volume 14 Number 12 1986 Nucleic Acids Research Structural variations In the Drosophila retrotransposon, 17.6 Satoshi Inouye, Kazue Hattori, Shunji Yuki and Kaoru Saigo* Department of Biochemistry, Kyushu University 60 School of Medicine, Fukuoka 812, Japan Received 23 April 1986; Revised and Accepted 23 May 1986 ABSTRACT More than 21 members of 17.6, a Drosophila retrotransposon, were isolated and t h e i r possible s t r u c t u r a l changes were examined by r e s t r i c t i o n mapping, blot hybridization, heteroduplex analysis and nucleotide sequence determination of long terminal repeats (LTRs). At least 7 members were found to suffer with terminal or internal long deletions. No pair of LTRs having an identical nucleotide sequence was found either within an element or between elements. Although an i n i t i a t i o n s i t e for the presumable genome-sized transcript of 17.6, a potential substrate for reverse transcription on trans location, was identified within the left-hand LTR, our r e s u l t s as a whole support the notion that the majority of 17.6s have continued to reside for a long period of time at their present chromosomal loci and hence the rate of translocation of 17.6 is very low. INTRODUCTION 17.6 i s a member of c££_ia-like t r a n s p o s a b l e g e n e t i c elements (retrotransposons) in Drosophila melanogaster and has been suggested to have about 40 copies per haploid chromosome (1). In a previous experiment (2), we determined the complete nucleotide sequence of a 17.6 element inserted in a histone gene and found the 17.6 genome to include three long open reading frames (ORFs) comparable in size and location with r e t r o v i r a l gag, pol and env. We also found the second ORF of 17.6 not only to contain the n u c l e o t i d e sequence coding for r e v e r s e transcriptase-like enzyme but al3o to be very similar in overall structure to the pol gene of Moloney murine leukaemia virus (2,3). Since subsequent nucleotide sequence analyses (4-10) have revealed the presence of similar pol-like genes in several other copia-like elements in Drosophila and yeast, i t is now quite reasonable to presume that the translocation of copia-like © IRL Pren Limited, Oxford, England. 4765 Nucleic Acids Research elements i s generally carried out via RNA intermediates by reverse t r a n s c r i p t i o n . In fact, Boeke e_t a_l. (11) have recently presented more direct evidence for t h i s notion at least in the case of a yeast copia-like element, Ty. Here, we examined possible structural changes among more than 21 members of a 17.6 family, representing about half the t o t a l per haploid chromosome, to see how fast these elements change their chromosomal positions. Although an initiation site for the presumable, genome-sized t r a n s c r i p t of 17.6 , a potential substrate for reverse transcription on translocation, was identified within the left-hand LTR, our results as a whole support the notion that the majority of 17.6s have continued to reside for a long period of time at t h e i r present chromosomal loci and hence the rate of translocation of 17.6, if i t actually occurs, is very low. MATERIAL AND METHODS Hateria"is. The r e s t r i c t i o n enzymes, DNase, DNA ligase and reverse transcriptase were obtained from commercial sources. P - l a b e l l e d nucleotides were purchased from New England Nuclear.An oligonucleotide primer(3'GGAACTACGCCATTGGTCTAAACGG5') for p r i m e r e x t e n t i o n was s y n t h e s i z e d using a Model 380A synthesizer (Applied Biosystems). General Methods. Restriction enzyme digestions, agarose gel e l e c t r o p h o r e s i s , subcloning of r e s t r i c t i o n segments and b l o t h y b r i d i z a t i o n were carried out e s s e n t i a l l y as described by Maniatis et a_l_. (12). As a cloning vehicle for sub-cloning., only pOC9 (13) was used. The DNA probe was labelled with 32 P by k i n a t i o n . DNA sequencing was conducted by the Maxam-Gilbert method (14). Heteroduplex analysis was carried out according to Modolell et al.