Makalowska I, Lin CF, Makalowski W: Overlapping genes in vertebrate genomes. Comput Biol Chem. 2005, 29 (1): 1-12. 10.1016/j.compbiolchem.2004.12.006.
Article
CAS
PubMed
Google Scholar
Rougeulle C, Heard E: Antisense RNA in imprinting: spreading silence through Air. Trends Genet. 2002, 18 (9): 434-437. 10.1016/S0168-9525(02)02749-X.
Article
CAS
PubMed
Google Scholar
Brantl S: Antisense-RNA regulation and RNA interference. Biochim Biophys Acta. 2002, 1575 (1-3): 15-25.
Article
CAS
PubMed
Google Scholar
Prescott EM, Proudfoot NJ: Transcriptional collision between convergent genes in budding yeast. Proc Natl Acad Sci U S A. 2002, 99 (13): 8796-8801. 10.1073/pnas.132270899.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hastings ML, Ingle HA, Lazar MA, Munroe SH: Post-transcriptional regulation of thyroid hormone receptor expression by cis-acting sequences and a naturally occurring antisense RNA. J Biol Chem. 2000, 275 (15): 11507-11513. 10.1074/jbc.275.15.11507.
Article
CAS
PubMed
Google Scholar
Ogawa Y, Lee JT: Antisense regulation in X inactivation and autosomal imprinting. Cytogenet Genome Res. 2002, 99 (1-4): 59-65. 10.1159/000071575.
Article
CAS
PubMed
Google Scholar
Marcelino J, Carpten JD, Suwairi WM, Gutierrez OM, Schwartz S, Robbins C, Sood R, Makalowska I, Baxevanis A, Johnstone B, Laxer RM, Zemel L, Kim CA, Herd JK, Ihle J, Williams C, Johnson M, Raman V, Alonso LG, Brunoni D, Gerstein A, Papadopoulos N, Bahabri SA, Trent JM, Warman ML: CACP, encoding a secreted proteoglycan, is mutated in camptodactyly-arthropathy-coxa vara-pericarditis syndrome. Nature genetics. 1999, 23 (3): 319-322. 10.1038/15496.
Article
CAS
PubMed
Google Scholar
Lamason RL, Mohideen MA, Mest JR, Wong AC, Norton HL, Aros MC, Jurynec MJ, Mao X, Humphreville VR, Humbert JE, Sinha S, Moore JL, Jagadeeswaran P, Zhao W, Ning G, Makalowska I, McKeigue PM, O'Donnell D, Kittles R, Parra EJ, Mangini NJ, Grunwald DJ, Shriver MD, Canfield VA, Cheng KC: SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans. Science. 2005, 310 (5755): 1782-1786. 10.1126/science.1116238.
Article
CAS
PubMed
Google Scholar
Keese PK, Gibbs A: Origins of genes: "big bang" or continuous creation?. Proc Natl Acad Sci U S A. 1992, 89 (20): 9489-9493. 10.1073/pnas.89.20.9489.
Article
PubMed Central
CAS
PubMed
Google Scholar
Shintani S, O'HUigin C, Toyosawa S, Michalova V, Klein J: Origin of gene overlap: the case of TCP1 and ACAT2. Genetics. 1999, 152 (2): 743-754.
PubMed Central
CAS
PubMed
Google Scholar
Dahary D, Elroy-Stein O, Sorek R: Naturally occurring antisense: transcriptional leakage or real overlap?. Genome Res. 2005, 15 (3): 364-368. 10.1101/gr.3308405.
Article
PubMed Central
CAS
PubMed
Google Scholar
Veeramachaneni V, Makalowski W, Galdzicki M, Sood R, Makalowska I: Mammalian overlapping genes: the comparative perspective. Genome Res. 2004, 14 (2): 280-286. 10.1101/gr.1590904.
