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

Abstract

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.

Recombination mediates production of an extrachromosomal circular DNA containing a transposon-like human element, THE-1

“…An alignment of the sequences surrounding the recombination points is compared to the sequence of the HeLa 5R circle in Fig. 6 (2,3,11,13,14). A variety of characteristics including the presence of an A-rich 3' tail and variably sized target site duplications have led to the classification of Alu and L-1 sequences as retroposons.…”

Isolation and characterization of a DNA fragment containing various kinds of repetitive sequences located on human chromosome 21

“…In addition to Alu and L1 sequences, O-family repetitive sequences (Sun et al, 1984) were found at the position between 1076 and 1418. The O-family repeat is flanked by 6 bp TSDs.…”

“…In addition to these SINES and LINES, retrovirus-like repetitive sequences have been identified. The O-family sequence is one such repetitive sequence and is considered to be a solitary LTR (long terminal repeat) (Sun et al, 1984;Paulson et al, 1985).…”

Human Endogenous Retrovirus-like Sequences

“…This group of elements, designated THE 1 repeats by Sun et al [62], was isolated from a human DNA library as clones hybridizing to human genomic DNA but not to an Alu family member. Like the other endogenous retroviral sequences discussed here, these elements possess features indicative of having been generated by the reverse flow of genetic information from RNA to DNA.…”