Analysis of a gene encoding two glycine transporter variants reveals alternative promoter usage and a novel gene structure.

Abstract The rat GLYT-1 gene encodes two glycine transporter variants, GLYT-1a and GLYT-1b, that differ in NH2 termini and 5′-noncoding regions as well as in tissue distribution. The GLYT-1 gene contains 15 exons, with the first two specific for GLYT-1a and the third specific for GLYT-1b. By combining RNase protection and rapid amplification of cDNA ends analysis, we have determined transcription start sites for GLYT-1a and GLYT-1b. By using a functional luciferase reporter assay, we demonstrate that distinct promoters regulate the expression of these transporters in several cell lines. Serially truncated GLYT-1b promoter constructs reveal a basal promoter within 304 base pairs of the transcription start site, possible negative regulatory elements between −304 and −1310, and additional positive regulatory elements between −1310 and −5264. The GLYT-1 gene contains three sets of dinucleotide repeats, two AC repeats, and one TG repeat which may form stem-loop structures to either facilitate or interfere with transcription of one of the transporter isoforms. The potential use of dinucleotide repeats in this manner would represent a novel mechanism for gene splicing. The use of distinct promoters for GLYT-1a and GLYT-1b suggests that these transporters have unique regulatory requirements that may reflect the differential tissue-specific expression patterns in white matter (GLYT-1b) and gray matter (GLYT-1a).