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

108

We present the DNA sequence of a 6.7-kilobase member of the rat long interspersed repeated DNA family (LINE or LlRn). This member (LINE 3) is flanked by a perfect 14-base-pair (bp) direct repeat and is a full-length, or close-to-full-length, member of this family. LINE 3 contains an approximately 100-bp A-rich right end, a number of long (>400-bp) open reading frames, and a ca. 200-bp G+C-rich (ca. 60%) cluster near each terminus. Comparison of the LINE 3 sequence with the sequence of about one-half of another member, which we also present, as well as restriction enzyme analysis of the genomic copies of this family, indicates that in length and overall structure LINE 3 is quite typical of the 40,000 or so other genomic members of this family which would account for as much as 10% of the rat genome. Therefore, the rat LINE family is relatively homogeneous, which contrasts with the heterogeneous LINE families in primates and mice. Transcripts corresponding to the entire LINE sequence are abundant in the nuclear RNA of rat liver. The characteristics of the rat LINE family are discussed with respect to the possible function and evolution of this family of DNA sequences.Repeated DNA sequences are present in the genomes of all metazoans (6). A class of highly repeated DNA that has been studied in primate and mouse genomes (1,10,14,18,19,31,32,37,49) has been called long interspersed repeated DNA (referred to as LINES [52] or, more recently, the Li family [59]). These families contain long members (several kilobases) that are repeated >20,000 times per genome and are responsible for the prominently stained electrophoretic bands that are seen when total genomic DNA is digested with the appropriate restriction endonuclease; the names of the endonucleases were originally used to denote these families.Extensive studies on mouse and primate LINEs (see references 43 and 53 for recent reviews) revealed several major features that these families share. First, many cloned members have, at what has been called the right or 3' end, a putative polyadenylation site, AATAAA, followed by an A-rich sequence (14,54,60). Second, although full-length members are 6 to 7 kilobases (kb) long (1, 14, 19), many cloned members are truncated and most often are missing a variable portion from their left end. Furthermore, there appear to be many more genomic copies of the right end than of the left end of certain cloned members of these families (14,19,59 by RNA polymerase 11 (20,50,56), although there are conflicting results about the extent to which transcripts are poly(A) + (26, 50) and to what extent LINE transcription may be asymmetric (50,56). It has been suggested that the truncated LINE members that end in A-rich 3' ends are incomplete DNA copies (retrotranscripts) of poly(A)+ LINE transcripts (14,43,55,59,60).The rat also contains a highly repeated family of transcribed LINE sequences (65). Members of this family have been (or still are) undergoing transposition in the rat genome, since at least three single-copy loci are polymorphic ow...

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

See 1 more Smart Citation

Structure of the highly repeated, long interspersed DNA family (LINE or L1Rn) of the rat.

D’Ambrosio¹,

Waitzkin²,

Witney³

et al. 1986

108

“…1). The proteins predicted by the ORFs include regions with homology to reverse transcriptase and nucleic acid-binding proteins (19,24,36).Li elements in other mammals are similar to those in primates with regard to abundance and overall organization (3,19,20,33,36,37,50,60,63). Moreover, both the nucleotide sequence of the ORF region and the polypeptides predicted from the ORFs are homologous in all mammalian orders that have been analyzed.…”

mentioning

confidence: 98%

Unit-length line-1 transcripts in human teratocarcinoma cells.

