Transcription of the KpnI families of long interspersed DNAs in human cells

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Abstract
The mammalian genome contains a variety of interspersed repetitive sequences of unknown function. It has, however, been suggested that interspersed repetitive sequences and their RNA transcripts are involved in the coordinate regulation of gene expression1. Two major families of interspersed sequences in primates are the so-called Alu and KpnI families2–13. Members of the KpnI families range in length from 1.2 to over 6 kilobases (kb). They exist in generally clustered arrangements, in 6 × 104 to 105 copies per diploid genome. Something is known of the arrangements of KpnI family sequences near human structural genes4,7,11,12, but there has been no information on transcription of the sequences. We report here that the KpnI sequences are transcribed in HeLa cells by RNA polymerase II into abundant and heterogeneous species of RNA. The transcripts range in length from about 200 bases to over 5 kb, and are found predominantly in the non-polyadenylated fraction of the nuclear RNA. Transcripts homologous to both of the complementary strands of the KpnI sequences are present, but with a strong bias towards one strand.