Some gene variants for 5 S RNA are dispersed in the rat genome

In the course of studies on genes for small nuclear RNAs, seven lambda phage clones containing sequences homologous to 5 S RNA were plaque purified from a rat genomic library. The seven clones were found to be from six different genomic loci. When the 5 S RNA hybridized to these clones was digested by T1 RNase, only clone 5S-2 protected the RNA completely. Moreover, clone 5S-2 which has five nucleotide substitutions in the internal control region was transcribed 10 times more efficiently than a bonafide Chinese hamster 5S gene. The other clones were less efficiently transcribed than a bonafide 5S gene or not transcribed at all. The number of gene variants for 5 S RNA in the rat genome was approximately 3000. In contrast to the clustering of 5S genes and gene variants found in Xenopus, Drosophila, hamster, mouse, and human cells, the 5S gene variants in the rat genome are dispersed and most contained conserved 3'-flanking sequences. These naturally occurring 5S gene variants may be useful in binding transcription factors that affect 5S genes.