Lines (Molecular Biology)

LINEs are long interspersed repeated segments (see Interspersed DNA Elements), first described in the genomes of mammals. They are over 5 kb long and are repeated approximately 10 4 times in the genome. A 6.4-kb member of one LINE family occurs downstream of the human beta- globin gene. This primate LINE family is called the Kpn family, because it generates restriction fragments of characteristic size when the genome is fragmented by the Kpn restriction enzyme.

LINEs of the mouse genome have been prepared by digesting reassociated DNA fragments with deoxyribonuclease specific for single strands. Separation of the resulting fragments on the basis of size reveals many discrete bands that are assigned to 15-kbp and 6-kbp groups. The 6-kbp LINE family, called MIF-1, has been described in several species of mice and other rodents. As with the primate Kpn family, MIF subfamilies are distinguishable within each of several genomes by restriction-site polymorphisms (see Restriction Fragment Length Polymorphism (RFLP)), and related genomes contain distinct divergent subfamilies. The rodent and primate LINEs are sufficiently different not to cross-hybridize.

A highly repeated DNA element has been described in the Xenopus laevis genome. It is present in about 8500 copies per haploid genome and accounts for about 2.4% of the genome. The copies range in size from 6 kbp to 10 kbp because of an expandable region containing variable numbers of a tandemly repeating 183- to 204 bp unit. The element is flanked by an imperfect 18 bp inverted sequence, and inverted repeats of 180 to 185 bp are nearby. This and other indirect evidence suggest that this element may be a transposable element (1).


DNA sequence analysis of a region contained within a LINE in mice reveals a long, open reading frame (ORF) of 978 bp between two stop codons. This sequence is conserved among three distantly related mice species and between mouse and monkey, in a manner that is claimed to be characteristic of regions undergoing selection for protein function (2).

The Drosophila mobile element jockey is similar in its structural organization and coding potential to the LINEs of various organisms. A complete copy of jockey (about 5 kbp) is terminated by a segment of oligo(dA), preceded by two long ORF that overlap with a -1 frameshift. On the basis of sequence analysis, the first ORF codes for a nucleic acid-binding protein and the second codes for a reverse transcriptase that is most similar in its sequence to the putative reverse transcriptase of other LINEs. The existence of a large number of jockey copies with a deletion in the second ORF may indicate that they can use reverse transcriptase in trans (3).

Sequence analysis of the rat vasopressin and oxytocin gene family reveals that the two genes are linked by a LINE containing seven ORFs encoding hypothetical proteins of 99 to 566 amino acid residues. Furthermore, both DNA strands of LINE serve as templates for transcription. Transcripts initiated at the 3′ end are more abundant than those started from the 5′ end. Transcription occurs preferentially in brain tissue, as analyzed by Northern blot, in situ hybridization, and nuclease protection experiments. Most LINEs are transcribed over their entire length, and a major fraction of the resulting RNA does not enter the cytoplasm, but remains in the cell nucleus (4).

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