Neural BC1 RNA: cDNA clones reveal nonrepetitive sequence content.

BC1 is a small developmentally regulated RNA that is prevalent in nervous tissue. In order to determine if BC1 RNA represents the transcriptional by-product of various repetitive brain identifier (ID) elements or the independent transcript of a single or a few genes, we compared the sequences of a population of cDNA clones derived from in vitro C-tailed BC1 RNA. Each of 10 randomly selected clones revealed a 5' domain that was identical in sequence to the ID element, followed by an internal region of poly(A). In 8 of the clones, we found an identical, nonrepetitive sequence domain located at the 3' end of each molecule. An oligonucleotide of 30 residues complementary to this section identified only BC1 RNA in blot-hybridization analysis. Our results strongly suggest that BC1 RNA is transcribed specifically from the BC1 gene(s) and is not a highly heterogeneous population of ID-containing RNA polymerase III transcripts. Moreover, the availability of a unique BC1 RNA sequence will facilitate studies on tissue- and stage-specific gene regulation and will help in clarifying the role of this small RNA in the brain.