US 2005OOO9771A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2005/0009771 A1 LeVanOn et al. (43) Pub. Date: Jan. 13, 2005 (54) METHODS AND SYSTEMS FOR (22) Filed: Jan. 27, 2004 IDENTIFYING NATURALLY OCCURRING ANTISENSE TRANSCRIPTS AND METHODS, Related U.S. Application Data KITS AND ARRAYS UTILIZING SAME (63) Continuation-in-part of application No. 10/441,281, (76) Inventors: Erez. Levanon, Petach Tikva (IL); filed on May 20, 2003. Jeanne Bernstein, Kfar Yona (IL); Sarah Pollock, Tel Aviv (IL); Alex Publication Classification Diber, Herzlia (IL); Zurit Levine, Herzlia (IL); Sergey Nemzer, Ramat 51)1) Int. Cl.C.7 ............................ A61K 48700 ; C12O 1/68; Gan (IL); Vladimir Grebinsky, G06F 19/00; G01N 33/48; Highland Park, NJ (US); Hanqing Xie, GO1N 33/50 Lambertville, NJ (US); Brian Meloon, (52) U.S. Cl. .................................... 514/44; 435/6; 702/20 Plainsboro, NJ (US); Andrew Olson, Westfield, NJ (US); Dvir Dahary, Tel Aviv (IL); Yossi Cohen, Woking (GB); (57) ABSTRACT Avi Shoshan, Kiryat Gat (IL); Shira Walach, Hod Hasharon (IL); Alon A method of identifying putative naturally occurring anti Wasserman, New York, NY (US); Sense transcripts is provided. The method is effected by (a) Rami Khosravi, Herzlia (IL); Galit computationally aligning a first database including Sense Rotman, Herzlia (IL) oriented polynucleotide Sequences with a Second database Correspondence Address: including expressed polynucleotide Sequences; and (b) iden G.E. EHRLICH (1995) LTD. tifying expressed polynucleotide Sequences from the Second c/o ANTHONY CASTORINA database being capable of forming a duplex with at least one 2001 JEFFERSON DAVIS HIGHWAY, SUITE Sense-oriented polynucleotide Sequence of the first database, 207 thereby identifying putative naturally occurring antisense ARLINGTON, VA 2.2202 (US) transcripts. Also provided are polynucleotides and polypep tide sequences identified by the above-described methodol (21) Appl. No.: 10/764,503 Ogy. Patent Application Publication Jan. 13, 2005 Sheet 1 of 48 US 2005/0009771 A1 No.==================--~~)=====::====::================= Patent Application Publication Jan. 13, 2005 Sheet 2 of 48 US 2005/0009771 A1 Patent Application Publication Jan. 13, 2005 Sheet 3 of 48 US 2005/0009771 A1 Fig. 4a 57oo Av7055320 90 Z4.4352.15 783 O. : 52 Query; l. gg acco agga tatgagcggaaaacactittct ct acttagatacaactttitt c 52 | | | | | | | Sbict : S2 ggaccCaggatatgagcggaaaacactittct ctact tagataca acttitt to 1 Fig. 4b 570 a Av705532 0 OO 2443.5214 649 O. : S2 Query: l ggacccaggatatgagcggaaaacactittctotacttagatacaacttitttc. 52 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Sbjct: 52 gga Cocaggatatgagcggaaaa cact ttctotact tagataca acttitt to l Fig. 4c 570 2 AV7055320 90 Z4.4352 l3 86. OLS 52 Query: l gg accCaggatatgagcggaaaacactittctotact tagataca acttittt c 52 . Sbjct: 52 ggacccaggatatgagcggaaaa cactittct ct acttagata caacttitt to l Fig. 4d 5710 AWO708600 2l 4 TBll 427 934 O. : 54 Query: 1 gtaaggga actittggcqact tagtgcgat cactgggaga attgtagagtccact 54 . Sbjct: l2.5 g taggga act t t gg.cgact tagtgcqat cactgggagaattgtagagt ccact ll 62 Score = 22 - 3 bits ( il), Expect r O. 66 Identities = 1 1/l ( l (O$ ) St. rand = Plus / Minus Query: 146 act tcca gagg l56 i ; Snjot.: 760 act tccagagg 750 Fig. 4e 571 l AWO708600 2l 4 T811426 2353 Os 54 Cuery gta agg gaa Ctttgg.cg act tagt gcgat cactgg gaga attgtagagt ccact 54 . Sajct. : l 215 gta agg gaa ct ttgg.cgact tagtgcgat cactgggaga attgtagagticcact lie2 Score = 22, 3 bits (ll, Expect s 0. 