Genomic organization, expression, and comparative analysis of noncoding region of the rat Ndrg4 gene

Rat Ndrg4 is a member of the NDRG gene family and has been suggested to relate to brain development. The structure of the rat Ndrg4 gene was studied to understand the mechanism for the expression of multiple forms of Ndrg4 protein, which were revealed in the brain. Subcloning and DNA sequencing analysis of a bacterial artificial chromosome (BAC) clone, together with analysis of a transcriptional start site by a cap-site hunting, indicated that the Ndrg4 gene spans about 39 kilobases (kb) and consists of 19 exons, in which the first and second exons were first found in rat. An alternative promoter usage at different transcriptional start sites may produce three types of messages, Ndrg4-A, Ndrg4-B, and Ndrg4-C, and there is a variant that lacks exon 18 for each type of transcript. Thereby, Ndrg4-A1, Ndrg4-A2, Ndrg4-B1, Ndrg4-B2, Ndrg4-C1, and Ndrg4-C2 were identified to be expressed. These six variants might explain the heterogeneity of the Ndrg4 protein in the brain. The variants without exon 18 were revealed in the embryonic and early postnatal brains while those with exon 18 were detected in the maturing and adult brains. Radiation hybrid mapping suggests that the rat Ndrg4 gene is located on chromosome 19 at 90.6 centirays (cR) from the top. Comparison of the noncoding sequence of the rat Ndrg4 gene to those of the orthologous mouse and human genes suggests that the AP-1 binding site is a candidate regulatory element.