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The Chinese Hamster Alu-Equivalent Sequence: a Conserved, Highly

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The Chinese Hamster Alu-Equivalent Sequence: a Conserved, Highly MOLECULAR AND CELLULAR BIoLocY, July 1981, p. 573-583 Vol. 1, No. 7 0270-7306/81/070573-11$02.00/0 The Chinese Hamster Alu-Equivalent Sequence: a Conserved, Highly Repetitious, Interspersed Deoxyribonucleic Acid Sequence in Mammals Has a Structure Suggestive of a Transposable Element SUSAN R. HAYNES, THOMAS P. TOOMEY, LESLIE LEINWAND,t AND WARREN R. JELINEK* The Rockefeller University, New York, New York 10021 Received 30 March 1981/Accepted 16 April 1981 A consensus sequence has been determined for a major interspersed deoxyri- bonucleic acid repeat in the genome of Chinese hamster ovary cells (CHO cells). This sequence is extensively homologous to (i) the human Alu sequence (P. L. Deininger et al., J. Mol. Biol., in press), (ii) the mouse Bl interspersed repetitious sequence (Krayev et al., Nucleic Acids Res. 8:1201-1215, 1980), (iii) an inter- spersed repetitious sequence from African green monkey deoxyribonucleic acid (Dhruva et al., Proc. Natl. Acad. Sci. U.S.A. 77:4514-4518, 1980) and (iv) the CHO and mouse 4.5S ribonucleic acid (this report; F. Harada and N. Kato, Nucleic Acids Res. 8:1273-1285, 1980). Because the CHO consensus sequence shows significant homology to the human Alu sequence it is termed the CHO Alu-equivalent sequence. A conserved structure surrounding CHO Alu-equivalent family members can be recognized. It is similar to that surrounding the human Alu and the mouse Bi sequences, and is represented as follows: direct repeat CHO-Alu-A-rich sequence-direct repeat. A composite interspersed repetitious sequence has been identified. Its structure is represented as follows: direct repeat-residue 47 to 107 of CHO-Alu-non-Alu repetitious sequence-A-rich sequence-direct repeat. Because the Alu flanking sequences resemble those that flank known transposable elements, we think it likely that the Alu sequence dispersed throughout the mammalian genome by transposition. The nuclear deoxyribonucleic acid (DNA) of stranded hnRNA [ds-hnRNA]) that resist diges- most eucaryotic organisms is interspersed with tion by single strand-specific ribonucleases short repetitive sequences approximately 100 to (RNases) (14-16, 24, 26). When ds-hnRNA was 300 base pairs long (6, 7, 27). Little is known used to screen libraries of cloned nuclear DNA concerning the function of these interspersed a large proportion of all clones were found to repeats. In humans one family of approximately contain sequences capable of hybridizing with 300-base-pair repetitive DNA, the Alu family, this class of repetitive RNA. Depending on the dominates the whole pattern of interspersed re- size of the cloned DNA fragments, between 25 peats (12). Members of the Alu family are pres- and 94% of all clones contained ds-hnRNA com- ent a minimum of 300,000 times in the haploid plementary sequences (14, 19; Jelinek, unpub- human genome (P. L. Deininger, C. M. Rubin, lished data), indicating that these sequences are D. Jolly, C. W. Schmid, and T. Friedmann, J. both highly repetitive and widely dispersed Mol. Biol., in press). Likewise, Chinese hamster throughout the mammalian genome. and mouse DNAs each contain a family of inter- The nucleotide sequences of extensive regions spersed repeats whose members occur at ap- of three such cloned nuclear DNA fragments proximately the same frequency as Alu family from Chinese hamster ovary (CHO) cells were members occur in human DNA (14, 19). These determined. This report describes six repetitive interspersed repetitive sequences are heavily sequences, all related to one another, that were transcribed as part of heterogeneous nuclear identified in these three clones. In addition, this ribonucleic acid (hnRNA) molecules in cultured report presents the nucleotide sequence of a cells from all three species and can be isolated CHO low-molecular-weight RNA, the so-called because they form base-paired duplexes (double- 4.5S RNA, that base pairs with polyadenylate- terminated nuclear and cytoplasmic RNA (17). t Present address: Department of Microbiology, Albert Its sequence, like that of the mouse 4.5S RNA Einstein College of Medicine, Bronx, NY 10461. (11), is extensively homologous to that of the 573 574 HAYNES ET AL. MOL. CELL. BIOL. interspersed repetitive DNA described here. Overlapping products from the 5' end of the molecule The nucleotide sequences of members of the were easily identified because the 5' nucleotide is human Alu family of interspersed repetitive guanosine 5'-triphosphate-3'-monophosphate. Unla- DNA have been published (1, 3, 18, 25), as have beled 4.5S RNA was purified and ligated with 3P- labeled cytidine 5'-monophosphate-3'-monophosphate the sequences of three examples of the mouse as described by Bruce and Uhlenbeck (4). The 3' end interspersed repetitive DNA that hybridized of the 4.58 RNA is heterogeneous. Three types of 3' with the mouse ds-hnRNA, the so-called mouse ends were identified, UU-OH, UUU-OH, and