66 identities - il f l l Qs Stranc = Plus in JS Cuery: l (; 6 attacca gagg St. ; : S: ct; F 63 a ci Patent Application Publication Jan. 13, 2005 Sheet 4 of 48 US 2005/0009.771 A1 Score = 22.3 bits (1 l), Expect = 0.66 Identities = hl/ (OO } Strand = Plus / Plus Query: l 00 ggaaaacacac il 0 Sbjct : 1900 ggaaaa.ca cac 910 Fig. 4f 5712 AW0708600 214 T811424 2500 O. : 54 Query: 1 gtaagggaact ttgg.cgact tagt gcg at Cactgggaga attgtagagtccact 54 | | | | | | | | | | | | Sbjct : 1317 gtaagggaactittggcgact tagtgcgat cactgggaga attgttgagt ccact l264 Score = 22.3 bits (li), Expect O. 66 Identities s ll Will ( i 00) Strand = Plus / Minus Query: 146 act tcca gagg 56 Sbict: 862 act tccagagg 852 Score = 22.3 bits (ll), Expect as 0. 66 identities s ll Ali ( 0.0%) St. rand a Plus / Plus Query: 100 gyaaaacacac l 10 Sbict : 284 ggaaaa.ca cac 2C5 S713 Aw0708600 2l 4 T811423 94 OL: 54 Query: 1 gta aggga actittgg.cg act tagt g c gat cact g g gagaattgtagagt coact 54 i | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Spict 224 gtaaggga a Ctttgg.cga ct tag togcq at Cactgg gaga attgtagagticcact ill 571.4 Awo708600 2l?. T8l. 1422 366 OL: S 4 Quer: gta agggia act t t ggag act tag toggat. cact gg gaga attgtagag tocact 54 i Shigt : 22 gta aggge & c. t.tggig act tag targat cactgg gaga attgtagag tecact lil Score = 22.3 bits l ; , Expect. is O. g. 6 Patent Application Publication Jan. 13, 2005 Sheet 5 of 48 US 2005/0009771 A1 Identities = lili fill (100) Strand = Plus / Plus Query : 10?) ggaaaa.ca cac l l () Sbct: 913 ggaaaacacac 923 Fig. 4i 572 O BE046369 O 422 W265533 1532 OL: 52 Query: aatctt cataatccCcatgtgtcaaaggaga gaccaggtggagglta actgaa 52 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Sbjct: l 48l aat ctitcataatccccatgtgtcaaaggagagaccaggtggaggta actgaa 532 Fig. 4.j 5721 BE046369 O 422 w26553 2 753 OL: 52 Query: ll aatct toataatcc.ccatgtgtcaaaggaga gaccaggtggaggta actgaa 52 | | | | | | | | | | | | | | | | | | | | | | | | | | | Sbjct : 1702 aatct tca taatcccCatgtgtcaaaggagagaccagg toggaggta act gaa i753 Fig. 4k 5722 BE0463690 A22 W265531 832 OL, 52 Query: datctt cata at coccat gt at Caaaggaga gaccaggtggaggta act gaa 52 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Sbjct : 78 aatctt cataatccc.catgttgttcaaaggaga gaccaggtggaggta actgaa l832 Patent Application Publication Jan. 13, 2005 Sheet 6 of 48 US 2005/0009771 A1 53BP1 76P 53BP1 lO394 6P 6837 OL: 304 6 OF : 54, 63 OF2: 208 Score = 1659 bits (837), Expect = 0.0 Identities - 840/84 (99%) Strand = P2 tas / Minus Query: 7432 gagacggaattitcgctottgttgccCaggctggaatgcaatggcacaatctoagct cact 749 | | | | | | | | | | | Sbict: 3il3 gagacggaattitcgcticttgttgcccagagctoggaatgcaatggcacaatctoragct cact 3054 Query: 7492 gcagogtctgct