Kpn I family of long interspersed repeated DNA sequences in primates: polymorphism of family members and evidence for transcription.

The complete nucleotide sequence of a human Kpn I element inserted into a-satellite DNA is presented.This sequence reveals several features of interest. First, a large block of DNA normally associated with Kpn I elements has been deleted. Second, the order of the remaining sequences is permuted in a manner that cannot be accounted for by simple inversion. Third, a significant open reading frame of 675 bases is detected. (5,8,11,12). This laboratory has isolated and characterized human DNA segments carrying unusual monomeric domains of asatellite sequence (13). Of particular interest are the nonsatellite sequences that have been found occasionally interrupting the long tandem arrays of satellites (10,13,14). Because satellite sequences undergo continual rectification by unequal crossover (15) and gene conversion, it seems possible that the interrupting sequences represent mobile elements that have inserted into satellite relatively recently in evolutionary time. In this study I focused on a part of the pa7 clone, which has been shown to carry a nonsatellite sequence inserted into a-satellite DNA (13). The invading sequence is shown here to be an unusual Kpn I element.The Kpn I elements are abundant (about 30,000 copies per haploid genome) and particularly interesting structurally. No terminal repeats have yet been found, making them unlike most transposable elements (16,17), and their variable constructions include deletions and inversions (11). In this paper the complete nucleotide sequence of an element inserted into human a-satellite DNA is presented. The sequence reveals the presence of a large sequence permutation, thereby describing yet another type of polymorphism found in the Kpn I family of primate dispersed repetitive elements. Moreover, a large open reading frame is found, suggesting a coding function. MATERIALS AND METHODSEnzymes and polynucleotide linkers were purchased from New England BioLabs, and isotopes were from New England Nuclear. DNA Sequence Determination. DNA sequence was determined by using the partial chemical cleavage method of Maxam and Gilbert (18). DNA was labeled at the 3' end with the Klenow fragment of DNA polymerase 1 and at the 5' end by polynucleotide kinase.Subcloning. The 4.0-kilobase (kb) Sal I-EcoRI DNA segment carrying a Kpn I element with flanking a-satellite DNA was purified from the previously described pa7 clone (13) and ligated into pBR322 DNA cut with Sal I and EcoRI.In order to facilitate the sequence determination, two experiments designed to introduce restriction sites at useful locations were performed. In the first experiment the subclone was opened at the Bgl II site and then treated for various periods with the exonuclease BAL-31. Progress of the digestion was followed by gel electrophoresis. Cla I linkers were blunt-end-ligated to the ends and cleaved by Cla I, and the molecules were recircularized by ligation. After transformation of Escherichia coli HB101 and selection on ampicillin plates, random colonies were used for "miniprep" (19) and restrict...

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confidence: 99%

Rearranged sequences of a human Kpn I element.

Potter¹

1984

“…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.…”

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confidence: 98%

“…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) …”

Section: Introductionmentioning

confidence: 99%

“…Recently, DNA sequences from portions of the monkey LI (Kpn I) family have been published (22,39). The available sequence includes a region that is homologous to the sequence from LJMd-4 and other published LJMd sequences (see ref The values for "possible sites" were determined by examining all three possible base substitutions at each position in the sequence and determining whether the altered codon represents a silent (S) or replacement (R) substitution.…”

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confidence: 99%

See 1 more Smart Citation

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

Martin¹,

Voliva²,

Burton³

et al. 1984

DNA sequence analysis of a region contained within a large, interspersed repetitive family of mice reveals a long open reading frame. This sequence extends 978 base pairs between two stop codons, creating a reading frame that is open for 326 amino acids. The DNA sequence in this region is conserved between three distantly related Mus species, as well as between mouse and monkey, in a manner that is characteristic of regions undergoing selection for protein function.Interspersed repetitive elements are ubiquitous in the DNA of higher eukaryotes. 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) 2308The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. §1734 solely to indicate this fact.

“…Mammalian DNA contains several families of highly repeated sequences, some of which have been suggested to be mobile elements (21)(22)(23). Part of the evidence for this notion is based on the finding that these elements, such as SINE and LINE (24), are bounded by direct repeats of 7-20 base pairs (bp), similar to the integrated provirus of the retroviruses.…”

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confidence: 99%

"Retroposon" insertion into the cellular oncogene c-myc in canine transmissible venereal tumor.

Katzir¹,

Rechavi²,

Cohen³

et al. 1985

112

We examined by Southern blotting the state of the cellular oncogene c-myc In the dog transmissible venereal tumor. The tumor DNA contains a 16.8-kilobase pair (kbp) rearranged c-myc fragment in addition to the normal 15-kbp and 7.5-kbp fragments. We compared the structure of the cloned rearranged c-myc (rc-myc) with that of a cloned normal c-myc and found that the rearrangement was due to the insertion of a 1.8-kbp DNA upstream to the first exon of c-myc. The inserted DNA is flanked by 10-base-pair direct repeats and contains a dA-rich tail, suggesting its origin from mRNA. Partial sequence of the inserted element showed 62% homology with the primate interdispersed Kpn I repetitive element. These results provide an example for the behavior of repetitive DNA sequences like the Kpn I family, as movable elements that can transpose nearby to oncogenes or other structural genes and perhaps affect their activity.