Skowroński¹,

Fanning²,

Singer³

1988

295

220

We have characterized the approximately 6.5-kilobase cytoplasmic poly(A)+ Line-i (Li) RNA present in a human teratocarcinoma cell line, NTera2Di, by primer extension and by analysis of cloned cDNAs. The bulk of the RNA begins (5' end) at the residue previously identffied as the 5' terminus of the longest known primate genomic Li elements, presumed to represent "unit" length. Several of the cDNA clones are close to 6 kilobase pairs, that is, close to full length. The partial sequences of 18 cDNA clones and full sequence of one (5,975 base pairs) indicate that many different genomic Li elements contribute transcripts to the 6.5-kilobase cytoplasmic poly(A)+ RNA in NTera2Dl cells because no 2 of the 19 cDNAs analyzed had identical sequences. The transcribed elements appear to represent a subset of the total genomic Lls, a subset that has a characteristic consensus sequence in the 3' noncoding region and a high degree of sequence conservation throughout. Two open reading frames (ORFs) of 1,122 (ORF1) and 3,852 (ORF2) bases, flanked by about 800 and 200 bases of sequence at the 5' and 3' ends, respectively, can be identified in the cDNAs. Both ORFs are in the same frame, and they are separated by 33 bases bracketed by two conserved in-frame stop codons. ORF 2 is interrupted by at least one randomly positioned stop codon in the majority of the cDNAs. The data support proposals suggesting that the human Li family includes one or more functional genes as well as an extraordinarily large number of pseudogenes whose ORFs are broken by stop codons. The cDNA structures suggest that both genes and pseudogenes are transcribed. At least one of the cDNAs (cD11), which was sequenced in its entirety, could, in principle, represent an mRNA for production of the ORF1 polypeptide. The similarity of mammalian Lls to several recently described invertebrate movable elements defines a new widely distributed class of elements which we term class 1I retrotransposons.Line-1 (Li) is a family of long highly repeated DNA sequences dispersed in all mammalian genomes (9-12, 14, 22, 23, 55, 58, 65). In primates, the longest known family members are about 6 kilobase pairs (kbp), although many family members are truncated and internally rearranged (1,22,23,31,35,39,48). The structure of randomly selected genomic Lls from various primates is similar to that of processed pseudogenes, including the presence on one strand of long but broken open reading frames (ORFs), an A-rich 3' terminus (on the strand containing the ORFs), the apparent lack of introns interrupting the ORFs, and variablesized target site duplications (Fig. 1). The proteins predicted by the ORFs include regions with homology to reverse transcriptase and nucleic acid-binding proteins (19,24,36).Li elements in other mammals are similar to those in primates with regard to abundance and overall organization (3,19,20,33,36,37,50,60,63). Moreover, both the nucleotide sequence of the ORF region and the polypeptides predicted from the ORFs are homologous in all mammalian orders that have be...

“…About 95% of the sequence was determined in both directions or from a series of overlapping Exolll deletion clones (11). Open reading frames have been identified in the corresponding region of mouse LINEs and primate LINEs (19) and thus appear to be a general feature of mammalian LINEs. We analyzed all of the non-LINE insulin 1 sequence for homology to all segments of the rat LINE diagrammed in Fig. 6 by computer methods suitable for detecting either general or local regions of homology.…”

mentioning

confidence: 99%

Long interspersed repeated DNA (LINE) causes polymorphism at the rat insulin 1 locus.

Lakshmikumaran¹,

D’Ambrosio²,

Laimins³

et al. 1985

The insulin 1, but not the insulin 2, locus is polymorphic (i.e., exhibits allelic variation) in rats. Restriction enzyme analysis and hybridization studies showed that the polymorphic region is 2.2 kilobases upstream of the insulin 1 coding region and is due to the presence or absence of an approximately 2.7-kilobase repeated DNA element. DNA sequence determination showed that this DNA element is a member of a long interspersed repeated DNA family (LINE) that is highly repeated (>50,000 copies) and highly transcribed in the rat. Although the presence or absence of LINE sequences at the insulin 1 locus occurs in both the homozygous and heterozygous states, LINE-containing insulin 1 alleles are more prevalent in the rat population than are alleles without LINEs. Restriction enzyme analysis of the LINE-containing alleles indicated that at least two versions of the LINE sequence may be present at the insulin 1 locus in different rats. Either repeated transposition of LINE sequences or gene conversion between the resident insulin 1 LINE and other LINE sequences in the genome are possible explanations for this.About one-third of various mammalian genomes is composed of families of repeated DNA sequences (4, 32). A major portion of this DNA is highly repeated (i.e., >20,000 copies per family) and is interspersed among nonrepeated DNA (7). Two classes of interspersed repeat DNA families have been identified, based on the length of the repeated element. Short interspersed repeated DNA families contain 100-to 300-base-pair (bp) repeat elements (12,28,32), whereas long interspersed repeated DNA families (LINE family) consist of elements that are quite complex and at least several kilobase pairs long (1,9,10,16,20,21,30,32,33).About one-third of the rat genome also is repeated DNA (25). This fraction is dominated by several highly repeated short interspersed repeated DNA families and at least one LINE family, as is the case for other mammalian genomes (42). These families, which did not reanneal as highly repeated DNA (25), are highly transcribed in the rat (42).Whatever their function, repeated DNA sequences may affect contiguous DNA sequences. These include effects on gene activity due to regulatory elements in the repeated DNA (28), as well as deletion, duplication, inversion, and translocation of the contiguous DNA sequences by homologous recombination between the resident repeated DNA sequence and other members of the repeat family in the genome. Such repeat DNA-mediated events are not just theoretical possibilities. One type of familial hypercholesteremia in humans, for example, is due to deletion of part of the gene for a lipoprotein receptor by recombination between two members of the human Alu short interspersed repeated DNA family (14).It recently was shown (8) that two single-copy DNA loci of rats are polymorphic due to the presence or absence of a full-length (-6.5-kilobase [kb]) member of the rat LINE family: the Igh locus and the Mlvi-2 locus, which is a site for the integration of Moloney leukemia virus (38)...