(15). Ph_£g_es a.£? pTa£raid£. The o r i g i n of X h i s t l 7 . 6 has been d~escrTbed previously (16). Other 17.6 containing phages were screened from an EcoRI p a r t i a l l i b r a r y of D. melanogaster (Oregon R) embryonic DNA e s s e n t i a l l y as descrTbed elsewhere (16) . Preparation of RNA and a primer extension experiment. GM2 c e lTT1 l s were c u l t u r e d inlOOml D20 medium to l a t e log phase as described previously (17) and c o l l e c t e d by low-speed centrifugation. RNA was prepared from GM2 c e l l s essentially as described by Deeley et aj_-(18). Using lmg/ml of GM2 total RNA, a primer e x t e n t i o n experiment was c a r r i e d out as described elsewhere (4). RESULTS AND DISCUSSION V a r i a t i o n j.n o v e r a l l s t r u c t u r e of 17.6 e l e m e n t s Using a 2.1 kb (kb=»1000 b a s e p a i r s ) H i n d l l l 4766 f r a g m e n t of Nucleic Acids Research 1 504 L±_ t t_ 2 2J t-LJ SOB t T t 511 514 516 518* 519* - 525 T t T T7 536 T t T t T tTt 530 5J4B d f T y T t T t O Q t 0 0 Ttt 1 Fig. 1. Restriction maps of cloned Drosophila fragments containing 17.6-related sequences along with tne locations and deduced structures of 17.6s. The top line labelled 17.6 shows the restriction map of the Drosophila insert in Xhistl7.6. The fragments used for probes for hybridization are marked by three underlines a, b and c. T , Hindlll; • , EcoRI; + , BamHI; O , Clal;V SinI. In the case of Clal and SinI, only the sites within some LTRs are shown. , homology with probe a for detection of LTR sequences; , homology with probe b; , homology with probe c. Asterisks show the presence of plural clones exhibiting identical restriction maps. The locations and the deduced structures of 17.6s are schematically illustrated just beneath the restriction map of each clone. The locations of deletions are shown by triangles, while those of LTRs, by boxes. The estimated lengths of the deletions are as follows; X510, 0.6 kb; X525, 0.5kb;X530, 3.3kb;X540, 1.0kb;X602, 2.2kb;X605, 1.2kb; X534B,0.4kb. 4767 Nucleic Acids Research 17.6 in Xhistl7.6 (see an underline b in Fig.l) as a probe, 50 recombinant clones were isolated from about 5x 10 phages in a cloned l i b r a r y of Drosophila me lanogaster DNA. Mapping of r e s t r i c t i o n enzyme s i t e s followed by Southern hybridization showed that these recombinant clones as a whole represent at least 21 chromosomal loci corresponding to half the total 17.6i n s e r t i o n s i t e s per haploid chromosome (Fig.l). Since 17.6 genomes in s e v e r a l clones were found to be a r t i f i c i a l l y truncated at i n t e r n a l EcoRI s i t e s , t h e i r structures were not analyzed furthermore except for that in X526. The precise locations of the ends of 17.6s together with those of possible i n t e r n a l deletions were determined in the majority of the remaining clones by mapping the cutting s i t e s of r e s t r i c t i o n enzymes, heteroduplex a n a l y s e s and/or p a r t i a l nucleotide sequencing. The structures of t h i r t e e n 17.6 elements thus determined are schematically shown in Fig.l. About half these t h i r t e e n elements ( those in X510, X525,X530, X534B,X540, X602 and X605) were each found to have a large deletion, internal or terminal, with respect to the authentic 17.6 in Xhistl7.6. The distribution of these deletions appears random. Some examples of electron micrographs of heteroduplex molecules between Xhistl7.6 and other clones are shown in Fig.2. In the case of 17.6 in X605, which contains a 1.2kb-long i n t e r n a l deletion, the duplex region with the right-hand LTR (see Fig.l) was occasionally observed to be single-stranded (see the regions with large arrowheads in Figs.2D and E). Though the reason for t h i s is unclear, i t i s unlikely that t h i s structural change a r i s e s from possible variation in nucleotide sequence in that particular region of 17.6 in X605. In fact, except for a 50bp(base pair)-long, highly reshuffled region located immediately next to the deletion s i t e (Fig.3), only one nucleotide change could be found in a t o t a l of 1100 nucleotides flanking the deletion s i t e in 17.6 in X605 (data not shown). 