Article
PubMed Central
CAS
PubMed
Google Scholar
Dan I, Watanabe NM, Kajikawa E, Ishida T, Pandey A, Kusumi A: Overlapping of MINK and CHRNE gene loci in the course of mammalian evolution. Nucleic Acids Res. 2002, 30 (13): 2906-2910. 10.1093/nar/gkf407.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kasper G, Taudien S, Staub E, Mennerich D, Rieder M, Hinzmann B, Dahl E, Schwidetzky U, Rosenthal A, Rump A: Different structural organization of the encephalopsin gene in man and mouse. Gene. 2002, 295 (1): 27-32. 10.1016/S0378-1119(02)00799-0.
Article
CAS
PubMed
Google Scholar
Steigele S, Nieselt K: Open reading frames provide a rich pool of potential natural antisense transcripts in fungal genomes. Nucleic Acids Res. 2005, 33 (16): 5034-5044. 10.1093/nar/gki804.
Article
PubMed Central
CAS
PubMed
Google Scholar
Su AI, Cooke MP, Ching KA, Hakak Y, Walker JR, Wiltshire T, Orth AP, Vega RG, Sapinoso LM, Moqrich A, Patapoutian A, Hampton GM, Schultz PG, Hogenesch JB: Large-scale analysis of the human and mouse transcriptomes. Proc Natl Acad Sci U S A. 2002, 99 (7): 4465-4470. 10.1073/pnas.012025199.
Article
PubMed Central
CAS
PubMed
Google Scholar
Yelin R, Dahary D, Sorek R, Levanon EY, Goldstein O, Shoshan A, Diber A, Biton S, Tamir Y, Khosravi R, Nemzer S, Pinner E, Walach S, Bernstein J, Savitsky K, Rotman G: Widespread occurrence of antisense transcription in the human genome. Nat Biotechnol. 2003, 21 (4): 379-386. 10.1038/nbt808.
Article
CAS
PubMed
Google Scholar
Lehner B, Williams G, Campbell RD, Sanderson CM: Antisense transcripts in the human genome. Trends Genet. 2002, 18 (2): 63-65. 10.1016/S0168-9525(02)02598-2.
Article
CAS
PubMed
Google Scholar
Zhang Y, Liu XS, Liu QR, Wei L: Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species. Nucleic Acids Res. 2006, 34 (12): 3465-3475. 10.1093/nar/gkl473.
Article
PubMed Central
CAS
PubMed
Google Scholar
Birney E, Andrews TD, Bevan P, Caccamo M, Chen Y, Clarke L, Coates G, Cuff J, Curwen V, Cutts T, Down T, Eyras E, Fernandez-Suarez XM, Gane P, Gibbins B, Gilbert J, Hammond M, Hotz HR, Iyer V, Jekosch K, Kahari A, Kasprzyk A, Keefe D, Keenan S, Lehvaslaiho H, McVicker G, Melsopp C, Meidl P, Mongin E, Pettett R, Potter S, Proctor G, Rae M, Searle S, Slater G, Smedley D, Smith J, Spooner W, Stabenau A, Stalker J, Storey R, Ureta-Vidal A, Woodwark KC, Cameron G, Durbin R, Cox A, Hubbard T, Clamp M: An overview of Ensembl. Genome Res. 2004, 14 (5): 925-928. 10.1101/gr.1860604.
