraction of mouse genomic DNA) were affinity-selected with recombinant AP-1 complexes. One of the selected AP-1-binding elements originated from 1 kb 3' of the transcription start site of SEZ-6. We show that the mouse SEZ-6 gene extends over 49 kbp and contains 17 exons. SEZ-6 has been reported as a mouse brain-specific transcript encoding an integral membrane protein with a short cytoplasmic tail which we note may have a signalling function. We show that SEZ-6 mRNA expression in rat brain is specific to neurons but shows sharp regional differences, unconnected with the localization of major neurotransmitters. Full-length and a 3' truncated transcript are also abundant in testis. We define the origins of all reported sequence variants. The hypothetical domain structure of the protein is in excellent agreement with the exonic structure of the gene. The SEZ-6 promoter is a CpG island. In transient transfections, even the smallest promoter fragment tested (157 bp) was extremely selective towards a mouse neuronal cell line, Neuro 2a, compared with NIH-3T3, a non-expressing line.

Two genetically separable steps in the differentiation of thymic epithelium

The development of the thymus depends initially on epithelial-mesenchymal and subsequently on reciprocal lympho-stromal interactions. The genetic steps governing development and differentiation of the thymic microenvironment are unknown. With the use of a targeted disruption of the whn gene, which recapitulates the phenotype of the athymic nude mouse, the WHN transcription factor was shown to be the product of the nude locus. Formation of the thymic epithelial primordium before the entry of lymphocyte progenitors did not require the activity of WHN. However, subsequent differentiation of primitive precursor cells into subcapsular, cortical, and medullary epithelial cells of the postnatal thymus did depend on activity of the whn gene. These results define the first genetically separable steps during thymic epithelial differentiation.