An overview of nested genes in eukaryotic genomes

Eukaryotic Cell

Volumn 8, Issue 9, 2009, Pages 1321-1329

  Kumar, Anui ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; ARTICLE; EUKARYOTIC CELL; GENE; GENE EXPRESSION REGULATION; GENOME; HUMAN; METABOLISM; MOLECULAR EVOLUTION;

ANIMALS; EUKARYOTIC CELLS; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION; GENOME; HUMANS; NESTED GENES;

EUKARYOTA;

EID: 69949115558     PISSN: 15359778     EISSN: None     Source Type: Journal    
DOI: 10.1128/EC.00143-09     Document Type: Article

References (74)

1. Ashburner, M., C. A. Ball, J. A. Blake, D. Botstein, H. Butler, J. M. Cherry, A. P. Davis, K. Dolinski, S. S. Dwight, J. T. Eppig, M. A. Harris, D. P. Hill, L. Issel-Tarver, A. Kasarskis, S. Lewis, J. C. Matese, J. E. Richardson, M. Ringwald, G. M. Rubin, and G. Sherlock. 2000. Gene Ontology: tool for the unification of biology. Nat. Genet. 25:25-29.
2. Assis, R., A. S. Kondrashov, E. V. Koonin, and F. A. Kondrashov. 2008. Nested genes and increasing organizational complexity of metazoan genomes. Trends Genet. 24:475-478.
3. Barrell, B. G., G. M. Air, and C. A. Hutchison III. 1976. Overlapping genes in bacteriophage phiX174. Nature 264:34-41.
4. 4. Bernardi, A., and F. Bernardi. 1981. Complete sequence of an IS element present in pSC101. Nucleic Acids Res. 9:2905-2911. (Pubitemid 11058661)
5. 5. Bertone, P., V. Stole, T. E. Royce, J. S. Rozowsky, A. E. Urban, X. Zhu, J. L. Rinn, W. Tongprasit, M. Samanta, S. Weissman, M. Gerstein, and M. Snyder. 2004. Global identification of human transcribed sequences with genome tiling arrays. Science 306:2242-2246. (Pubitemid 40024458)
6. Blattner, F. R., G. Plunkett III, C. A. Bloch, N. T. Perna, V. Burland, M. Riley, J. Collado-Vides, J. D. Glasner, C. K. Rode, G. F. Mayhew, J. Gregor, N. W. Davis, H. A. Kirkpatrick, M. A. Goeden, D. J. Rose, B. Mau, and Y. Shao. 1997. The complete genome sequence of Escherichia coli K-12. Science 277:1453-1474.
7. Braun, B. R., M. van Het Hoog, C. d'Enfert, M. Martchenko, J. Dungan, A. Kuo, D. O. Inglis, M. A. Uhl, H. Hogues, M. Berriman, M. Lorenz, A. Levitin, U. Oberholzer, C. Bachewich, D. Harcus, A. Marcil, D. Dignard, T. Iouk, R. Zito, L. Frangeul, F. Tekaia, K. Rutherford, E. Wang, C. A. Munro, S. Bates, N. A. Gow, L. L. Hoyer, G. Kohler, J. Morschhauser, G. Newport, S. Znaidi, M. Raymond, B. Turcotte, G. Sherlock, M. Costanzo, J. Ihmels, J. Berman, D. Sanglard, N. Agabian, A. P. Mitchell, A. D. Johnson, M. Whiteway, and A. Nantel. 2005. A human-curated annotation of the Candida albicans genome. PLoS Genet. 1:36-57.
