Two novel CNRs from the CNR gene cluster have molecular features distinct from those of CNR1 to 8

Sorting out a promiscuous superfamily: towards cadherin connectomics

Members of the cadherin superfamily of proteins are involved in diverse biological processes such as morphogenesis, sound transduction, and neuronal connectivity. Key to cadherin function is their extracellular domain containing cadherin repeats, which can mediate interactions involved in adhesion and cell signaling. Recent cellular, biochemical, and structural studies have revealed that physical interaction among cadherins is more complex than originally thought. Here we review work on new cadherin complexes and discuss how the classification of the mammalian family can be used to search for additional cadherin-interacting partners. We also highlight some of the challenges in cadherin research; namely, the characterization of a cadherin connectome in biochemical and structural terms, as well as the elucidation of molecular mechanisms underlying the functional diversity of nonclassical cadherins in vivo.

Clustered protocadherins and neuronal diversity

Neuronal diversity is a fundamental requirement for complex neuronal networks and brain function. The clustered protocadherin (Pcdh) family possesses several characteristic features that are important for the molecular basis of neuronal diversity. Clustered Pcdhs are expressed predominantly in the central nervous system, in neurites, growth cones, and synapses. They consist of about 60 isoforms, and their expression is stochastically and combinatorially regulated in individual neurons. The multiple clustered Pcdhs expressed in individual neurons form heteromultimeric protein complexes that exhibit homophilic adhesion properties. Theoretically, the clustered Pcdhs could generate more than 3×10(10) possible variations in each neuron and 12,720 types of cis-tetramers per neuron. The clustered Pcdhs are important for normal neuronal development. The clustered Pcdh genes have also attracted attention as a target for epigenetic regulation.

Identification of the cluster control region for the protocadherin-beta genes located beyond the protocadherin-gamma cluster

The clustered protocadherins (Pcdhs), Pcdh-α, -β, and -γ, are transmembrane proteins constituting a subgroup of the cadherin superfamily. Each Pcdh cluster is arranged in tandem on the same chromosome. Each of the three Pcdh clusters shows stochastic and combinatorial expression in individual neurons, thus generating a hugely diverse set of possible cell surface molecules. Therefore, the clustered Pcdhs are candidates for determining neuronal molecular diversity. Here, we showed that the targeted deletion of DNase I hypersensitive (HS) site HS5-1, previously identified as a Pcdh-α regulatory element in vitro, affects especially the expression of specific Pcdh-α isoforms in vivo. We also identified a Pcdh-β cluster control region (CCR) containing six HS sites (HS16, 17, 17', 18, 19, and 20) downstream of the Pcdh-γ cluster. This CCR comprehensively activates the expression of the Pcdh-β gene cluster in cis, and its deletion dramatically decreases their expression levels. Deleting the CCR nonuniformly down-regulates some Pcdh-γ isoforms and does not affect Pcdh-α expression. Thus, the CCR effect extends beyond the 320-kb region containing the Pcdh-γ cluster to activate the upstream Pcdh-β genes. Thus, we concluded that the CCR is a highly specific regulatory unit for Pcdh-β expression on the clustered Pcdh genomic locus. These findings suggest that each Pcdh cluster is controlled by distinct regulatory elements that activate their expression and that the stochastic gene regulation of the clustered Pcdhs is controlled by the complex chromatin architecture of the clustered Pcdh locus.

Total expression and dual gene-regulatory mechanisms maintained in deletions and duplications of the Pcdha cluster

The clustered protocadherin-alpha (Pcdha) genes, which are expressed in the vertebrate brain, encode diverse membrane proteins whose functions are involved in axonal projection and in learning and memory. The Pcdha cluster consists of 14 tandemly arranged genes (Pcdha1-Pcdha12, Pcdhac1, and Pcdhac2, from 5' to 3'). Each first exon (the variable exons) is transcribed from its own promoter, and spliced to the constant exons, which are common to all the Pcdha genes. Cerebellar Purkinje cells show dual expression patterns for Pcdha. In individual Purkinje cells, different sets of the 5' genes in the cluster, Pcdha1-12, are randomly expressed, whereas both 3' genes, Pcdhac1 and Pcdhac2, are expressed constitutively. To elucidate the relationship between the genomic structure of the Pcdha cluster and their expression in Purkinje cells, we deleted or duplicated multiple variable exons and analyzed the expression of Pcdha genes in the mouse brain. In all mutant mice, transcript levels of the constant exons and the dual expression patterns were maintained. In the deletion mutants, the missing genes were flexibly compensated by the remaining variable exons. On the other hand, in duplication mutants, the levels of the duplicated genes were trimmed. These results indicate that the Pcdha genes are comprehensively regulated as a cluster unit, and that the regulators that randomly and constitutively drive Pcdha gene expression are intact in the deleted or duplicated mutant alleles. These dual regulatory mechanisms may play important roles in the diversity and fundamental functions of neurons.