17.6 in X534B contained a very short (about 200bp-long), internal deletion which could not be clearly visualized by electrontnicroscope (Fig.2B): the location of t h i s short deletion was determined by fine r e s t r i c t i o n mapping not shown here. 4768 Nucleic Acids Research Fig. 2. Electron micrographs of heteroduplex molecules between the DNA from a cloned phage having 17.6-related sequence and Ahistl7.6 DNA. A, X530; B, X534B; C, X540; D and E, two different examples of X605; F,X634. M, marker DNA (pBR322 with a molecular weight of 4.4kb); D, double-stranded region; S, single-stranded region. Large arrows in D and E show two variations in the heteroduplex molecules of Xhistl7.6 and X 605. Arrows labelled X indicate stem and loop structures found in the DNA from X605. The lengths of the duplex regions expected to include 17.6 are estimated as follows. A, (4.1 ± 0.2)kb. B, (7.0 ± 0.3)kb. C; (5.3 ± 0.3 and 1.1 ± l.OJkb; D, (3.9 ± 0.2)kb; E, (3.8 ±0.2 and 2.5 ± 0.2)kb; F, (7.1 ± 0.3)kb. (A slightly reduced value in F with respect to the authentic 17.6 is at least partly due to a high degree of variation in nucleotide sequence at the 3'terminal regions of LTRs (see Fig.3) .) 4769 Nucleic Acids Research 605 17.6 AAUCTTTTCTTGGACTUAI AGGATATTATCGTAAATTTATTXCAAACTTTGCAGACAT AAGCTTTTCTTGGACTGACAGGATATTATCGTAAATTTATTCCAAACTTTGCAGACAT AGCCAAACCCATGACTAACTGTTTAAAAAAGAACATGAAAATTGACACTACCAACCCAGAATAT AGCCAAACCCATGACTAAGTGTTTAAAAAAGAACATGAAAATTGACACTACCAACCCAGAArAT CCCGA] CCCGACTTTI rr> 12|l lit IGAGATGCOT'GGAGACTGAGGAAGTCGAAT rGCAGC TTAACA(;AACAAAAACTGGTCT(K3CGGACATAGAAAGACTACATAAAACAATTAATGAAAAGAT TTAACACAACAAAAACTGGTGTGGCGGACATAGAAAGACTACATAAAACAAT1AATGAAAAGAT Fig. 3. Nucleotide sequence variation near the deletion site in X605. Horizontal lines with arrowheads and numbers show the locations and sizes of direct repeats. Note that, although repeats 1 and 3 are located at identical loci in the 17.6s of X605 and Xhistl7.6, respectively, their sequences differ considerably from each other. One additional finding that should be mentioned is that the restriction map of 17.6 in X602 extensively differs from those of other 17.6s including the authentic 17.6 in Xhistl7.6. That is, 17.6 in X602 lacks all the conserved cutting sites of EcoRI, BamHI and Sail, although no deletion/insertion was observed in the corresponding regions by electronmicroscopy (see Fig.l). Because of the deletion of its left-hand LTR-containing region, 17.6 in X602 must be a kind of dead element at least with respect to translocation. There is the possibility that this 17.6 became a dead element a very long time ago, followed by introduction of the observed variations in the restriction sites. Variations j^n nucleotide sequences of LTRs. To ascertain the degree of variation at the level of nucleotide sequence, we determined the complete nucleotide sequences of the right-hand LTRs of nine 17.6 elements. As shown in Fig.4, these nucleotide sequences are similar but not identical to one another. Since we determined the LTR sequences of about one quarter of 17.6s in a haploid chromosome, the above finding that there is no pair of 17.6s with LTRs having identical sequences may suggest that the last duplication and insertion of the majority of these 17.6s occurred long ago so that even newly inserted 17.6a have become the targets for additional mutations with respect to parental ones. 4770 Nucleic Acids Research In addition to many 1-3 bp long nucleotide changes, several long (6-34bp) insertions and deletions were detected, most explainable by duplication of neighbouring sequences or deletion of already duplicated sequences, as indicated by the horizontal lines with arrowheads in Fig.4. In particular, the 3'terminal one third of the LTR of 17.6 in X634 was found to have