The interleukin-4 receptor gene (IL4R) maps to 16p11.2-16p12.1 in human and to the distal region of mouse chromosome 7.

The chromosomal location of both the human and the mouse interleukin-4 receptor (IL4R) genes have been determined. The human gene was localized to 16p11.2-16p12.1 by in situ hybridization and confirmed by Southern blot analysis of DNA from a panel of mouse-human hybrid somatic cell lines. The mouse homolog was positioned in the distal region of chromosome 7 by interspecific backcross analysis. The results suggest that the IL4R locus is unlinked to other members of the hematopoietin receptor family. Interestingly, the position on human chromosome 16 suggests that the IL4R may be a candidate for rearrangements, as 12;16 translocations are often associated with myxoid liposarcomas.     

The amplified mouse squamous cell carcinoma antigen gene locus contains a serpin (Serpinb3b) that inhibits both papain-like cysteine and trypsin-like serine proteinases

The clade B serpins occupy a unique niche among a larger superfamily by predominantly regulating intracellular proteolysis. In humans, there are 13 family members that map to serpin gene clusters at either 6p25 or 18q21. While most of these serpins display a unique inhibitory profile and appear to be well conserved in mammals, the clade B loci of several species show evidence of relatively recent genomic amplification events. However, it is not clear whether these serpin gene amplification events yield paralogs with functional redundancy or, through selective pressure, inhibitors with more diverse biochemical activities. A recent comparative genomic analysis of the mouse clade B cluster at 1D found nearly complete conservation of gene number, order, and orientation relative to those of 18q21 in humans. The only exception was the squamous cell carcinoma antigen (SCCA) locus. The human SCCA locus contains two genes, SERPINB3 (SCCA1) and SERPINB4 (SCCA2), whereas the mouse locus contains four serpins and three pseudogenes. At least two of these genes encoded functional, dual cross-class proteinase inhibitors. Mouse Serpinb3a was shown previously to inhibit both chymotrypsin-like serine and papain-like cysteine proteinases. We now report that mouse Serpinb3b extends the inhibitory repertoire of the mouse SCCA locus to include a second cross-class inhibitor with activity against both papain-like cysteine and trypsin-like serine proteinases. These findings confirmed that the genomic expansion of the clade B serpins in the mouse was associated with a functional diversification of inhibitory activity.     

Interleukin-1 receptor cluster: gene organization of IL1R2, IL1R1, IL1RL2 (IL-1Rrp2), IL1RL1 (T1/ST2), and IL18R1 (IL-1Rrp) on human chromosome 2q

The family of interleukin-1 receptor-like genes currently has six known members. We have constructed a contig of 10 overlapping human PAC clones that covers 530 kb and includes five of the six family members. The termini of the contig were mapped to the interval between D2S373 and D2S176 (chromosome 2q12) by radiation hybrid mapping. The contig contains the genes (cen --> tel), in the order given, for the type II interleukin-1 (IL-1) receptor (IL1R2), the type I IL-1 receptor (IL1R1), the IL-1 receptor-related protein 2 (IL1RL2), T1/ST2/fit-1 (IL1RL1), and the IL-1 receptor-related protein 1, which has recently been shown to be a component of the IL-18 receptor (IL18R1). We show that all the genes are transcribed in the same direction, with IL1R2 being transcribed toward the cluster. The only known family member that is absent from the human contig is the IL-1 receptor accessory protein gene (IL1RAP), which maps to 3q28.     

Isolation and mapping of EVX1, a human homeobox gene homologous to even-skipped, localized at the 5' end of HOX1 locus on chromosome 7.

We isolated and mapped the human homeobox gene EVX1. This gene encodes a protein of 407 amino acid residues containing a homeodomain closely related to the Drosophila even-skipped (eve) segmentation gene of the pair-rule class. EVX1 belongs to a small family of vertebrate eve-related homeobox genes including human EVX1 and EVX2 genes, their murine homologs, Evx 1 and Evx 2, and the frog Xhox-3 gene. We previously reported that EVX2 is localized at the 5' end of the HOX4 locus on chromosome 2. We show here that EVX1 is localized at the 5' end of the HOX1 locus on chromosome 7, 48 kb upstream from the most 5' of the eleven HOX1 genes, namely HOX1J. Both EVX genes are transcribed in an opposite orientation as compared to that of adjacent HOX genes. Human HOX1 and HOX4 complex loci appear to be both closely linked to a homeobox gene of the EVX family.     

Mapping of the thrombospondin gene to human chromosome 15 and mouse chromosome 2 by in situ hybridization

We have mapped the thrombospondin gene (THBS1) to a single locus on human chromosome 15 (band q15) and on mouse chromosome 2 (region F). Thrombospondin has been implicated in a variety of cell-matrix and cell-cell interactions. The finding of a single locus suggests that the different functions of thrombospondin are not due to a closely related family of genes. These results also confirm a region of homology between the proximal part of human chromosome 15 and region F of mouse chromosome 2.     