The protocadherin-alpha family is involved in axonal coalescence of olfactory sensory neurons into glomeruli of the olfactory bulb in mouse

Olfactory sensory neurons (OSNs) that express the same odorant receptor project their axons to specific glomeruli in the main olfactory bulb. Protocadherin-alpha (Pcdha) proteins, diverse cadherin-related molecules that are encoded as a gene cluster, are highly concentrated in OSN axons and olfactory glomeruli. Here, we describe Pcdha mutant mice, in which the constant region of the Pcdha gene cluster has been deleted by gene targeting. The mutant mice show abnormal sorting of OSN axons into glomeruli. There are multiple, small, extraneous glomeruli for the odorant receptors M71 and MOR23. These abnormal patterns of M71 and MOR23 glomeruli persist until adulthood. Many M71 glomeruli, but apparently not MOR23 glomeruli, are heterogeneous in axonal innervation. Thus, Pcdha molecules are involved in coalescence of OSN axons into OR-specific glomeruli of the olfactory bulb.

Identification of long-range regulatory elements in the protocadherin-alpha gene cluster

The clustered protocadherins (Pcdh) are encoded by three closely linked gene clusters (Pcdh-alpha, -beta, and -gamma) that span nearly 1 million base pairs of DNA. The Pcdh-alpha gene cluster encodes a family of 14 distinct cadherin-like cell surface proteins that are expressed in neurons and are present at synaptic junctions. Individual Pcdh-alpha mRNAs are assembled from one of 14 "variable" (V) exons and three "constant" exons in a process that involves both differential promoter activation and alternative pre-mRNA splicing. In individual neurons, only one (and rarely two) of the Pcdh alpha1-12 promoters is independently and randomly activated on each chromosome. Thus, in most cells, this unusual form of monoallelic expression leads to the expression of two different Pcdh-alpha 1-12 V exons, one from each chromosome. The two remaining V exons in the cluster (Pcdh-alphaC1 and alphaC2) are expressed biallelically in every neuron. The mechanisms that underlie promoter choice and monoallelic expression in the Pcdh-alpha gene cluster are not understood. Here we report the identification of two long-range cis-regulatory elements in the Pcdh-alpha gene cluster, HS5-1 and HS7. We show that HS5-1 is required for maximal levels of expression from the Pcdh alpha1-12 and alphaC1 promoters, but not the Pcdh-alphaC2 promoter. The nearly cluster-wide requirement of the HS5-1 element is consistent with the possibility that the monoallelic expression of Pcdh-alpha V exons is a consequence of competition between individual V exon promoters for the two regulatory elements.

Allelic gene regulation of Pcdh-alpha and Pcdh-gamma clusters involving both monoallelic and biallelic expression in single Purkinje cells

The molecular basis for providing the identity and diversity of single neurons is a key for realizing the brain system. Diverse protocadherin isoforms encoded by the Pcdh-alpha and Pcdh-gamma gene clusters are expressed in all of the vertebrates studied. For the Pcdh-alpha isoforms, differential expression patterns have been found in single Purkinje cells by unusual monoallelic and combinatorial types of gene regulation. Here we investigated total allelic gene regulation in the Pcdh-alpha and -gamma clusters, including the C-type variable exons (C1 to C5) and the Pcdh-gammaA and -gammaB variable exons in single Purkinje cells. Using split single-cell reverse transcription-PCR analysis, almost all of the Purkinje cells at postnatal day 21 biallelically expressed all the C-type isoforms, whereas the Pcdh-alpha isoforms showed both monoallelic and combinatorial expression. The Pcdh-gammaA and -gammaB isoforms also showed differential regulation in each cell with both monoallelic and combinatorial gene regulation. These data indicated that different types of allelic gene regulation (monoallelic versus biallelic) occurred in the Pcdh-alpha and -gamma clusters, although they were spliced into the same constant exons. It has been reported that each C-type Pcdh-alpha or -gamma transcript has a different expression pattern during brain development, suggesting that the different C-type variable exons may code temporal diversity, although the Pcdh-alpha, -gammaA, and -gammaB isoforms were differential and combinatorial gene regulation within a single cell. Thus, the multiple gene regulations in the Pcdh-alpha and -gamma clusters had a potential mechanism for increasing the diversity of individual neurons in the brain.

