Non-Alu family interspersed repeats in human DNA and their transcriptional activity

Randomly selected human genomic clones have been surveyed for the presence of non-Alu family interspersed repeats. Four such families of repeats have been isolated and characterized with respect to repetition frequency, interspersion, base sequence, sequence divergence, in vitro RNA polymerase III transcription, elongation of transcripts in isolated nuclei, and in vivo transcription. The two most abundant of the four families of repeats correspond to previously reported families of repeats, namely the kpn I family and poly (CA). We conclude that most of the highly repetitive (greater than 50,000 copies) human interspersed repeats have already been identified. Two lower abundance repeats families are also described here. The abundance with which each of these families is represented in nuclear RNA qualitatively corresponds to their genomic reiteration frequencies. Further, the complementary strands of each repeat family are approximately symmetrically transcribed. The abundance of these repeats in cytoplasmic RNA is qualitatively less than in nuclear RNA. The bulk of the in vivo transcriptional activity of these repeats thus appears to be nonspecific read through from other promoters.