UUUU- B1 sequence (19). Nucleotide sequence compar- OH. Therefore, after ligation with 3P-labeled cytidine isons described here demonstrate that all of 5'-monophosphate-3'-monophosphate the 4.5S RNA these sequences are closely related to one an- was subjected to electrophoresis in a thin acrylamide other. Thus, the Alu family sequence has been gel to separate each of these three species. The RNAs highly conserved during mammalian evolution. were eluted from the gel and subjected to the chemical Some, but not all, CHO Alu-equivalent family degradations described by Peattie (22) for RNA se- quence determinations. By aligning the T, partial oli- members are flanked by short direct repeats of gonucleotides at the 5' end of the molecule with the 7 to 20 base pairs. The sequences of these direct sequence determined by the chemical degradation repeats are unique to eachAlu-equivalent family method from the 3' end of the molecule each of the T, member. Presumably, they arose during the dis- and pancreatic RNase digestion products were or- persal of the Alu sequence throughout the CHO dered. In addition, the chemical sequencing method DNA. If so, then the Alu-equivalent sequence allowed an independent confirmation of the sequence may have been inserted at many sites in CHO of each of the T, and pancreatic RNase products. DNA by a mechanism related in some aspects Hybridization to nitrocellulose replicas ofaga- to that used by bacterial transposable elements rose gels. DNA restriction fragments were separated by electrophoresis in agarose gels and transferred to (28). The sequences flanking CHO Alu-equiva- nitrocellulose filters by the method of Southern (29). lent family members are similar in structure to Before hybridization of labeled probe DNA the filters those that flank some members of the human were treated with a solution containing 50% formam- Alu family of interspersed repeats and the ide, 5x SSC (lx SSC is 0.15 M NaCl plus 0.015 M mouse Bi family of interspersed repeats. They sodium citrate), 50 mM NaPO4 (pH 7.4) and lx Den- are not structures unique to complete Alu se- hart solution (0.02 g of polyvinylpyrrolidone, 0.02 g of quences. A composite repetitive sequence was Ficoll, and 0.057 ml of a 35% solution of bovine serum identified during the course of the work pre- albumin per 100 ml of solution). Hybridization of sented here. In this structure the middle portion labeled probe DNA was accomplished in the same solution containing 10% dextran sulfate at 40°C. After of the Alu sequence is juxtaposed next to an- hybridization the filters were washed with three other repetitive sequence, one side of this com- changes of 2x SSC at room temperature for 15 min posite repeat is flanked by an endoreduplicated each followed by three washes in 0.1x SSC at room A-rich sequence, and the entire sequence is temperature for 15 min each. flanked by short direct repeats. This sequence represents a previously undescribed repetitive RESULTS DNA element having the same overall flanking Nuclear DNA from CHO cells was cleaved structure as most Alu and Alu-equivalent family with EcoRI endonuclease and ligated with members. EcoRI-cleaved Charon 16A lambda phage DNA. MATERIALS AND METHODS The recombinant DNA was then used to trans- fect spheroplasts prepared from Escherichia Cloning of CHO DNA fragments and identifi- coli strain K802, and the resulting plaques were cation of clones contining ds-hnRNA comple- screened for DNA sequences capable of hybrid- mentary sequences. The cloning of EcoRI DNA fragments from Chinese hamster nuclear DNA in ization with CHO ds-hnRNA as previously de- Charon 16A lambda phage has been described previ- scribed (14). Three such clones, numbers 34, 49, ously, as has the identification of clones containing and 63, were chosen for sequence analysis. The sequences complementary to ds-hnRNA (14). nucleotide sequences ofextensive regions ofeach Nucleic acid sequence determinations. All of these three clones were determined. The se- DNA sequence determinations were performed by the quences were then searched by computer for method of Maxam and Gilbert (20, 21). For sequence regions of internal homology and for regions of analysis, the 4.5S RNA was labeled with 3P by incu- homology with the human Alu sequence and the bating CHO cells with carrier-free H3mPO4. The 4.5S mouse Bl sequence, each ofwhich has extensive RNA was purified as described previously (17). The and sequence homology with the ds-hnRNA from nucleotide sequences of each of the RNase T, were pancreatic RNase products were determined by the these respective species. Six such regions methods of Barrell (2). Partial T, RNase digestion detected, four in clone 49 and one each in clones followed by two-dimensional fingerprinting allowed 34 and 63. Because members of a repetitive the purification ofincreasingly longer oligonucleotides. sequence family are similar but not identical in VOL. 1, 1981 Alu-EQUIVALENT SEQUENCE IN CHO CELLS 575 sequence they are best represented as a consen- Lr over their entire lengths, with the excep- sus, or most common sequence.
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