The H-2 complex of mice contains many genes in addition to the gene families involved in immune reactions. Some of them are believed to function in mouse development, as suggested by the findings that several embryonic lethal mutations map within or near the H-2 complex. We have analyzed the H-2K/tw5 region in an attempt to study non-H-2 genes encoded in this region. Overlapping cosmid clones spanning about 170 kilobase pairs of DNA, including the H-2K/tw5 region of the mouse, have been screened for genes expressed in embryonic carcinoma cells. A transcript of 2.8 kilobase pairs (K. Abe. J.-F. Wei, F.-S. Wei, Y.-C. Hsu, H. Uehara, K. Artzt, and D. Bennett, EMBO J. 7:3441-3449, 1988) encoded by the KE 4 gene flanking H-2K distally was identified. The transcript was abundantly expressed in embryonic carcinoma cells but was present at low levels in other tissues in adults. A cDNA for this transcript was isolated from the F9 embryonic carcinoma cell line and sequenced. It potentially encodes a protein of 436 amino acids with several interesting features. First, it contains two regions made of well-conserved repeats unusually rich in histidine residues. In the repeats, histidine alternates with other amino acids, notably glycine or serine. Second, the two histidine-rich regions are separated by three putative membrane-spanning domains. Third, the N-terminal part of the sequence shows characteristics of a signal peptide. The results indicate that the protein coded by the gene may be a transmembrane protein with histidine-rich charge clusters. A similar sequence motif found in other known genes allows speculation on the possible functional of this gene.
The H-2 complex of mice contains many genes in addition to the gene families involved in immune reactions. Some of them are believed to function in mouse development, as suggested by the findings that several embryonic lethal mutations map within or near the H-2 complex. We have analyzed the H-2K/tw5 region in an attempt to study non-H-2 genes encoded in this region. Overlapping cosmid clones spanning about 170 kilobase pairs of DNA, including the H-2K/tw5 region of the mouse, have been screened for genes expressed in embryonic carcinoma cells. A transcript of 2.8 kilobase pairs (K. Abe. J.-F. Wei, F.-S. Wei, Y.-C. Hsu, H. Uehara, K. Artzt, and D. Bennett, EMBO J. 7:3441-3449, 1988) encoded by the KE 4 gene flanking H-2K distally was identified. The transcript was abundantly expressed in embryonic carcinoma cells but was present at low levels in other tissues in adults. A cDNA for this transcript was isolated from the F9 embryonic carcinoma cell line and sequenced. It potentially encodes a protein of 436 amino acids with several interesting features. First, it contains two regions made of well-conserved repeats unusually rich in histidine residues. In the repeats, histidine alternates with other amino acids, notably glycine or serine. Second, the two histidine-rich regions are separated by three putative membrane-spanning domains. Third, the N-terminal part of the sequence shows characteristics of a signal peptide. The results indicate that the protein coded by the gene may be a transmembrane protein with histidine-rich charge clusters. A similar sequence motif found in other known genes allows speculation on the possible functional of this gene.
Abstract We have studied 27 cell lines homozygous by consanguinity for the major histocompatibility complex to establish the restriction fragment length polymorphism (RFLP) patterns seen with six different restriction enzymes (Bam HI, Bg1 II, Eco RI, Hinc II, Hind III, Pvu II) and DR beta chain probes. The probes used were a full-length cDNA DR beta probe and a probe specific for the 3' untranslated region. The RFLP obtained represent the first standard patterns for the individual haplotypes DR1 through 7 and DR9 as defined by genetically homozygous lines. The patterns obtained reflect the DR specificities closely, as well as the DRw52 and DRw53 specificities. These latter specificities are associated with the most prominent patterns of RFLP. Bands are present which are unique for the haplotypes DR1, DR2, DR4, DR7, DRw52, and DRw53, and could be used for typing these haplotypes in heterozygotes. Subtypes can be identified for all of the haplotypes except DR1. These subtypes indicate that there is an extensive amount of polymorphism in the DR subregion that has not been identified serologically.
