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

Abstract The clustered protocadherins (Pcdh) are encoded by three closely linked gene clusters (Pcdh-α, -β, and -γ) that span nearly 1 million base pairs of DNA. The Pcdh-α 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-α 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 α1–12 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-α 1–12 V exons, one from each chromosome. The two remaining V exons in the cluster (Pcdh-αC1 and αC2) are expressed biallelically in every neuron. The mechanisms that underlie promoter choice and monoallelic expression in the Pcdh-α gene cluster are not understood. Here we report the identification of two long-range cis-regulatory elements in the Pcdh-α gene cluster, HS5–1 and HS7. We show that HS5–1 is required for maximal levels of expression from the Pcdh α1–12 and αC1 promoters, but not the Pcdh-αC2 promoter. The nearly cluster-wide requirement of the HS5–1 element is consistent with the possibility that the monoallelic expression of Pcdh-α V exons is a consequence of competition between individual V exon promoters for the two regulatory elements. gene regulation transcription enhancer monoallelic expression