Search

We present a systematic study of the clustering of genes within the human genome based on homology inferred from both sequence and structural similarity. The 3D-Genomics automated proteome annotation pipeline () was utilised to infer homology for each protein domain in the genome, for the 26 superfamilies most highly represented in the Structural Classification Of Proteins (SCOP) database. This approach enabled us to identify homologues that could not be detected by sequence-based methods alone. For each superfamily, we investigated the distribution, both within and among chromosomes, of genes encoding at least one domain within the superfamily. The results indicate a diversity of clustering behaviours: some superfamilies showed no evidence of any clustering, and others displayed significant clustering either within or among chromosomes, or both. Removal of tandem repeats reduced the levels of clustering observed, but some superfamilies still displayed highly significant clustering. Thus, our study suggests that either the process of gene duplication, or the evolution of the resulting clusters, differs between structural superfamilies.

We screened for variation in the 12 protocadherin gamma A (PCDHGA) genes of the protocadherin cluster on chromosome 5q31. We used denaturing high-performance liquid chromatography followed by sequencing to identify changes in the DNA sequence. We identified 24 nonsynonymous changes, 24 synonymous SNPs, and 9 polymorphisms in the 5' flanking regions. The variant with the greatest predicted impact on the encoded protein was a frameshift polymorphism in PCDHGA8, caused by a deletion of one C base (Pro174fsdelC). The del variant was more common in 512 controls compared to 506 schizophrenic (SZ) cases (10.6% vs 7.2%, p=0.007) but this trend was not replicated in an independent sample of 403 trios, in which it was transmitted 47 times and not transmitted 55 times from heterozygous parents (p=0.43). We screened 10 of the common polymorphisms for association with schizophrenia by genotyping pooled DNA from 540 SZ cases and 540 controls, but none of them showed a significant difference. It will be important to identify the phenotype associated with the loss of the PCDHGA8 gene.

The cadherin superfamily is a large protein family with diverse structures and functions. Because of this diversity and the growing biological interest in cell adhesion and signaling processes, in which many members of the cadherin superfamily play a crucial role, it is becoming increasingly important to develop tools to manage, distribute and analyze sequences in this protein family. Current profile and motif databases classify protein sequences into a broad spectrum of protein superfamilies, however to provide a more specific functional annotation, the next step should include classification of subfamilies of these protein superfamilies. Here, we present a tool that classified greater than 90% of the proteins belonging to the cadherin superfamily found in the SWISS PROT database. Therefore, for most members of the cadherin superfamily, this tool can assist in adding more specific functional annotations than can be achieved with current profile and motif databases. Finally, the classification tool and the results of our analysis were integrated into a web-accessible database (http://calcium.uhnres. utoronto.ca/cadherin).

Cadherins play an important role in specific cell-cell adhesion events. Their expression appears to be tightly regulated during development and each tissue or cell type shows a characteristic pattern of cadherin molecules. Inappropriate regulation of their expression levels or functionality has been observed in human malignancies, in many cases leading to aggravated cancer cell invasion and metastasis. The cadherins form a superfamily with at least six subfamilies, which can be distinguished on the basis of protein domain composition, genomic structure, and phylogenetic analysis of the protein sequences. These subfamilies comprise classical or type-I cadherins, atypical or type-II cadherins, desmocollins, desmogleins, protocadherins and Flamingo cadherins. In addition, several cadherins clearly occupy isolated positions in the cadherin superfamily (cadherin-13, -15, -16, -17, Dachsous, RET, FAT, MEGF1 and most invertebrate cadherins). We suggest a different evolutionary origin of the protocadherin and Flamingo cadherin genes versus the genes encoding desmogleins, desmocollins, classical cadherins, and atypical cadherins. The present phylogenetic analysis may accelerate the functional investigation of the whole cadherin superfamily by allowing focused research of prototype cadherins within each subfamily., (Copyright 2000 Academic Press.)

We have identified 52 novel human cadherin-like genes organized into three closely linked clusters. Comparison of the genomic DNA sequences with those of representative cDNAs reveals a striking genomic organization similar to that of immunoglobulin and T cell receptor gene clusters. The N-terminal extracellular and transmembrane domains of each cadherin protein are encoded by a distinct and unusually large exon. These exons are organized in a tandem array. By contrast, the C-terminal cytoplasmic domain of each protein is identical and is encoded by three small exons located downstream from the cluster of N-terminal exons. This unusual organization has interesting implications regarding the molecular code required to establish complex networks of neuronal connections in the brain and the mechanisms of cell-specific cadherin-like gene expression.

The formation of supracellular structures, i.e. tissues and organs, is dependent on the spatially and temporally regulated formation of semistable cell-cell contacts. In recent years, the molecular components of such cell junctions, especially those occurring in epithelial cells, have been studied extensively, and the main proteins and glycoproteins of the 'adhering junctions' such as the desmosomes and the zonula adherens of polar epithelial cells have been characterized. We are now beginning to understand the complex protein-protein interactions that contribute to the assembly and disassembly of these structures and their roles in the attachment of specific filaments of the cytoskeleton.

Cadherins are a multigene family of proteins which mediate homophilic calcium-dependent cell adhesion and are thought to play an important role in morphogenesis by mediating specific intercellular adhesion. Different lines of experimental evidence have recently indicated that the site responsible for mediating adhesive interactions is localized to the first extracellular domain of cadherin. Based upon an analysis of the sequence of this domain, I show that cadherins can be classified into three groups with distinct structural features. Furthermore, using this sequence information a phylogenetic tree relating the known cadherins was assembled. This is the first such tree to be published for the cadherins. One cadherin subtype, neural cadherin (N-cadherin), shows very little sequence divergence between species, whereas all other cadherin subtypes show more substantial divergence, suggesting that selective pressure upon this domain may be greater for N-cadherin than for other cadherins. Phylogenetic analysis also suggests that the gene duplications which established the main branches leading to the different cadherin subtypes occurred very early in their history. These duplications set the stage for the diversified superfamily we now observe.