8. Carninci, P., T. Kasukawa, S. Katayama, J. Gough, M. C. Frith, N. Maeda, R. Oyama, T. Ravasi, B. Lenhard, C. Wells, R. Kodzius, K. Shimokawa, V. B. Bajic, S. E. Brenner, S. Batalov, A. R. Forrest, M. Zavolan, M. J. Davis, L. G. Wilming, V. Aidinis, J. E. Allen, A. Ambesi-Impiombato, R. Apweiler, R. N. Aturaliya, T. L. Bailey, M. Bansal, L. Baxter, K. W. Beisel, T. Bersano, H. Bono, A. M. Chalk, K. P. Chiu, V. Choudhary, A. Christoffels, D. R. Clutterbuck, M. L. Crowe, E. Dalla, B. P. Dalrymple, B. de Bono, G. Della Gatta, D. di Bernardo, T. Down, P. Engstrom, M. Fagiolini, G. Faulkner, C. F. Fletcher, T. Fukushima, M. Furuno, S. Futaki, M. Gariboldi, P. Georgii-Hemming, T. R. Gingeras, T. Gojobori, R. E. Green, S. Gustincich, M. Harbers, Y. Hayashi, T. K. Herrsch, N. Hirokawa, D. Hill, L. Huminiecki, M. Iacono, K. Ikeo, A. Iwama, T. Ishikawa, M. Jakt, A. Kanapin, M. Katoh, Y. Kawasawa, J. Kelso, H. Kitamura, H. Kitano, G. Kollias, S. P. Krishnan, A. Kruger, S. K. Kummerfeld, I. V. Kurochkin, L. F. Lareau, D. Lazarevic, L. Lipovich, J. Liu, S. Liuni, S. McWilliam, M. Madan Babu, M. Madera, L. Marchionni, H. Matsuda, S. Matsuzawa, H. Miki, F. Mignone, S. Miyake, K Morris, S. Mottagui-Tabar, N. Mulder, N. Nakano, H. Nakauchi, P. Ng, R. Nilsson, S. Nishiguchi, S. Nishikawa, F. Nori, O. Ohara, Y. Okazaki, V. Orlando, K. C. Pang, W. J. Pavan, G. Pavesi, G. Pesole, N. Petrovsky, S. Piazza, J. Reed, J. F. Reid, B. Z. Ring, M. Ringwald, B. Rost, Y. Ruan, S. L. Salzberg, A. Sandelin, C. Schneider, C. Schonbach, K. Sekiguchi, C. A. Semple, S. Seno, L. Sessa, Y. Sheng, Y. Shibata, H. Shimada, K Shimada, D. Silva, B. Sinclair, S. Sperling, E. Stupka, K. Suglura, R. Suitana, Y. Takenaka, K. Taki, K. Tammoja, S. L. Tan, S. Tang, M. S. Taylor, J. Tegner, S. A. Teichmann, H. R. Ueda, E. van Nimwegen, R. Verardo, C. L. Wei, K Yagi, H. Yamanishi, E. Zabarovsky, S. Zhu, A. Zimmer, W. Hide, C. Bult, S. M. Grimmond, R. D. Teasdale, E. T. Liu, V. Brusič, J. Quackenbush, C. Wahlestedt, J. S. Mattick, D. A. Hume, C. Kai, D. Sasaki, Y. Tomara, S. Fukuda, M. Kanamori-Katayama, M. Suzuki, J. Aoki, T. Arakawa, J. Iida, K. Imamura, M. Itoh, T. Kato, H. Kawaji, N. Kawagashira, T. Kawashima, M. Kojima, S. Kondo, H. Konno, K. Nakano, N. Ninomiya, T. Nishio, M. Okada, C. Plessy, K. Shibata, T. Shiraki, S. Suzuki, M. Tagami, K Waki, A. Watahiki, Y. Okamura-Oho, H. Suzuki, J. Kawai, and Y. Hayashizaki. 2005. The transcriptional landscape of the mammalian genome. Science 309:1559-1563.
9. 9. Cheng, J., P. Kapranov, J. Drenkow, S. Dike, S. Brubaker, S. Patel, J. Long, D. Stern, H. Tammana, G. Helt, V. Sementchenko, A. Piccolboni, S. Bekiranov, D. K. Bailey, M. Ganesh, S. Ghosh, I. Bell, D. S. Gerhard, and T. R. Gingeras. 2005. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308:1149-1154. (Pubitemid 40696429)
10. Coelho, P. S., A. C. Bryan, A. Kumar, G. S. Shadel, and M. Snyder. 2002. A novel mitochondrial protein, Tarlp, is encoded on the antisense strand of the nuclear 25S rDNA. Genes Dev. 16:2755-2760.
