Repeated deoxyribonucleic acid clusters in the chicken genome contain homologous sequence elements in scrambled order

Musti, Anna Maria; Sobieski, Donna A.; Chen, Bessie B.; Eden, Francine C.

doi:10.1021/bi00514a001

Cited by 22 publications

(15 citation statements)

References 28 publications

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“…If the Kpn I elements are eventually found to be "scrambled clusters" as described in Drosophila (34) and chicken (35), then this sequence data will help to define the subunits. In any event, the rearrangements present in Kpn A indicate a remarkable structural plasticity in this family of sequences.…”

Section: Discussionmentioning

confidence: 99%

Rearranged sequences of a human Kpn I element.

Potter¹

1984

Proc. Natl. Acad. Sci. U.S.A.

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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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Section: Discussionmentioning

confidence: 99%

Rearranged sequences of a human Kpn I element.

Potter¹

1984

Proc. Natl. Acad. Sci. U.S.A.

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“…At the 3' end, as written, both terminate in homologous segments, including an A-rich stretch (see Fig. 3A) family members might be constructed from discrete elements that are joined in a scrambled fashion at different genomic localities, analogous to the scrambled clusters of short repetitive elements in chickens (33) and Drosophila (34); the mechanism by which such clusters form remains obscure. Another possibility is that all family members might have been typical long units at first, with some being shortened by deletions both at the ends and within the element itself.…”

Section: ="Ilmentioning

confidence: 99%

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

Lerman¹,

Thayer²,

Singer³

1983

Proc. Natl. Acad. Sci. U.S.A.

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An ==2-kilobase-pair-long member (Kpn. I-LS1) of the African green monkey Kpn I family of repeated sequences has been cloned, subjected to sequence analysis, and compared to other family members which are over 6 kilobase pairs (Kpn I-a7) and 829 base pairs (Kpn I-RET) long. Both Kpn I-LS1 and Kpn I-RET lack sequences found at the ends of the longer family member and their structures resemble those of processed genes. Kpn I-LS1 sequences are colinear with part of the long family member, Kpn I-a7. However, although all sequences in Kpn I-RET are represented in Kpn I-LS1, the two are not colinear; Kpn I-RET is missing 731 base pairs found in Kpn I-LS1 and one segment flanking the deletion is inverted. The results demonstrate that Kpn I family members are not only of different lengths but may also contain scrambled arrangements of common sequences. Sequences in Kpn I-LS1 hybridize to RNA from monkey and human cells, indicating that some family members are transcribed.Eukaryote genomes typically contain multiple families of repeated DNA sequences that are interspersed among other genomic segments. In primates, the Kpn I family members are polymorphic in length and sequence, occur on the order of 104 times, and have been observed flanking genes and within satellite DNA (1)(2)(3)(4)(5)(6)(7)(8) (Fig. 1A) (10-12). The structure of Kpn I-LS1 is compared here with that of Kpn I-RET and Kpn I-a7, a typical long AGM family member (6). Also, we report that transcripts homologous to Kpn I family sequences have been detected in both AGM and human cells. METHODSMaterials. The recombinant phages ACaa7 (6) and ACaOri7 (9-12) were described previously; the Kpn I family members included in these clones are called Kpn I-a7 and Kpn I-LS1, respectively. For convenience we refer to them as a7 and LS1 in this paper and Kpn I-RET (8) is called RET. DNA was isolated (13) and purified (14) from monkey liver. Phage and plasmid DNAs were isolated as described (9). Total RNA from AGM liver and HeLa cells was isolated by the guanidinium isothiocyanate method (15) and the polyadenylylated RNA was selected as described (16). Total liver nuclear RNA was isolated from purified nuclei and was treated with DNase I (17). The primary human fibroblast cDNA library was kindly supplied by H. Okayama and P. Berg (18); two cDNA plasmids, pcDKl and pcDK2, were selected by screening (19) the library with sequences from LS1 (see Results).Subcloning. DNA fragments were isolated from phage or plasmid digests by preparative agarose gel electrophoresis and were ligated into pBR322 directly or after attaching HindIII linkers (Collaborative Research, Waltham, MA).Hybridization Analyses. Procedures for labeling plasmid and genomic DNA and for restriction endonuclease digestion, gel electrophoresis, transfer to nitrocellulose filters, and hybridization were as described (6,8,9). Nucleotide Sequence Analysis. The nucleotide sequence determinations were by the Maxam and Gilbert procedure (20) as modified (21). Computer analysis (22) and alignment (23) of seque...

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“…More complex families have been described where several small "discrete" repetitive elements are found mixed together into larger arrays but with no apparent conserved ordering of the smaller elements with respect to each other within the larger array. This organization has been called a "scrambled and clustered organization" (5) and examples have been described in Drosophila (5), chicken (7) and within the rabbit beta globin locus (8). Length variation exists in both of these two types of repeats.…”

Section: Introductionmentioning

confidence: 99%

The L1Md long interspersed repeat family in the mouse: almost all examples are truncated at one end

et al. 1983

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We have characterized a large repetitive element which has been found at seven different locations within the beta globin locus of the BALB/c mouse. This repeat has an unusual structure in that each of the different members has the same end of the element conserved while the other end terminates at a different point in each repeat member. The sequences within the repeats from the beta globin locus have homology with other repetitive families such as the MIF-1, Bam-5, R, and the BamHl families. These were recently proposed (T. Fanning, (1983) Nucleic Acids Res. 11, 5073-5091) to be part of a structure with the same organization which we found in the globin locus. Probing plaques from a BALB/c genomic library with sequences derived from the repeats in the globin locus shows that virtually all of the repeats from this family are organized in a manner consistent with the proposed structure.

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Repeated deoxyribonucleic acid clusters in the chicken genome contain homologous sequence elements in scrambled order

Cited by 22 publications

References 28 publications

Rearranged sequences of a human Kpn I element.

Rearranged sequences of a human Kpn I element.

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

The L1Md long interspersed repeat family in the mouse: almost all examples are truncated at one end

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