Article
PubMed Central
CAS
PubMed
Google Scholar
Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, Dugan-Rocha S, Miner G, Morgan M, Hawes A, Gill R, Celera, Holt RA, Adams MD, Amanatides PG, Baden-Tillson H, Barnstead M, Chin S, Evans CA, Ferriera S, Fosler C, Glodek A, Gu Z, Jennings D, Kraft CL, Nguyen T, Pfannkoch CM, Sitter C, Sutton GG, Venter JC, Woodage T, Smith D, Lee HM, Gustafson E, Cahill P, Kana A, Doucette-Stamm L, Weinstock K, Fechtel K, Weiss RB, Dunn DM, Green ED, Blakesley RW, Bouffard GG, De Jong PJ, Osoegawa K, Zhu B, Marra M, Schein J, Bosdet I, Fjell C, Jones S, Krzywinski M, Mathewson C, Siddiqui A, Wye N, McPherson J, Zhao S, Fraser CM, Shetty J, Shatsman S, Geer K, Chen Y, Abramzon S, Nierman WC, Havlak PH, Chen R, Durbin KJ, Egan A, Ren Y, Song XZ, Li B, Liu Y, Qin X, Cawley S, Worley KC, Cooney AJ, D'Souza LM, Martin K, Wu JQ, Gonzalez-Garay ML, Jackson AR, Kalafus KJ, McLeod MP, Milosavljevic A, Virk D, Volkov A, Wheeler DA, Zhang Z, Bailey JA, Eichler EE, Tuzun E, Birney E, Mongin E, Ureta-Vidal A, Woodwark C, Zdobnov E, Bork P, Suyama M, Torrents D, Alexandersson M, Trask BJ, Young JM, Huang H, Wang H, Xing H, Daniels S, Gietzen D, Schmidt J, Stevens K, Vitt U, Wingrove J, Camara F, Mar Alba M, Abril JF, Guigo R, Smit A, Dubchak I, Rubin EM, Couronne O, Poliakov A, Hubner N, Ganten D, Goesele C, Hummel O, Kreitler T, Lee YA, Monti J, Schulz H, Zimdahl H, Himmelbauer H, Lehrach H, Jacob HJ, Bromberg S, Gullings-Handley J, Jensen-Seaman MI, Kwitek AE, Lazar J, Pasko D, Tonellato PJ, Twigger S, Ponting CP, Duarte JM, Rice S, Goodstadt L, Beatson SA, Emes RD, Winter EE, Webber C, Brandt P, Nyakatura G, Adetobi M, Chiaromonte F, Elnitski L, Eswara P, Hardison RC, Hou M, Kolbe D, Makova K, Miller W, Nekrutenko A, Riemer C, Schwartz S, Taylor J, Yang S, Zhang Y, Lindpaintner K, Andrews TD, Caccamo M, Clamp M, Clarke L, Curwen V, Durbin R, Eyras E, Searle SM, Cooper GM, Batzoglou S, Brudno M, Sidow A, Stone EA, Venter JC, Payseur BA, Bourque G, Lopez-Otin C, Puente XS, Chakrabarti K, Chatterji S, Dewey C, Pachter L, Bray N, Yap VB, Caspi A, Tesler G, Pevzner PA, Haussler D, Roskin KM, Baertsch R, Clawson H, Furey TS, Hinrichs AS, Karolchik D, Kent WJ, Rosenbloom KR, Trumbower H, Weirauch M, Cooper DN, Stenson PD, Ma B, Brent M, Arumugam M, Shteynberg D, Copley RR, Taylor MS, Riethman H, Mudunuri U, Peterson J, Guyer M, Felsenfeld A, Old S, Mockrin S, Collins F: Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 2004, 428 (6982): 493-521. 10.1038/nature02426.
Article
CAS
PubMed
Google Scholar
Aparicio S, Chapman J, Stupka E, Putnam N, Chia JM, Dehal P, Christoffels A, Rash S, Hoon S, Smit A, Gelpke MD, Roach J, Oh T, Ho IY, Wong M, Detter C, Verhoef F, Predki P, Tay A, Lucas S, Richardson P, Smith SF, Clark MS, Edwards YJ, Doggett N, Zharkikh A, Tavtigian SV, Pruss D, Barnstead M, Evans C, Baden H, Powell J, Glusman G, Rowen L, Hood L, Tan YH, Elgar G, Hawkins T, Venkatesh B, Rokhsar D, Brenner S: Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science. 2002, 297 (5585): 1301-1310. 10.1126/science.1072104.
Article
CAS
PubMed
Google Scholar
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature. 2004, 432 (7018): 695-716. 10.1038/nature03154.
Long M, Betran E, Thornton K, Wang W: The origin of new genes: glimpses from the young and old. Nat Rev Genet. 2003, 4 (11): 865-875. 10.1038/nrg1204.