11. Crampton, N., W. A. Bonass, J. Kirkham, C. Rivetti, and N. H. Thomson. 2006. Collision events between RNA polymerases in convergent transcription studied by atomic force microscopy. Nucleic Acids Res. 34: 5416-5425.
12. Crampton, N., N. H. Thomson, J. Kirkham, C. W. Gibson, and W. A. Bonass. 2006. Imaging RNA polymerase-amelogenin gene complexes with single molecule resolution using atomic force microscopy. Eur. J. Oral Sci. 114(Suppl. 1):133-138; discussion, 164-165, 380-381.
13. David, L., W. Huber, M. Granovskaia, J. Toedling, C. J. Palm, L. Bofkin, T. Jones, R. W. Davis, and L. M. Steinmetz. 2006. A high-resolution map of transcription in the yeast genome. Proc. Natl. Acad. Sci. USA 103:5320-5325.
14. 14. de Nobel, H., C. Ruiz, H. Martin, W. Morris, S. Bral, M. Molina, and F. M. Klis. 2000. Cell wall perturbation in yeast results in dual phosphorylation of the Slt2/Mpk1 MAP kinase and in an Slt2-mediated increase in FKS2-lacZ expression, glucanase resistance and thermotolerance. Microbiology 146(Pt. 9):2121-2132. (Pubitemid 30702340)
15. Dodou, E., and R. Treisman. 1997. The Saccharomyces cerevisiae MADS-box transcription factor Rlm1 is a target for the Mpk1 mitogen-activated protein kinase pathway. Mol. Cell. Biol. 17:1848-1859.
16. Elbashir, S. M., J. Harborth, W. Lendeckel, A. Yalcin, K. Weber, and T. Tuschl. 2001. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411:494-498.
17. Engler, J. A., and M. P. van Bree. 1981. The nucleotide sequence and protein-coding capability of the transposable element IS5. Gene 14:155-163.
18. Farrell, C. M., and L. N. Lukens. 1995. Naturally occurring antisense transcripts are present in chick embryo chondrocytes simultaneously with the down-regulation of the α1(I) collagen gene. J. Biol. Chem. 270:3400-3408.
19. Fisk, D. G., C. A. Ball, K. Dolinski, S. R. Engel, E. L. Hong, L. Issel-Tarver, K. Schwartz, A. Sethuraman, D. Botstein, and J. M. Cherry. 2006. Saccharomyces cerevisiae S288C genome annotation: a working hypothesis. Yeast 23:857-865.
20. Ghosal, D., H. Sommer, and H. Saedler. 1979. Nucleotide sequence of the transposable DNA-element IS2. Nucleic Acids Res. 6:1111-1122.
21. Gibson, C. W., N. H. Thomson, W. R. Abrams, and J. Kirkham. 2005. Nested genes: biological implications and use of AFM for analysis. Gene 350:15-23.
22. Godson, G. N., B. G. Barrell, R. Staden, and J. C. Fiddes. 1978. Nucleotide sequence of bacteriophage G4 DNA. Nature 276:236-247.
23. Goffeau, A., B. G. Barrell, H. Bussey, R. W. Davis, B. Dujon, H. Feldmann, F. Galibert, J. D. Hoheisel, C. Jacq, M. Johnston, E. J. Louis, H. W. Mewes, Y. Murakami, P. Philippsen, H. Tettelin, and S. G. Oliver. 1996. Life with 6000 genes. Science 274:546, 563-567.
24. Henikoff, S., and M. K. Eghtedarzadeh. 1987. Conserved arrangement of nested genes at the Drosophila Gart locus. Genetics 117:711-725.
25. 25. Henikoff, S., M. A. Keene, K. Fechtel, and J. W. Fristrom. 1986. Gene within a gene: nested Drosophila genes encode unrelated proteins on opposite DNA strands. Cell 44:33-42. (Pubitemid 16036711)
26. Henikoff, S., M. A. Keene, J. S. Sloan, J. Bleskan, R. Hards, and D. Patterson. 1986. Multiple purine pathway enzyme activities are encoded at a single genetic locus in Drosophila. Proc. Natl. Acad. Sci. USA 83:720-724.
27. Igual, J. C., A. L. Johnson, and L. H. Johnston. 1996. Coordinated regulation of gene expression by the cell cycle transcription factor Swi4 and the protein kinase C MAP kinase pathway for yeast cell integrity. EMBO J. 15:5001-5013.
