Sequence, organization, and expression of the human FEM1B gene

The FEM-1 protein of Caenorhabditis elegans functions within the nematode sex-determination pathway. Two mouse homologs, encoded by the Fem1a and Fem1b genes, have been reported. We report here the characterization of a novel human gene, designated FEM1B, that is highly homologous to the mouse Fem1b gene. FEM1B encodes a protein, designated FEM1beta, that shows >99% amino acid identity to the corresponding mouse Fem1b protein, including 100% amino acid identity in the N-terminal ANK repeat domain. FEM1beta represents the first characterized human member of the FEM-1 protein family. The human and mouse genes show conservation of coding sequence and its intron/exon organization, flanking untranslated and genomic sequences, and expression pattern in adult tissues. These findings suggest that there may be evolutionary conservation of regulation and function between the mouse and human FEM1B genes.     

Cloning, mapping and expression of UBL3, a novel ubiquitin-like gene.

A novel Drosophila melanogaster gene UBL3 was characterized and shown to be highly conserved in man and Caenorhabditis elegans (C. elegans). The human and mouse homologues were cloned and sequenced. UBL3 is a ubiquitin-like protein of unknown function with no conserved homologues in yeast. Mapping of the human and mouse UBL3 genes places them within a region of shared gene order between human and mouse chromosomes on human chromosome 13q12-13 and telomeric mouse chromosome 5 (MMU5).     

Identification,genomic organization and mRNA expression of CRELD1, the founding member of a unique family of matricellular proteins

We have isolated and characterized a unique gene that encodes a highly conserved membrane bound extracellular protein that defines a new epidermal growth factor-related gene family. The CRELD1 (Cysteine-Rich with EGF-Like Domains 1) gene (previously known as cirrin) was cloned from a human chromosome 3 BAC. Mapping of the gene confirmed its position at chromosome 3p25.3. The gene is ubiquitously expressed in early development and later becomes more markedly expressed in the developing heart, limb buds, mandible and central nervous system. Expression persists in adulthood in most tissues. Sequence analysis suggests that this is a cell adhesion protein. The mouse orthologue was cloned and mapped to the syntenic region of mouse chromosome 6. Orthologues or homologues have also been identified for cow, Chinese hamster, Drosophila and Caenorhabditis elegans. The CRELD1 gene is deleted in the human cytogenetic disorder 3p- syndrome and is in the region of loss of heterozygosity for several types of cancer. A potential role for this protein in these disorders is discussed.     

The C1orf9 gene encodes a putative transmembrane member of a novel protein family

Here we report the characterization of a human mRNA encoding a novel protein denoted C1orf9 (chromosome 1 open reading frame 9). The cDNA sequence, derived from a testis cDNA library, contains 5700 bp which encodes an open reading frame of 1254 amino acids. The deduced protein contains a putative N-terminal signal peptide and one putative transmembrane region, indicating membrane localization. No significant homology was found with known characterized proteins. However, a 150 amino acid region has significant homology to deduced protein sequences from other organisms, including Caenorhabditis elegans (43% identity), Saccharomyces cerevisiae (47% identity), Schizosaccharomyces pombe (48% identity), and two proteins from Arabidopsis thaliana (42% and 40% identity), suggesting a novel family of conserved domains. The C1orf9 gene was assigned to chromosome 1q24. The gene spans approximately 78.7 kb and is organized into at least 24 exons. Expression analysis revealed a single C1orf9 mRNA species of approximately 6.0 kb with a predominant expression in pancreas and testis, and only low levels of expression in other tissues examined.     

Identification and characterization of the rat homologue of LAIR-1

Leukocyte-associated immunoglobulin-like receptor-1 (LAIR-1) is a cell-surface molecule that functions as an inhibitory receptor on various immune cells in both humans and mice. We have cloned a LAIR-1 homologue from the rat that we have named rat LAIR-1. The LAIR-1 gene maps to rat chromosome 1q12 in a region showing conserved synteny with human chromosome 19q13.4 and mouse chromosome 7, where the leukocyte receptor cluster is located. Rat LAIR-1 shows 40 and 71% protein sequence identity with human LAIR-1 and mouse LAIR-1, respectively, has a single Ig-like domain and contains two immunoreceptor tyrosine-based inhibitory motif-like sequences in its cytoplasmic tail. Soluble rat LAIR-1 fusion proteins bind to the same adherent cell lines as human LAIR-1 and mouse LAIR-1, indicating that a putative ligand for all the LAIR-1 molecules is expressed on these cells. Furthermore, we show that rat and mouse LAIR-1 bind the same molecule expressed on human HT29 cells. Since many autoimmune diseases are studied in rat models, identification of rat LAIR-1 allows for in vivo studies on the function of LAIR molecules in these systems.     

Identification of the mouse and rat orthologs of the gene mutated in Usher syndrome type IIA and the cellular source of USH2A mRNA in retina,a target tissue of the disease

Usher syndrome type IIA (MIM: 27601) is an autosomal recessive disorder characterized by moderate to severe congenital deafness and progressive retinitis pigmentosa. We recently identified the human Usher syndrome type IIA gene (USH2A) on chromosome 1q41, which encodes a protein possessing 10 laminin epidermal growth factor and four fibronectin type 3 domains, both commonly observed in extracellular matrix proteins. To gain insight into the pathogenesis of Usher syndrome type IIA, we isolated and characterized the murine (Ush2a) and rat (rat Ush2a) orthologs of human USH2A. We mapped mouse Ush2a by fluorescence in situ hybridization to mouse chromosome 1 in the region syntenic to human chromosome 1q41. Rat Ush2a has been localized by radiation hybrid mapping to rat chromosome 13 between d13rat49 and d13rat76. The mouse and rat genes, similar to human USH2A, are expressed primarily in retina and cochlea. Mouse Ush2a encodes a 161-kDa protein that shows 68% identity and 9% similarity to the human USH2A protein. Rat Ush2a encodes a 167-kDa protein with 64% identity and 10% similarity to the human protein and 81% identity and 5% similarity to the mouse USH2A protein. The predicted amino acid sequence of the mouse and rat proteins, like their human counterpart, contains a leader sequence, an amino-terminal globular domain, 10 laminin epidermal growth factor domains, and four carboxy-terminal fibronectin type III motifs. With in situ hybridization, we compared the cellular expression of the USH2A gene in rat, mouse, and human retinas. USH2A mRNA in the adult rat, mouse, and human is expressed in the cells of the outer nuclear layer of the retina, one of the target tissues of the disease. In the developing rat retina, Ush2a mRNA expression appears in the neuroepithelium at embryonic day 17.