A fine physical map of the CACNA1A gene region on 19p13.1–p13.2 chromosome

Abstract

The P/Q-type Ca²⁺ channel α_1A subunit gene (CACNA1A) was cloned on the short arm of chromosome 19 between the markers D19S221 and D19S179 and found to be responsible for Episodic Ataxia type 2, Familial Hemiplegic Migraine and Spinocerebellar Ataxia type 6. This region was physically mapped by 11 cosmid contigs spanning about 1.4 Mb, corresponding to less than 70% of the whole region. The cosmid contig used to characterize the CACNA1A gene accounted only for the coding region of the gene lacking, therefore, the promoter and possible regulation regions. The present study improves the physical map around and within the CACNA1A by giving a complete cosmid or BAC contig coverage of the D19S221–D19S179 interval. A number of new STSs, whether polymorphic or not, were characterized and physically mapped within this region. Four ESTs were also assigned to cosmids belonging to specific contigs.

Introduction

The gene responsible for Episodic Ataxia type 2 (EA2) was mapped within a region of the short arm of chromosome 19 between D19S221 and D19S226 markers (Calandriello et al., 1996). In this region, the P/Q-type Ca²⁺ channel α_1A subunit gene (CACNA1A) was recently cloned and found to be responsible for EA2 and for Familial Hemiplegic Migraine (FHM) (Ophoff et al., 1996). Although, the coding region of the CACNA1A gene has been completely sequenced, the characterization of the gene does not comprise the promoter, the 5′ and 3′ UTR regions and possible transcriptional and translational regulating segments located in introns and flanking regions.

The portion of the ‘high-resolution metric map of chromosome 19’ spanning from D19S221 to D19S179 consisted of 11 ordered cosmid contigs (Ashworth et al., 1995). The sum of intercosmid distances and cosmid sizes suggested the span between the proximal marker D19S179 and the distal marker D19S221 to be about 1.8 Mb. This physical distance corresponds to a recombination distance of about 6 cM on the genetic map (Dib et al., 1996). As determined by EcoRI mapping, these 11 contigs ranged from 55 to 341 kb in size and covered a total of 1396 kb, corresponding to less than 70% of the actual whole region. The present study improves the physical map around and within the CACNA1A gene by giving a complete cosmid/BAC contig coverage. This was done by extending and merging the cosmid contigs coverage of the CACNA1A gene and its controlling region and in a change of the 5′–3′ direction of the gene previously reported (Ophoff et al., 1996), with respect to the centromere. Furthermore, a number of new STSs were characterized and physically mapped within this region. Some were found to be polymorphic, whereas other were not. Four ESTs previously located by radiation hybrid in the region were assigned to cosmids belonging to specific contigs.