A single point mutation in a novel immune-associated nucleotide gene 5 (Ian5) coincides with severe T cell lymphopenia in BB rats. We used a transgenic rescue approach in lymphopenic BB-derived congenic F344.lyp/lyp rats to determine whether this mutation is responsible for lymphopenia and to establish the functional importance of this novel gene. A 150-kb P1 artificial chromosome (PAC) transgene harboring a wild-type allele of the rat Ian5 gene restored Ian5 transcript and protein levels, completely rescuing the T cell lymphopenia in the F344.lyp/lyp rats. This successful complementation provides direct functional evidence that the Ian5 gene product is essential for maintaining normal T cell levels. It also demonstrates that transgenic rescue in the rat is a practical and definitive method for revealing the function of a novel gene.
Abstract The T locus on mouse chromosome 17 is haploid-insufficient: deletion/+ heterozygous mice have a short tail. One exceptional allele, Tc, produces a tailless phenotype in heterozygous mice. Thus, Tc has a more severe phenotype than that of a deletion allele, suggesting either that Tc is further deleted for a neighboring locus, resulting in the additional phenotype, or that Tc is a gain-of-function mutation. We have shown that Tc is not deleted for the D17Leh119 and D17RP17 loci flanking T, which are deleted in some T alleles. Thus, the severity of the Tc phenotype is not due to the deletion of an adjacent locus. We have also examined the genetic nature of the Tc allele by placing it in trans with a T-locus duplication, twLub2, which has previously been independently confirmed at the molecular level to have a duplication in the chromosomal region including the T locus. We have shown that Tc is partially complemented by twLub2, unlike a null allele (deletion) which was previously shown to be fully complemented by twLub2. These results indicate that Tc behaves genetically as an antimorph, exerting its effect by antagonizing the function of a wild-type allele at the T locus. The apparent correlation between the gene dosage at the T locus and the length of the body axis is discussed.
The BB (BioBreeding) rat is one of the best models of spontaneous autoimmune diabetes and is used to study non-MHC loci contributing to Type 1 diabetes. Type 1 diabetes in the diabetes-prone BB (BBDP) rat is polygenic, dependent upon mutations at several loci. Iddm1 , on chromosome 4, is responsible for a lymphopenia ( lyp ) phenotype and is essential to diabetes. In this study, we report the positional cloning of the Iddm1/lyp locus. We show that lymphopenia is due to a frameshift deletion in a novel member ( Ian5 ) of the Immune-Associated Nucleotide (IAN)-related gene family, resulting in truncation of a significant portion of the protein. This mutation was absent in 37 other inbred rat strains that are nonlymphopenic and nondiabetic. The IAN gene family, lying within a tight cluster on rat chromosome 4, mouse chromosome 6, and human chromosome 7, is poorly characterized. Some members of the family have been shown to be expressed in mature T cells and switched on during thymic T-cell development, suggesting that Ian5 may be a key factor in T-cell development. The lymphopenia mutation may thus be useful not only to elucidate Type 1 diabetes, but also in the function of the Ian gene family as a whole. [Sequence data reported in this paper has been deposited in GenBank and assigned the following accession nos: AF517674 , AF517675 , AF517676 , and AF517677 . Supplemental material is available online at http://depts.washington.edu/rhwlab/ and http: www.genome.org . ] The following individuals and institutions kindly provided reagents, samples, or unpublished information as indicated in the paper: K. Matsumoto and the Sir Frederick Banting Research Centre.
DIGICALC * is a program designed to aid in the acquisition, storage, and analysis of nucleic acid restriction fragment data. The chief considerations during program design were (i) ease of use for people with varying degrees of computer experience, (ii) minimal hardware requirements (e.g. an IBM PC), (iii) portability and ease of modification, and (iv) improved functionality in sizing and comparing restriction fragments over manual methods. The program accepts manual or digitizer input of nucleic acid fragment mobility, calculates the fragments' sizes, and provides the means to search the fragment database and to produce charts of fragment sizes.