28. Inoue, S. B., N. Takewaki, T. Takasuka, T. Mio, M. Adachi, Y. Fujii, C. Miyamoto, M. Arisawa, Y. Furuichi, and T. Watanabe. 1995. Characterization and gene cloning of 1,3-β-D-glucan synthase from Saccharomyces cerevisiae. Eur. J. Biochem. 231:845-854.
29. Johnstone, M. E., D. Nash, and F. N. Naguib. 1985. Three purine auxotrophic loci on the second chromosome of Drosophila melanogaster. Biochem. Genet. 23:539-555.
30. Jung, U. S., A. K. Sobering, M. J. Romeo, and D. E. Levin. 2002. Regulation of the yeast Rlml transcription factor by the Mpk1 cell wall integrity MAP kinase. Mol. Microbiol. 46:781-789.
31. 31. Kaeberlein, M., and L. Guarente. 2002. Saccharomyces cerevisiae MPT5 and SSD1 function in parallel pathways to promote cell wall integrity. Genetics 160:83-95. (Pubitemid 34118273)
32. Kapranov, P., A. T. Willingham, and T. R. Gingeras. 2007. Genome-wide transcription and the implications for genomic organization. Nat. Rev. Genet. 8:413-423.
33. Karlin, S., C. Chen, A. J. Gentles, and M. Cleary. 2002. Associations between human disease genes and overlapping gene groups and multiple amino acid runs. Proc. Natl. Acad. Sci. USA 99:17008-17013.
34. Ketela, T., R. Green, and H. Bussey. 1999. Saccharomyces cerevisiae Mid2p is a potential cell wall stress sensor and upstream activator of the PKC1-MPK1 cell integrity pathway. J. Bacteriol. 181:3330-3340.
35. Klaer, R., S. Kuhn, E. Tillmann, H. J. Fritz, and P. Starlingen 1981. The sequence of IS4. Mol. Gen. Genet. 181:169-175.
36. 36. Kröger, M., and G. Hobom. 1982. Structural analysis of insertion sequence IS5. Nature 297:159-162. (Pubitemid 12051840)
37. Kumar, A., P. M. Harrison, K. H. Cheung, N. Lan, N. Echols, P. Bertone, P. Miller, M. B. Gerstein, and M. Snyder. 2002. An integrated approach for finding overlooked genes in yeast. Nat. Biotechnol. 20:58-63.
38. 38. Kumar, A., M. Seringhaus, M. Biery, R. J. Sarnovsky, L. Umansky, S. Piccirillo, M. Heidtman, K.-H. Cheung, C. J. Dobry, M. Gerstein, N. Craig, and M. Snyder. 2004. Large-scale mutagenesis of the yeast genome using a Tn7-derived multipurpose transposon. Genome Res. 14:1975-1986. (Pubitemid 39386512)
39. Lee, K. S., K. Irie, Y. Gotoh, Y. Watanabe, H. Araki, E. Nishida, K. Matsumoto, and D. E. Levin. 1993. A yeast mitogen-activated protein kinase homolog (Mpklp) mediates signalling by protein kinase C. Mol. Cell. Biol. 13:3067-3075.
40. Lynch, M. 2002. Intron evolution as a population-genetic process. Proc. Natl. Acad. Sci. USA 99:6118-6123.
41. Lynch, M., and J. S. Conery. 2003. The origins of genome complexity. Science 302:1401-1404.
42. Ma, J., C. J. Dobry, D. J. Krysan, and A. Kumar. 2008. Unconventional genomic architecture in the budding yeast Saccharomyces cerevisiae masks the nested antisense gene NAG1. Eukaryot. Cell 7:1289-1298.
43. 43. Mackiewicz, P., M. Kowalczuk, A. Gierlik, M. R. Dudek, and S. Cebrat. 1999. Origin and properties of non-coding ORFs in the yeast genome. Nucleic Acids Res. 27:3503-3509. (Pubitemid 29414678)
44. Makalowska, I., C. F. Lin, and W. Makalowski. 2005. Overlapping genes in vertebrate genomes. Comput. Biol. Chem. 29:1-12.
