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

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 expression. Two major families of interspersed sequences in primates are the so-called Alu and KpnI families. Members of the KpnI families range in length from 1.2 to over 6 kilobases (kb). They exist in generally clustered arrangements, in 6 X 10(4) to 10(5) copies per diploid genome. Something is known of the arrangements of KpnI family sequences near human structural genes, 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.

Transcriptional "silencer" element in rat repetitive sequences associated with the rat insulin 1 gene locus.

“…Variation in sequences at this locus may, in fact, influence expression of the rI gene in the particular strain of rat. While a subset of LINE sequences are transcribed as nuclear RNA, not all LINES are thought to be transcriptionally active (20). It is difficult to determine if the rat repetitive element found upstream of the rat insulin I gene is expressed due to the extensive homologies shown by all rat LINE sequences.…”

Antisense Promoter of Human L1 Retrotransposon Drives Transcription of Adjacent Cellular Genes

“…These transcripts corresponded to both L1Hs strands, and some contained unrelated sequences apparently derived from readthrough transcription directed by adjacent cellular promoters (29). Recently, high-frequency retrotransposition of the engineered L1Hs into transcribed genes in HeLa cells yielded promiscuous mobilization of the L1Hs 3Ј flanking sequences into new genomic regions (25).…”

A large interspersed repeat found in mouse DNA contains a long open reading frame that evolves as if it encodes a protein.

“…13 and references therein). Transcripts from portions of these large repeats have been detected in both mice (11,16,20) and primates (19,(21)(22)(23). There is some evidence that these sequences are associated with polyribosomes in mouse liver (16), although they were not detected in polyribosomal preparations from human culture cells (21 codons, TGA and TAG; the longest distance between a posthe 500-bp (20) sible initiation codon and a terminator is 864 bp (Fig.…”

“…They are found in organisms as diverse as frogs (1), sea urchins (2), flies (3), birds (4), rodents (5), and humans (6); nevertheless, the reason for their existence is not understood. Hypotheses concerning their contribution to the normal patterns of gene expression in differentiated cells range from a model in which they are seen as the main perpetrators of regulation (7,8) (11,16,20) and primates (19,(21)(22)(23) …”

“…The model proposed above does not preclude the possibility that the repeat exerts effects on the expression of nearby genes. For (23). Thus, it seems likely that the LI repeat family is not merely junk DNA.…”