Total DNA transcription reveals the existence of highly repetitive transcribable sequences in higher animals

Using HeLa S-100 extracts, we have transcribed total DNA isolated from several species of higher animals. Transcription of the total DNA from rat, mouse, or hamster gives a discrete product of 6S RNA (about 180 nucleotides) in addition to a smeared background, whereas transcription from chick, calf, or human DNA gives a discrete band of 5S RNA (about 120 nucleotides). In view of the sensitivity to a-amanitin, these transcripts are produced by RNA polymerase III. Fingerprint analysis demonstrated that the 6S RNA species transcribed from rodent DNA have conserved sequences. The composition of dinucleotides in these bands having a guanosine residue on the 3' side was analyzed by RNase T2 digestion. The results show that the CG ratios of the transcripts of rodent, calf and chick are quite low in comparison with AG, UG, or GG except in the case of the human transcript, suggesting that these highly repetitive transcribable sequences are derived from a common prototype sequence, except in human cells. We have isolated two phage clones and one phage clone from a rat and mouse genomic library, respectively, which give a transcript of 180 nucleotides in size, and whose pattern of RNase T2 digests is the same as that of the conserved transcriptional products of total DNA. These highly repetitive transcribable sequences appear to be reiterated at several to ten thousand copies per haploid genome. The relationship of these sequences with the highly repetitive interspersed sequence B1 or Alu family is discussed.