Assignment of the genes encoding human interleukin-8 receptor types 1 and 2 and an interleukin-8 receptor pseudogene to chromosome 2q35.

Two human cDNA clones that encode different interleukin-8 (IL8) receptors have recently been isolated. The interleukin-8 receptor type 1 (IL8R1) binds IL8 only, whereas the interleukin-8 receptor type 2 (IL8R2) (previously designated IL8RA) also binds growth regulated gene (GRO), and neutrophil activating protein-2 (NAP-2) with high affinity. In the process of screening a genomic library with these cDNAs to obtain large clones for use in chromosomal localization studies, we isolated an interleukin-8 receptor pseudogene (IL8RP) that bears greatest similarity to IL8R2. Using Southern hybridization analysis of human x rodent somatic cell hybrid DNAs with cDNA probes for IL8R1 and IL8R2 and probes from the IL8RP locus, we assigned the three loci to chromosome 2; fluorescence in situ hybridization (FISH) to metaphase chromosome preparations using genomic clones from each locus refined this localization to chromosome 2, band q35, for all three. By virtue of their chromosomal location, IL8R1 and IL8R2 may be considered candidate genes for several human disorders in which the involved locus has been mapped to distal 2q or that are associated with structural abnormalities of this segment, including van der Woude syndrome and the neoplastic diseases rhabdomyosarcoma and uterine leiomyomata. In addition, because this region of chromosome 2q is homologous to proximal mouse chromosome 1 in the segment containing the Lsh-Ity-Bcg locus involved in mediating host resistance to infection with intracellular pathogens, examination for abnormalities of the murine homologues of the IL8R genes should be considered in mice affected by mutations of this locus.     

Mapping, Phylogenetic and Expression Analysis of the RNase (RNaseA) Locus in Cattle

The mammalian secreted ribonucleases (RNases) comprise a large family of structurally related proteins displaying considerable sequence variation, and have been used in evolutionary studies. RNase 1 (RNase A) has been assumed to play a role in digestion, while other members have been suggested to contribute to host defence. Using the recently assembled bovine genome sequence, we characterised the complete repertoire of genes present in the RNaseA family locus in cattle, and compared this with the equivalent locus in the human and mouse genomes. Several additions and corrections to the earlier analysis of the RNase locus in the mouse genome are presented. The bovine locus encodes 19 RNases, of which only six have unambiguous equivalent genes in the other two species. Chromosomal mapping and phylogenetic analysis indicate that a number of distinct gene duplication events have occurred in the cattle lineage since divergence from the human and mouse lineages. Substitution analysis suggests that some of these duplicated genes are under evolutionary pressure for purifying selection and may therefore be important to the physiology of cattle. Expression analysis revealed that individual RNases have a wide pattern of expression, including diverse mucosal epithelia and immune-related cells and tissues. These data clarify the full repertoire of bovine RNases and their relationships to those in humans and mice. They also suggest that RNase gene duplication within the bovine lineage accompanied by altered tissue-specific expression has contributed a survival advantage.     

Comparative genomic analysis of the clade B serpin cluster at human chromosome 18q21: amplification within the mouse squamous cell carcinoma antigen gene locus

The human clade B serpins neutralize serine or cysteine proteinases and reside predominantly within the intracellular compartment. Genomic analysis shows that the 13 human clade B serpins map to either 6p25 (n = 3) or 18q21 (n = 10). Similarly, the mouse clade B serpins map to syntenic loci at 13A3.2 and 1D, respectively. The mouse clade B cluster at 13A3.2 shows a marked expansion in the number of serpin genes (n = 15). The purpose of this study was to determine whether a similar expansion occurred at 1D. Using STS-content mapping, comparative genomic DNA sequence analysis, and cDNA cloning, we found that the mouse clade B cluster at 1D showed nearly complete conservation of gene number, order, and orientation relative to those of 18q21. The only exception was the squamous cell carcinoma antigen (SCCA) locus. The human SCCA locus contains two genes, SERPINB3 (SCCA1) and SERPINB4 (SCCA2), whereas the mouse locus contains four serpins and three pseudogenes. Based on phylogenetic analysis and predicted amino acid sequences, amplification of the mouse SCCA locus occurred after rodents and primates diverged and was associated with some diversification of proteinase inhibitory activity relative to that of humans.     

The cloning and nucleotide sequence of human ST2L cDNA

The ST2 gene is a member of the IL-1 receptor family and is hypothesized to be involved in helper T cell function, but its functional ligand and physiological role remain unknown. We have cloned the human ST2L cDNA that encodes a distinct type of membrane-bound ST2 protein. The predicted 556-amino-acid sequence showed 67% identity to the mouse ST2L protein. The human ST2 gene (IL1RL1) contains 13 exons and spans 40 kb in length. Its exon-intron organization was elucidated from a registered human genomic sequence derived from chromosome 2q, which contains three other genes belonging to the IL-1 receptor family in an approximately 202-kb genomic region. The tissue distribution of ST2 expression was examined by RT-PCR, and the soluble form (ST2, IL1RL1-a) and ST2L (IL1RL1-b) appear to be expressed differentially. We also established stable transfectants of a human glioblastoma cell line, T98G, that express human ST2L constitutively, and we confirmed cell-surface expression of human ST2L protein on the transfectants.     

