Protocadherin-Gamma Gene Cluster

A number sign (#) is used with this entry because it represents what has historically been considered a gene cluster on chromosome 5q31. The 22 tandemly arranged genes within this cluster, PCDHGA1 (606288), PCDHGA2 (606289), PCDHGA3 (606290), PCDHGA4 (606291), PCDHGA5 (606292), PCDHGA6 (606293), PCDHGA7 (606294), PCDHGA8 (606295), PCDHGA9 (606296), PCDHGA10 (606297), PCDHGA11 (606298), PCDHGA12 (603059), PCDHGB1 (606299), PCDHGB2 (606300), PCDHGB3 (606301), PCDHGB4 (603058), PCDHGB5 (606302), PCDHGB6 (606303), PCDHGB7 (606304), PCDHGC3 (603627), PCDHGC4 (606305), and PCDHGC5 (606306), function as 'variable' exons that are individually spliced to a downstream constant region (PCDHGCT) to form distinct PCDHG transcripts.

Description

Cadherins are calcium-dependent cell-cell adhesion molecules, and protocadherins constitute a subfamily of nonclassic cadherins. The PCDHG gene cluster encodes a family of protocadherins. Multiple PCDHG mRNAs are produced by splicing a single variable exon to 3 constant region exons. Each variable exon encodes the extracellular and transmembrane domains of the protocadherin protein, and the constant region exons encode the intracellular domain (Wu et al., 2001).

Cloning and Expression

By EST database searching for cadherin-like sequences, Wu and Maniatis (1999) identified 52 novel genes organized into 3 closely linked tandem clusters, alpha (604966), beta (604967), and gamma, on human chromosome 5q31. A distinct large, uninterrupted exon of approximately 2,400 nucleotides encodes the 6 N-terminal extracellular domains and the transmembrane domain of each protocadherin. The C termini of the PCDHA and PCDHG proteins are identical within each cluster and are encoded by 3 small exons located downstream from each array of N-terminal exons. Each large exon is independently spliced to the first exon encoding the intracellular domain. Wu and Maniatis (1999) denoted the extracellular portion as the variable region and the cytoplasmic portion as the constant region. In contrast to the PCDHA and PCDHG clusters, the PCDHB gene cluster does not have a downstream constant region, and the C-terminal cytoplasmic domains of PCDHB proteins are therefore encoded by the single-exon PCDHB genes (Vanhalst et al., 2001). Wu and Maniatis (1999) proposed 4 models to explain protocadherin gene regulation and noted that several neurologic disorders map to chromosome 5q31.

Wu and Maniatis (1999) determined that the PCDHG cluster contains at least 22 genes. Based on sequence similarities, the PCDHG cluster could be divided into subfamilies A, B, and C. In general, the N-terminal extracellular and transmembrane domains of PCDHG proteins are similar to those of PCDHA and PCDHB proteins. The exons encoding the variable regions of the PCDHGC proteins are distinct from those encoding the PCDHGA and PCDHGB variable regions and are located relatively far from the PCDHGA and PCDHGB variable exons. PCDHGC variable exons are more closely related to the C-type protocadherins in the PCDHA cluster. The cytoplasmic regions of the PCDHA and PCDHG proteins are distinct, although both share a similarly located lysine-rich motif. The first 2 exons of the PCDHA constant region encode 2 PXXP motifs, a putative SH3 protein-binding site, whereas those of the PCDHG constant region do not.

By in situ hybridization using a probe directed against the Pcdhg common exons, Wang et al. (2002) found strong Pcdhg expression in the central and peripheral nervous systems of embryonic mice, with weaker expression in meninges and skeletal muscle. In brain, broad Pcdhg expression persisted into adulthood, with highest levels in cortex, hippocampus, and cerebellum. Using probes directed against Pcdhg variable exons, Wang et al. (2002) found that individual neurons expressed subsets of Pcdhg genes. Western blot analysis of fractionated brain lysates showed that Pcdhg proteins were present in synaptosomes and enriched in the postsynaptic density fraction.

By in situ hybridization and PCR analysis, Zou et al. (2007) found that some Pcdha and Pcdhg isoforms were widely expressed in specific cell types throughout various rat brain regions and spinal cord. In most central nervous system regions, labeling with a constant region probe was stronger and appeared in more cells than labeling with individual variable exon probes, consistent with splicing of variable exons to a common set of constant exons. However, in some cases, such as cerebellum for the PCDHA cluster, signals from the constant region probe were not much stronger than those from individual variable exon probes, suggesting expression of variable-only isoforms.