Article
CAS
PubMed
Google Scholar
Ohno S: Evolution by gene duplication. 1970, Berlin; New York , Springer-Verlag
Chapter
Google Scholar
Brosius J: RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements. Gene. 1999, 238 (1): 115-134. 10.1016/S0378-1119(99)00227-9.
Article
CAS
PubMed
Google Scholar
Makalowski W: Genomics. Not junk after all. Science. 2003, 300 (5623): 1246-1247. 10.1126/science.1085690.
Article
CAS
PubMed
Google Scholar
van Duin M, van Den Tol J, Hoeijmakers JH, Bootsma D, Rupp IP, Reynolds P, Prakash L, Prakash S: Conserved pattern of antisense overlapping transcription in the homologous human ERCC-1 and yeast RAD10 DNA repair gene regions. Mol Cell Biol. 1989, 9 (4): 1794-1798.
Article
PubMed Central
CAS
PubMed
Google Scholar
Brosius J: On "genomencature": a comprehensive (and respectful) taxonomy for pseudogenes amd other "junk DNA". Proc Natl Acad Sci. 1992, 89 (22): 10706-10710. 10.1073/pnas.89.22.10706.
Article
PubMed Central
CAS
PubMed
Google Scholar
Thornburg BG, Gotea V, Makalowski W: Transposable elements as a significant source of transcription regulating signals. Gene. 2006, 365: 104-110. 10.1016/j.gene.2005.09.036.
Article
CAS
PubMed
Google Scholar
Romanish MT, Lock WM, de Lagemaat LN, Dunn CA, Mager DL: Repeated Recruitment of LTR Retrotransposons as Promoters by the Anti-Apoptotic Locus NAIP during Mammalian Evolution. PLoS Genet. 2007, 3 (1): e10-10.1371/journal.pgen.0030010.
Article
PubMed Central
PubMed
Google Scholar
Lorenc A, Makalowski W: Transposable elements and vertebrate protein diversity. Genetica. 2003, 118 (2-3): 183-191. 10.1023/A:1024105726123.
Article
CAS
PubMed
Google Scholar
Gotea V, Makalowski W: Do transposable elements really contribute to proteomes?. Trends Genet. 2006, 22 (5): 260-267. 10.1016/j.tig.2006.03.006.
Article
CAS
PubMed
Google Scholar
Nei M, Rooney AP: Concerted and birth-and-death evolution of multigene families. Annual review of genetics. 2005, 39: 121-152. 10.1146/annurev.genet.39.073003.112240.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ensembl: Gene Orthology/Paralogy prediction method. [http://www.ensembl.org/info/data/compara/homology_method.html]
Pertea G, Huang X, Liang F, Antonescu V, Sultana R, Karamycheva S, Lee Y, White J, Cheung F, Parvizi B, Tsai J, Quackenbush J: TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics. 2003, 19 (5): 651-652. 10.1093/bioinformatics/btg034.
Article
CAS
PubMed
Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol. 1990, 215 (3): 403-410.
Article
CAS
PubMed
Google Scholar
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL: GenBank. Nucleic Acids Res. 2005, 33 (Database issue): D34-8. 10.1093/nar/gki063.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hinrichs AS, Karolchik D, Baertsch R, Barber GP, Bejerano G, Clawson H, Diekhans M, Furey TS, Harte RA, Hsu F, Hillman-Jackson J, Kuhn RM, Pedersen JS, Pohl A, Raney BJ, Rosenbloom KR, Siepel A, Smith KE, Sugnet CW, Sultan-Qurraie A, Thomas DJ, Trumbower H, Weber RJ, Weirauch M, Zweig AS, Haussler D, Kent WJ: The UCSC Genome Browser Database: update 2006. Nucleic Acids Res. 2006, 34 (Database issue): D590-8. 10.1093/nar/gkj144.
Article
PubMed Central
CAS
PubMed
Google Scholar
Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22 (22): 4673-4680. 10.1093/nar/22.22.4673.
Article
PubMed Central
CAS
PubMed
Google Scholar