an exceptionally varied nucleotide sequence with only 45 % homology with the counterpart of the authentic 17.6 in Xhistl7.6. As described below, this highly varied region corresponds to R + U5 in the LTR of the authentic 17.6. To our knowledge, no other copia-like elements have been shown to include a member having LTRs with such a high degree of variation (19-23). However, this unusual variation in LTR- of 17.6 in X6J4 appears not to influence the sequence-specific insertion of 17.6 (24), since, as shown previously (24), the insertion of this 17.6 resulted in a duplication of ATAT as also in the case of all other 17.6 elements. In addition to these, 9 changes in nucleotide sequences were found to be shared by plural elements (Fig.4) , indicating 17.6 LTR to possibly contain many polymorphic nucleotide sequences having equal biological activity. Since combinations of polymorphic changes among 17.6s appear to be rather random, the present distribution of combinations of polymorphic changes in 17.6s may possibly result in part from either cumulative recombinations between LTRs of different 17.6s or plural independent mutational events or both. The nucleotide sequences of both LTRs of a copia-like element must be perfectly corrected at the time of insertion, if its translocation is carried out via an RNA intermediate by a mechanism similar to that in retrovirus (25). In fact, in the case of copia, such a phenomenon has been reported (19). To examine this possibility in 17.6, all or some of the nucleotide sequences of the left-hand LTRs of five 17.6 elements were determined and compared with those of their right-hand counterparts.The results shown in Fig.4 are consistent to some degree with our expectation, since all the 17.6 elments examined here as well as the authentic 17.6 in Xhistl7.6 have at least a few minor base differences in both LTRs. In particular, the LTRs 4771 Nucleic Acids Research 17.1 ACTGACATATTCACATACAAAACCACATAACATAGAGTAAACATATTGAAAAaXC-- M5 -CAT-ACGTAAACAATAAGTGACCACCATGCTAATGTGGATCAAA -C- 134 534B T T T. T. :«.:::•::•?:. ..fl.». . . . . .. ] C- jf. / A.A • A . A . .A.A. 17 a TAACAAAAATATCCACTCTOCATTTTC- •03 T.CA cTTT-S34 T 5J4B CT Q 53U 540 S2fl 314 SU G t.*...A.A m"- : • g : -ACAaXCC-ATACTCTATGCC-ATCTGCCCAGTATGCATTCTAATAAACAAATTCTTTC .T CAG. G . . CAG..G. •:.:: .. .c .CA.. . . .c . . .c T .CA.. . . . c 334S 341 17.8 •OB T .CA.. -B-CA ...c C CAG..G.. .CAG - G . . . :*.? - TTACCO>TTCnOTAAA<^UUTCTTAAAcicTlgCTCCTCTCTCTgAaarrrcTCCTCC - - ACTTAAC-AATCCAAGA R+U5 420 b GAACGTTAATCAATAAAC TCATTTGA . . .GT TTTGAI 11 IlL CATTTCATTTm TCATTTGATTTTlT AC...AATC...A.C AC. . .AATC.. & C AC...AATC..X.C TCATTTGA1111C P- ^ T l A C . . AATC . . A . . C AC...AATC...A..C AC...AATC . . A . . C T- S- - - - -H5341 529 514 533 HI 53«a S40 A..A.AA..GA' A..A.AA..SA' ..A.AA..SA' ..A.AA..SA' ..A.AA..SA' ..A.AA..CA' ..A.AA..GATT.C -.A...CT - T- S^l -.A...ST -.A...ST T- . . . . I T-. -.A...CT -.A...CT - . A . . .GT -.A...CT TTTT- A AAAACTCAATT AAAACTCAATT.. . . AAAAC1QUTT.. . . G.C. G.C. C.C. G.C. G.C. G.C. G.C. .TTCOSA...G.C .TTCCOA...C.C .TTCCSA...G.C .TTCGGA...G.C .TTCSCA ..G.C .TTCGOA...G.C .TTCCSA ..G.C US at 514B 523 514 in 5U 33(0 ...C..TTTATT.C...C.TTTATTT.C ...C..TTTATT.C...C.IlBllll.C .. .c..TTTATT.C. . . c . r W c . . .C. .TTTATT.C. . .C.mATTT.C ...C..TTTATT.C...C.TTTATTT.C ...C..TTTATT.C...C.TTTATTT.C Fig. 4. The nucleotide sequences of LTRs of 17.6s from various clones. Capital letters on the line labelleH 5y 17.6 show the nucleotide sequence of the left-hand LTR of the authentic 17.6 in Xhistl7.6, whereas those on other lines 4772 Nucleic Acids Research exhibit the sequences of the right-hand LTRs of the 17.6s from various clones examined in the present research. Small letters appearing above these sequences indicate nucleotide sequence changes observed in the opposite LTRs of the same elements. Note that the complete nucleotide sequences of the left-hand LTRs were determined in 17.6s in X605, X634 and X508, while only the 5'terminal one third