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

In order to identify trinucleotide- and tandem repeat-containing transcript s in human spinal cord, hybridization of a high-density spinal cord cDNA li brary filter was carried out using a radioactively labeled degenerate oligo nucleotide designed to detect different trinucleotide repeats including tho se known to occur in disease-associated expansions, in a single step. The s equence analysis of the trinucleotide repeat-containing transcripts (TNRTs) revealed 23 known mammalian genes with trinucleotide repeat-containing reg ions (TNRs), some of which were not previously reported to contain TNRs, an d 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 ca lcium-dependent protease, ATBF1-A, ferritin H chain, and the G protein Gs a lpha(2). Ten sequences containing perfect TNRs and two sequences containing perfect tandem repeats (derived from 11 TNRTs) were further analyzed for a llelic variation using primers flanking the TNR, and five were shown to exh ibit two to five alleles per TNR, These transcripts were further investigat ed for their chromosomal localization where unknown or only partially chara cterized. The transcripts that were polymorphic in the TNR region were ATBF 1-A (a homeodomain protein), clone 390013 on chromosome Xp11, a member of t he family of the 14.3.3 protein kinase C regulators, a human translation in itiation factor (an isolog of the yeast Suilisol gene 1), and a novel seque nce (TR21), Only the first two transcripts showed the presence of rare expa nded alleles, Characterization of polymorphic TNRs in novel and even known genes expressed in human spinal cord is likely to help in the identificatio n of new candidates for genes involved in neurodegenerative disorders.