Cytoplasmic domain of protocadherin-α enhances homophilic interactions and recognizes cytoskeletal elements

Cell adhesion molecules of the protocadherin-alpha (pcdh-alpha), -beta, and -gamma families have been proposed to be synaptic specifiers. Pcdh-alpha and -gamma family members localize in part to synapses, and deletion of all pcdh-gammas in mouse affects synaptogenesis. Little is known, however, about the binding specificities and intracellular signaling of protocadherins. Using heterologous expression of tagged constructs, immunostaining, and biotinylation of surface components followed by Western blots we demonstrate that pcdh-alphas undergo homophilic interactions that are significantly enhanced by the cytoplasmic domain. Pcdh-alphas cloned from chick ciliary ganglion have one of two cytoplasmic constant regions (A- and B-types). Screening a yeast two-hybrid library of ciliary ganglion cDNA with the A-type domain yielded a fragment of neurofilament M (NFM); screening with B-type domain yielded a fragment of the actin-bundling protein fascin. Cotransfection of HEK cells with the constructs indicated that the NFM and A-type fragments codistributed as did the fascin and B-type fragments, and the latter could be coimmunoprecipitated. Antibody-induced clustering of full-length pcdh-alphas on the surface of transfected HEK cells induced coclustering of the interacting NFM fragment. Native full-length NFM in tissue extracts bound specifically to the A-type domain on beads, while native full-length fascin in tissue extracts specifically coimmunoprecipitated with pcdh-alpha. Immunostaining neurons demonstrated codistribution of full-length pcdh-alpha with both NFM and actin filaments. These findings suggest cytoskeletal links for pcdh-alphas and identify candidate targets. They also demonstrate homophilic interactions for pcdh-alphas as described for classical cadherins.

CNR/Pcdhalpha family in subplate neurons, and developing cortical connectivity

The cadherin-related neuronal receptor (CNR)/protocadherin (Pcdh) alpha family is one of the diverse protocadherin families identified as a candidate diversified membrane-associated component regulating the formation of neuronal connectivity. However, its expression during neural circuit formation has not been examined in detail. Here, we used a conserved sequence to study the expression of this protein family during the development of neocortical connectivity, by immunohistochemistry and in situ hybridization. The proteins were detected in developing thalamocortical and corticofugal axons, and in subplate neurons, which pioneer these axon tracts. The expression in subplate neurons was confirmed by birth-date labeling with BrdU, and by examination in homozygous reeler mice. This pattern of CNR/Pcdhalpha expression suggests its involvement in the development of neocortical connectivity.

Interaction with Protocadherin-γ Regulates the Cell Surface Expression of Protocadherin-α

The protocadherin-alpha (CNR/Pcdhalpha) and protocadherin-gamma (Pcdhgamma) proteins, members of the cadherin superfamily, are putative cell recognition/adhesion molecules in the brain. Overexpressed cadherins are generally expressed on the cell surface and elicit cell adhesion activity in several cell lines, although hardly any overexpressed CNR/Pcdhalpha proteins are expressed on the cell surface, except on HEK293T cells, which show low expression. We analyzed the expression of CNR/Pcdhalpha and Pcdhgamma in HEK293T cells and found that they formed a protein complex and that Pcdhgamma enhanced the surface expression of CNR/Pcdhalpha. This enhanced surface expression was confirmed by flow cytometry analysis and by marking cell surface proteins with biotin. The enhancement was observed using different combinations of CNR/Pcdhalpha and Pcdhgamma proteins. The surface expression activity was enhanced by the extracellular domains of the proteins, which could bind each other. Their cytoplasmic domains also had binding activity and influenced their localization. Their protein-protein interaction was also detected in extracts of mouse brain and two neuroblastoma cell lines. Thus, interactions between CNR/Pcdhalpha and Pcdhgamma regulate their surface expression and contribute to the combinatorial diversity of cell recognition proteins in the brain.

