Characterization of trinucleotide- and tandem repeat-containing transcripts obtained from human spinal cord cDNA library by high-density filter hybridization.

Abstract

In order to identify trinucleotide- and tandem repeat-containing transcripts in human spinal cord, hybridization of a high-density spinal cord cDNA library filter was carried out using a radioactively labeled degenerate oligonucleotide designed to detect different trinucleotide repeats including those known to occur in disease-associated expansions, in a single step. The sequence analysis of the trinucleotide repeat-containing transcripts (TNRTs) revealed 23 known mammalian genes with trinucleotide repeat-containing regions (TNRs), some of which were not previously reported to contain TNRs, and 18 cDNA clones with no or insignificant sequence homology to known genes. Amongst the known genes detected was the fragile X gene (FMR-1) containing (CGG)30. Other genes containing extended TNRs of 9 to 21 repeats were calcium-dependent protease, ATBF1-A, ferritin H chain, and the G protein Gsalpha2. Ten sequences containing perfect TNRs and two sequences containing perfect tandem repeats (derived from 11 TNRTs) were further analyzed for allelic variation using primers flanking the TNR, and five were shown to exhibit two to five alleles per TNR. These transcripts were further investigated for their chromosomal localization where unknown or only partially characterized. The transcripts that were polymorphic in the TNR region were ATBF1-A (a homeodomain protein), clone 390013 on chromosome Xp11, a member of the family of the 14.3.3 protein kinase C regulators, a human translation initiation factor (an isolog of the yeast Suilisol gene 1), and a novel sequence (TR21). Only the first two transcripts showed the presence of rare expanded alleles. Characterization of polymorphic TNRs in novel and even known genes expressed in human spinal cord is likely to help in the identification of new candidates for genes involved in neurodegenerative disorders.