and two thirds of the left-hand LTRs were sequenced for 17.6s in X535 and X538B, respectively. Bars indicate deletions, and dotted lines the absence of nucleotide change with respect to the left-hand LTR of the authentic 17.6. Boxes indicate variation in the nucleotide sequences from the left-hand LTR of the authentic 17.6. Direct repeats and locations of RNA starts are indicated by horizontal and L-shaped arrowheads, respectively. Dots in some horizontal arrowed lines denote mismatches and X identifies a particular repeat discussed in the text. A large lozenge and triangle, located respectively at 450 and 536 nucleotides from the 51 end, indicate the locations of Clal and SinI characteristic of 17.6 LTR. of 17.6 in X538B was found to have many right-left differences. However, at the same time, that the degree of difference in LTR sequence within an element is much less than that among different elements in most cases should be mentioned. Note the right-left difference in LTR sequence in 17.6 in X634 having an unusually high degree of variation, is also very small. We interpret these results as indicating that 17.6 possibly has, b a s i c a l l y , the a b i l i t y to c o r r e c t LTR s e q u e n c e s on translocation, but since they may have resided for a long period of time at the present chromosomal loci, the LTRs of the majority of 17.6s have incurred mutations, the number and extent of which depending on the duration of this period. Variation in RNA start sites from within left-hand LTR. Our previous nucleotide sequence analysis of the entire 17.6 element (2) showed the direction of transcription of all three major open reading frames of 17.6 to be from left to right in the case of orientation of 17.6s as in Fig.l. The genomesized RNA of copia was also shown to be transcribed from within LTR (4,27). To see if transcription of the 17.6 genome starts from within left-hand LTR, all the RNA extracted from Drosophila tissue cultured cells (GM2 cells) was examined by primer extension, using a 25 nucleotide-long synthetic oligonucleotide complementary to the region P in Fig.5 as a primer. In Fig.6, seven intensive bands along with many faint ones and smear in 4773 Nucleic Acids Research 297 5'_ 17.6 i 297 GTTCAAATACT i A G G C T T c T C C T C A l M T C A A T T T G C A T T T i 17 6 AAGCAAGCAf AliAGGCTTCTCCTCA r T T T C A C T T T C A T T T 297 CTTAAIJCTGAGATCCAAAO 17.6 CTTAAGCTGAACGTTAATC AATAAA CAACACAATCGATACCGAAATTT JTCGTGAAACTATTTCTCCTAAA ( 3 3 2 ) I 401)) Fig. 5. Locations of RNA s t a r t s and n u c l e o t i d e sequence conservation between 17.6 and 297. The locations of RNA s t a r t s a-g of 17.6 (see Fig.6 ) a n d T h a t of the major RNA of 222 (unpublished observation) are shown by vertical arrowheads. Wavy l i n e s i n d i c a t e host DNA, while the boxes show the s i z e and l o c a t i o n s of LTRs. A bar l a b e l l e d P i n d i c a t e s the l o c a t i o n of the primer used for primer extention (region P; nucleotides 542547 from the 5'end of the a u t h e n t i c 17.6 (see Fig.l of ref. 2).). Triangles show t h e l o c a t i o n s of t h e putative polyadenylation s i g n a l s . The nucleotide sequences of 17.6 and 297, d e l i m i t e d by broken l i n e s , are shown in the lower h a l f . Note t h a t the l o c a t i o n of RNA s t a r t b of 17.6 and t h a t of the major 29 7 RNA are i d e n t i c a l to each other within a l i m i t of e r r o r . Boxes A and B i n d i c a t e the nucleotide sequences assumed in a previous experiment to correspond to the Hogness box and polyadenylation signal of avian leukaemia-saroma v i r u s (1), while box X shows the sequence conserved between 17.6 and 2 9 7. As shown by arrowheads X in Fig.4, t h i s conserved sequence Fs repeated within the 17.6 LTR. A s t e r i s k s show the homology between 17.6 and 297 sequences. the high molecular-weight region can be seen. Since t h i s banding p a t t e r n did not change with the further a d d i t i o n of r e v e r s e t r a n s c r