A sequence-based map of the nine genes of the human interleukin-1 cluster

Six novel genes encoding proteins with the interleukin (IL)-1 fold have been identified recently. The classical family members are involved in inflammatory signaling. Previous work has placed the novel genes close to or within the same cluster as IL1A, IL1B, and IL1RN, which occupy an approximately 400-kb interval on chromosome 2. We have combined the incomplete public database sequence with our own sequence to generate a reference sequence and map that encompass all of the novel genes, allowing determination of the gene structures, precise localization of exons, and determination of distances between conventional SNP and microsatellite markers. Gene order from centromere to telomere is IL1A-IL1B-IL1F7-IL1F9-IL1F6-IL1F8-IL1F5-IL1F10-IL1RN, of which only IL1A, IL1B, and IL1F8 are transcribed towards the centromere. The gene order relates to the evolutionary relationship between the genes. Key features of exon boundaries are conserved. There is no evidence for other IL-1 family members within the cluster.     

Synaptophysin: structure of the human gene and assignment to the X chromosome in man and mouse.

Synaptophysin is an integral membrane protein of small synaptic vesicles in brain and endocrine cells. We have determined the structure and organization of the human synaptophysin gene and have established the chromosome localizations in man and mouse. Analysis of a cosmid clone containing the human synaptophysin gene (SYP) revealed seven exons distributed over approximately 20 kb, when compared with the previously published cDNA sequence. The exon-intron boundaries have been identified and do not correlate with functional domains. One intron interrupts the 3' untranslated region. Chromosomal localization of the human and murine genes for synaptophysin established the human SYP locus on the X chromosome in subbands Xp11.22-p11.23 and the mouse synaptophysin gene locus (Syp) on the X chromosome in region A-D. In addition, an Eco0109 RFLP has been identified and used in genetic mapping of the human SYP locus and supports the order TIMP-SYP-DXS14 within a span of approximately 4-7 centimorgans.     

The genes of the lysosomal cysteine proteinases cathepsin B, H, L, and S map to different mouse chromosomes

The mouse genes for the lysosomal cysteine proteinases cathepsin B, H, L, and S were mapped to Chromosomes (Chrs) 14, 9, 13, and 3, respectively. Two of the DNA probes used in this study detected an additional, independently segregating locus. The cathepsin B-specific probe hybridized to a locus on Chr 2, and the cathepsin H probe to a locus on the X Chr. These loci either correspond to pseudogenes or to cathepsin B- and cathepsin H-related genes. The four cysteine proteinases mapped in this study lie within known regions of conserved synteny between mouse and human chromosomes, when compared with the corresponding positions of their human homologs. Assuming that the genes of the cysteine proteinase gene family arose from a common ancestral gene, our results suggest that these four cysteine proteinases had been dispersed over different chromosomes before separation of mouse and human in evolution. Received: 22 August 1996 / Accepted: 20 November 1996     

Chromosomal localization of seven neuronal nicotinic acetylcholine receptor subunit genes in humans.

We have determined the chromosomal location of seven human neuronal nicotinic acetylcholine receptor subunit genes by genomic Southern analysis of hamster/human somatic cell hybrid DNAs. The beta 2 subunit gene was localized to human chromosome 1, the alpha 2 and beta 3 subunit genes were localized to human chromosome 8, the alpha 3, alpha 5, and beta 4 subunit genes were localized to human chromosome 15, and the alpha 4 subunit gene was localized to human chromosome 20. Mapping of the beta 2 subunit gene to chromosome 1 establishes a syntenic group with the amylase gene locus on human chromosome 1 and mouse chromosome 3, while mapping of the alpha 3 subunit gene to chromosome 15 confirms the existence of a syntenic group with the mannose phosphate isomerase gene locus on human chromosome 15 and mouse chromosome 9.     

Human homologs of two testes-expressed loci on mouse chromosome 17 map to opposite arms of chromosome 6

Our laboratory has recently cloned and characterized two testes-expressed loci--the Tcp-10 gene family cluster and the D17Si11 gene--that map to the proximal portion of mouse chromosome 17. Human homologs of both loci have been identified and cloned. Somatic cell hybrid lines have been used to map the human homolog of D17Si11 to the short arm of chromosome 6 (p11-p21.1) along with homologs of other genes from the (Pim-1)-(Pgk-2) region of the mouse chromosome. The human TCP 10 locus maps to the long arm of chromosome 6 (q21-qter) along with homologs of other genes from the mouse chromosome 17 region between the centromere and Pim-1. The mapping of large portions of the mouse t haplotype to unlinked regions on human chromosome 6 rules out the possibility that a t-haplotype-like chromosome could exist in humans.