tcccaggttcaa.gcaattctectgtctoagcct cotgagtagctggga 755 . | | | | | | | | | | | | | | | | | | | | | Sbjct: 3053 gCagcgtotgct tcc.caggttcaagcaattct cotgtctoagcctoct9agtagctggga 2994 Query: 7552 ttacaggcacatgccaccacacctggctaattitttgtatttittagtagaatcgaggttt c 75. Sbict : 2993 ttacaggcacatgccaccacacctggctaattitttgtattitt tag tagaatcgaggtttc 2934 Que Ly: 7612 dually liggu digg.cgyuct caaact cuttgact tcaggtgat cog CCC90ct.cggcct 767 Sbict: 2933 at catgttgg toaggctgg totcaaacticctgact tcaggtgatcc.gc.ccgcctcggcct 287.4 Query : 7672 cccaaaq togct g g g atta caggtgtgagccaccatgccoggcctaagaaatacttittaag 77 3 | | | | | | | | | | | | | | Sbjct : 2873 cucaaagtgctgggatta caggtgtgagccaccatgcccggcctaagaaa cacttittaag 284 Query : 7732 tatattitt cattagctagaattgcccaatctgttgtaggtataaattact toggtataggga Sbict: 28 l3 tata t t t t cattagctaga attgcc.caatctgttgtagg tataa attacttggtataggga ry: F2 gaga gaaag.cct atct tacct gttgct ttct tacttggtgg taa.catccagoagittagt c | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ct: 2753 gaga gaaagcci.atct tacct gttgctittct tact toggtgg taa.catccagoagttagt c Fig. 5a Patent Application Publication Jan. 13, 2005 Sheet 7 of 48 US 2005/0009771 A1 Query : 7852 tatttataaacataattact tttt cacatatgaaccataaaatatttaactittctgctict 791 | | | | | | | | | | | | | | | | | | | | | | | | | Sbjct: 2693 tatttataaacataattacttitt toacatatgaaccataaaatatttaactittctgctict 2634 Query: 792 a tattgtttgtttaccgct g tat ct cocacagottgaacagtaccaaggtacg tagtagg 7971. Sbjct: 2633 at attgtttgttctaccgctgtatic toccacagottgaacagtacca aggtacgtagtagg 2574 Query 7.972 togctcaataaatgactattgaataaatgaacatatocaacaaatgttctoaatgtaaagg 803 Sbjct : 2573 tyctoaataaatgactattgaataaatgaacatatocaacaaatgttctoaatgtaaagg 254 Query 8032 atcagagatgccacatgttct cottgatgggagaga.ccct tcca catgggaatgatggga 809 Sbjct: 25l3 at Cagagatgccacatgttct cottgatgggagagaccott.ccacatgggaatgatggga 245 4 Query : 8092 aggagttgtact cotggatgttcagta actgcttctaggagaaaagg tagagt cetatica 85. Sbct: 2453 aggagttgtacticctggatgttcagtaactgct tctaggagaaaaggtagagt cotatoa 23.93 Query : 8152 cta agcc.gcagatatttatttgttgtgtggctagaatgggatgttittgaatct tctgttac 82. Sbict : 2393 ct aag.ccgcag at attt atttgttge gtggetagaatgggatgtt t t gaatct tctgttac 2334 Query: 82l2 aacct togggaacgtggct gttatt toaattitatgagccagaaattitt cacatcccgaaac 8271 | | | | | | | | | | | | | | Sbj ct: 2333 a accttgggaacgtggctgttatt toaatt tatgagccagaaattt toacatcccgaaac 227. Query: 8272 822 ct: 2273 it 22 S Score = 1655 bits 835), Expect = O. C. Identi ties s. 849/85 6 (99& Strand Plus / Minus Fig. 5a continued Patent Application Publication Jan. 13, 2005 Sheet 8 of 48 US 2005/0009771 A1 Query: 5903 agatattgctittagggg tatttgatgtggtggtgacggaccCcticatgcc.cagoctoggt 59.62 | | | | | | | | | | | | | | | | | | | | | | | | | Sbct: 4642 aga tattgctt tagggg tatttgatgtggtggtgacggaCCCCtcatgcccagcctcggit 4583 Query: 5963 gctgaagtgtgctgaagcattgcagct gcctgtggtgtcaca agagtgggtgat coagtg 6022 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Sbict: 4582 gctgaagtgtgctgaag cattgcagct gcctgtggtgtcaca agagtgggtgatccagtg 1523 Query: 6023 cct cattgttggggagaga attggatt caagcagoat coaaaatataaacacgattatgt 6082 Sbjct