i p t a s e (data not shown), 17.6s may p o s s i b l y have heterogeneous RNA s t a r t s i t e s in or near left-hand LTRs. As summarized in Fig.7, RNA s t a r t s , c-g, are located near or w i t h i n a 9 n u c l e o t i d e - l o n g canonical sequence, CCATTTATT, whereas RNA s t a r t b i s localized in the very v i c i n i t y of TCAGT, a sequence proposed as being near the major RNA s t a r t s of v a r i o u s Drosophila c o p i a - l i k e elements including mdgl (26). Since a p u t a t i v e polyadenylation signal AATAAA i s located upstream of RNA s t a r t s c-g for a l l LTR sequences presented in F i g . 4 , t h e s e s i t e s do not appear t o p a r t i c i p a t e in t h e transcription of the genome-sized RNA of 17.6 expected to serve 4774 Nucleic Acids Research 160 147 122 110 J 76 - « • 67 J • e • g Fig. 6. A primer extention pattern of 17.6 RNA. Horizontal arrowheads labelled by alphabetical letters show the major RNA starts of 17.6 in or near the left-hand LTR. Minor RNA starts are indicated by dots. The range of left-hand LTR is shown by an L-shaped arrowhead. The markers used were HpalI digests of pBR322 (4). as a substrate for reverse transcription on translocation. RNA start a .located upstream of the 5'end of the left-hand LTR of the authentic 17.6, must be the strongest initiation site for the transcription of 17.6 from an outside promoter. Similar transcription from outside of LTR has been found in the case of 4775 Nucleic Acids Research 17.6 c ] 7.6 d 17.6 AATTATTTfTTI efg 17.6 b 297 TTtpSUDCTTA »dg 1 Fig.7. Consensus sequences near RNA starts. Deduced consensus sequences are enclosed by boxes. Thick bars with L-shaped arrowheads indicate the uncertainty in determining RNA starts. The RNA start of mdgl is as shown by Arkhipova et. al.(26). copia (27). RNA start b is located within a region previously proposed as corresponding to Hogness box of avian leukaemiasarcoma virus (1). In Fig.5, the location of RNA start b is within the region corresponding to that with the major RNA start of 29 7, a sibling of 17.6, within a limit of error. Since it is the only major RNA start located within 17.6 LTR and upstream of a putative polyadenylation signal (see box B in Fig.5), RNA start b is tentatively concluded to be the initiation site of transcription of the 17.6 genome RNA expected to be reverse transcribed. It is also suggested from these results that, as with copia (4), LTR of 17.6 can be divided into three regions U3, R, and U5 and the location of the boundary between U3 and R + U5 is as indicated in Fig.4. (Note that this location differs somewhat from that proposed on the basis of the homology with the avian retrovirus (1).) However, the above findings do not necessarily mean that the genome RNA of 17.6 is always reverse transcribable for its translocation. In fact, no change was found in the blotting hybridization pattern of 17.6 among DNAs extracted from GM2 cells cultured separately for more than two years (unpublished observation). In this connection, it should perhaps be mentioned that a 14-nucleotide-long sequence, GAGGCTTCTCCTCA, is present 20-30 nucleotides upstream of both 17.6 RNA b and the major RNA of 297 (see box labelled by arrowed underline X in Fig.5). Because of its location, this sequence is likely related to the transcriptional regulation of these RNAs. Interestingly, the 4776 Nucleic Acids Research same sequence is repeated in the 5'-upstream region in the case of 17.6 and is the longest in the repeated sequences found in the LTR of the authentic 17.6 (see arrowed underlines X in Fig.4) . ACKNOWLEDGEMENTS The authors express their appreciation to Prof. M. Sekiguchi for. his critical comments. This work was supported in part by grants from the Ministry of Education, Science and Culture, Japan to K.S. T o whom correspondence should be addressed REFERENCES 1. Kugimiya, W. , Ikenaga, H. and Saigo, K. (1983) Proc. Natl. Acad. Sci. USA 80, 3193-3197. 2. 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