Alpha-protocadherins are presynaptic and axonal in nicotinic pathways

The protocadherin families pcdh-alpha, beta, and gamma have been proposed to mediate synaptic specificity via homophilic interactions. Here we report isolation of two pcdh-alpha family members from chick. We find pcdh-alpha mRNA in multiple regions of chick CNS including cerebellum, tectum, olfactory bulb, and forebrain, and in the autonomic nervous system. Immunoblots identify major components of 120 and 140 kDa both in brain and ciliary ganglion extracts. Immunohistochemistry reveals pcdh-alphas in axons and perisynaptically in preganglionic terminals, adjacent to transmitter release sites. Pcdh-alphas appear to be absent from postsynaptic sites: They are nonoverlapping with postsynaptic receptor clusters in the ganglion and are rapidly lost after ganglionic denervation. Similar pcdh-alpha patterns are found in motor axons and at neuromuscular junctions of birds and mammals, and persist into adulthood. The results indicate that pcdh-alphas are widely expressed in nicotinic cholinergic pathways and may engage in heterophilic interactions at synapses and on axons.

Cadherin-related neuronal receptor 1 (CNR1) has cell adhesion activity with β1 integrin mediated through the RGD site of CNR1

Cadherin-related neuronal receptor (CNR) proteins are a diverse set of synaptic protocadherins, but little is known about its adhesive properties. We found that overexpressed CNR1 protein localized on the cell surface of HEK293T cells and increased the calcium-dependent cell aggregation potential. However, we could not detect the strong homophilic binding activity of CNR1 EC-Fc fusion protein in vitro. Parental HEK293T cells adhered to Arg-Gly-Asp (RGD) motif of EC1 domain of CNR1-Fc fusion protein. The fusion protein that the Asp73 of EC1 point-mutated to Glu (RGE-Fc) lost the adhesive activity. The adhesion activity of HEK293T cells to CNR1 EC-Fc fusion protein was completely blocked by inhibitors of integrins, including RGDS peptide and anti-beta1 integrin antibodies. The increased cell-aggregative property of CNR1 transfectants was also blocked by RGDS peptides. At cell-cell junctions of the CNR1 transfectants, co-localization between CNR1 and HEK293T endogenous beta1 integrin was observed. Furthermore, the spatiotemporal expression patterns of CNR and beta1 integrin nearly overlapped in the molecular layer of the developing mouse cerebellum in the main stage of synaptogenesis. These results indicate that CNR1 has a heterophilic, calcium-dependent cell adhesion activity with the beta1 integrin subfamily, and raise the possibility of CNR-beta1 integrin association in synaptogenesis.

Protocadherins

Protocadherins constitute the largest subgroup within the cadherin family of calcium-dependent cell-cell adhesion molecules. Recent progress in genome sequencing has enabled a refined phylogenetic analysis of protocadherins and led to the discovery of three large protocadherin clusters on human chromosome 5/mouse chromosome 18. Interestingly, many of the circa 70 protocadherins in mammals are highly expressed in the central nervous system. Roles in tissue morphogenesis and formation of neuronal circuits during early vertebrate development have been inferred. In the postnatal brain, protocadherins are possibly involved in the modulation of synaptic transmission and the generation of specific synaptic connections.

The cadherin-related neuronal receptor family: a novel diversified cadherin family at the synapse

The cadherin-related neuronal receptor (CNR) family has been identified as a receptor family that cooperates with Fyn, a member of the Src family of tyrosine kinases. The CNR family is composed of 14 members in mice and 15 members in humans. The mRNAs of CNRs are highly expressed in the brain and CNR1 protein is localized at synaptic junctions. Hence CNR family proteins are synaptic cadherins. The unique structure of CNR family cDNAs, which is characterized by complete DNA sequence identity among their 3'-termini including a part of the coding region, prompted us to investigate the genomic organization of this family. The genomic organization of CNRs is divided into 'variable' and 'constant' region exons, analogous to immunoglobulin and T cell receptor gene clusters. This organization raised the possibility that the CNR gene cluster may undergo somatic DNA rearrangement or trans-splicing and produce diversified gene products. Although it is not yet clear that the CNR gene cluster in the neuronal genomic DNA is somatically changed, a recent study suggested the occurrence of trans-transcripts and accumulation of somatic mutations in CNR transcripts (Genes Cells 6 (2001) 151). These results suggested that the proteins from the CNR gene cluster are enormously diversified by unique mechanisms. The localization of CNR1 protein at the synapse and the diversity of CNRs led us to the hypothesis that gene regulation of the CNR family dictates the formation and reorganization of synaptic connections in the nervous system.