PCDHG Antisense Transcripts

A cis-antisense gene pair is defined as a pair of genes residing on opposite strands in the same locus with at least 1 exon of one gene overlapping at least 1 exon of the other gene. Cis-antisense transcripts function in gene regulation at both the transcriptional and posttranscriptional levels. By in silico analysis of the PCDH gene clusters, Lipovich et al. (2006) identified 12 cis-antisense transcriptional units. Those with greatest EST support were anti-PCDHA12 (606318), anti-PCDHB3 (606329), and anti-PCDH5 pseudogene, which is located in the PCDHG gene cluster. All appeared to be noncoding. These antisense transcripts were conserved in chimpanzee and rhesus, but not in mouse. PCR analysis verified expression of these antisense transcripts in adult and fetal human brain and in rhesus brain, and the presence of antisense transcripts was associated with significantly reduced sense expression levels across all orthologs.

Gene Structure

Wu et al. (2001) determined that the PCDHG gene cluster spans about 300 kb and contains 22 genes, which function as variable first exons, followed by 3 small constant region exons. By comparative sequence analysis of human and mouse PCDH gene clusters, Wu et al. (2001) determined that there are high ratios of CpG dinucleotide islands near the 5-prime ends of each PCDH variable region exon. Their results indicated that each variable region exon has its own promoter, which is highly conserved between orthologous variable region exons in mouse and human. They also found that regions 5-prime of the PCDHGC variable region exons have large conserved segments. In addition, the regions downstream of the last C-type variable region exons in the alpha and gamma clusters, PCDHAC2 (606321) and PCDHGC5, respectively, are also conserved.

Tasic et al. (2002) showed that each PCDH variable exon is preceded by a promoter and that promoter choice determines which variable exon is included in a PCDH mRNA. In addition, they provided evidence that alternative splicing of variable exons within a gene cluster occurs via a cis-splicing mechanism. However, virtually every variable exon can engage in trans-splicing with constant exons from another cluster, albeit at a far lower level.

Gene Function

Lefebvre et al. (2012) found that deletion of all 22 Pcdh genes in the mouse gamma-subcluster (Pcdhg genes) disrupts self-avoidance of dendrites in retinal starburst amacrine cells (SACs) and cerebellar Purkinje cells. Further genetic analysis of the SACs showed that Pcdhg proteins act cell-autonomously during development, and that replacement of the 22 Pcdhg proteins with a single isoform restores self-avoidance. Moreover, expression of the same single isoform in all SACs decreased interactions among dendrites of neighboring SACs (heteroneuronal interactions). These results suggested that homophilic Pcdhg interactions between 'sibling neurites' (isoneuronal interactions) generate a repulsive signal that leads to self-avoidance. In this model, heteroneuronal interactions are normally permitted because dendrites seldom encounter a matched set of Pcdhg proteins unless they emanate from the same soma. Lefebvre et al. (2012) concluded that in many respects, their results mirrored those reported for Dscam1 (Down syndrome cell adhesion molecule; 602523) in Drosophila: this complex gene encodes thousands of recognition molecules that exhibit stochastic expression and isoform-specific interactions, and mediate both self-avoidance and self/nonself discrimination. Although Dscam and Pcdh proteins share no sequence homology, they seem to underlie similar strategies for endowing neurons with distinct molecular identities and patterning their arborizations.

Mountoufaris et al. (2017) showed that the PCDH-alpha (604966), PCDH-beta (604967), and PCDH-gamma gene clusters functionally cooperate to provide individual mouse olfactory sensory neurons with the cell surface diversity required for their assembly into distinct glomeruli in the olfactory bulb. Although deletion of individual Pcdh clusters had subtle phenotypic consequences, the loss of all 3 clusters led to a severe axonal arborization defect and loss of self-avoidance. By contrast, when endogenous Pcdh diversity is overridden by the expression of a single-tricluster gene repertoire (alpha and beta and gamma), olfactory sensory neuron axons fail to converge to form glomeruli, likely owing to contact-mediated repulsion between axons expressing identical combinations of Pcdh isoforms.

Mapping

By genomic sequence analysis, Wu and Maniatis (1999) mapped the PCDHG gene cluster to chromosome 5q31.

Animal Model

Wang et al. (2002) found that deletion of the entire Pcdhg region in mice did not alter early steps in neuronal migration, axon outgrowth, and synapse formation. However, at late embryonic stages, mice lacking Pcdhg showed dramatic neurodegeneration leading to neonatal death. Many interneurons were lost in mutant spinal cord, but sensory and motor neurons were relatively spared. In culture, mutant spinal cord neurons differentiated and formed synapses, but then died, whereas mutant hippocampal neurons flourished. Wang et al. (2002) concluded that the PCDHG genes are required for survival of specific neuronal subtypes.