Isolation and genomic arrangement of active and inactive forms of mammalian 5 S RNA genes

Genomic DNA fragments containing sequences homologous to 5 S rRNA have been isolated from humans and mice. When transcribed in a cell-free system (S100) derived from human HeLa cells, these cloned fragments show qualitative and quantitative differences with respect to 5 S rRNA synthesis and with respect to the synthesis of larger RNA polymerase III transcripts in the 300-600-nucleotide range. One mouse and one human clone have been characterized in detail. The clone containing the mouse 5 S gene is active in an in vitro transcription system and generates a 5 S transcript which differs in five RNase T1 oligonucleotides from mouse 5 S rRNA. In contrast, the clone containing the human 5 S gene is transcriptionally inactive for a 5 S-sized RNA product in vitro. Both clones serve as active templates for multiple RNA transcripts which share sequence homology with the human Alu family. These transcripts, as well as cloned Alu sequences used as hybridization probes, map to sites within close proximity of the 5 S gene in both the mouse and human clones. These functionally heterogeneous 5 S genes are arranged in a manner similar to the bulk of 5 S rRNA genes within their respective genomes and may be interspersed among them. The repeat lengths for DNA fragments containing these genes are considerably longer (2.8 and 6 kilobases) than observed for 5 S genes in other organisms and may indicate that larger repeat units are a characteristic feature of mammalian 5 S genes.