45. Mewes, H. W., K. Albermann, M. Bahr, D. Frishman, A. Gleissner, J. Hani, K. Heumann, K. Kleine, A. Maierl, S. G. Oliver, F. Pfeiffer, and A. Zollner. 1997. Overview of the yeast genome. Nature 387:7-65.
46. Misra, S., M. A. Crosby, C. J. Mungall, B. B. Matthews, K. S. Campbell, P. Hradecky, Y. Huang, J. S. Kaminker, G. H. Millburn, S. E. Prochnik, C. D. Smith, J. L. Tupy, E. J. Whittled, L. Bayraktaroglu, B. P. Berman, B. R. Bettencourt, S. E. Celniker, A. D. de Grey, R. A. Drysdale, N. L. Harris, J. Richter, S. Russo, A. J. Schroeder, S. Q. Shu, M. Stapleton, C. Yamada, M. Ashburner, W. M. Gelbart, G. M. Rubin, and S. E. Lewis. 2002. Annotation of the Drosophila melanogaster euchromatic genome: a systematic review. Genome Biol. 3:RESEARCH0083.
47. Mitrovich, Q. M., B. B. Tuch, C. Guthrie, and A. D. Johnson. 2007. Computational and experimental approaches double the number of known introns in the pathogenic yeast Candida albicans. Genome Res. 17:492-502.
48. Miura, F., N. Kawaguchi, J. Sese, A. Toyoda, M. Hattori, S. Morishita, and T. Ito. 2006. A large-scale full-length cDNA analysis to explore the budding yeast transcriptome. Proc. Natl. Acad. Sci. USA 103:17846-17851.
49. 49. Nagalakshmi, U., Z. Wang, K. Waern, C. Shou, D. Raha, M. Gerstein, and M. Snyder. 2008. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320:1344-1349. (Pubitemid 351929471)
50. Pallejà, A., E. D. Harrington, and P. Bork. 2008. Large gene overlaps in prokaryotic genomes: result of functional constraints or mispredictions? BMC Genomics 9:335.
51. 51. Philippsen, P., K. Kleine, R. Pohlmann, A. Dusterhoft, K. Hamberg, J. H. Hegemann, B. Obermaier, L. A. Urrestarazu, R. Aert, K. Albermann, R. Altmann, B. Andre, V. Baladron, J. P. Ballesta, A. M. Becam, J. Beinhauer, J. Boskovic, M. J. Buitrago, F. Bussereau, F. Coster, M. Crouzet, M. D'Angelo, F. Dal Pero, A. De Antoni, J. Hani, et al. 1997. The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its evolutionary implications. Nature 387:93-98. (Pubitemid 27334675)
52. 52. Rak, B., M. Lusky, and M. Hable. 1982. Expression of two proteins from overlapping and oppositely oriented genes on transposable DNA insertion element IS5. Nature 297:124-128. (Pubitemid 12051833)
53. Rodeheffer, M. S., B. E. Boone, A. C. Bryan, and G. S. Shadel. 2001. Namlp, a protein involved in RNA processing and translation, is coupled to transcription through an interaction with yeast mitochondrial RNA polymerase. J. Biol. Chem. 276:8616-8622.
54. 54. Ross-Macdonald, P., P. S. Coelho, T. Roemer, S. Agarwal, A. Kumar, R. Jansen, K. H. Cheung, A. Sheehan, D. Symoniatis, L. Umansky, M. Heidtman, F. K. Nelson, H. Iwasaki, K. Hager, M. Gerstein, P. Miller, G. S. Roeder, and M. Snyder. 1999. Large-scale analysis of the yeast genome by transposon tagging and gene disruption. Nature 402:413-418. (Pubitemid 129544829)
55. Sanger, F., G. M. Air, B. G. Barrell, N. L. Brown, A. R. Coulson, C. A. Fiddes, C. A. Hutchison, P. M. Slocombe, and M. Smith. 1977. Nucleotide sequence of bacteriophage phi X174 DNA. Nature 265:687-695.
56. Sanna, C. R., W. H. Li, and L. Zhang. 2008. Overlapping genes in the human and mouse genomes. BMC Genomics 9:169.
57. Sawers, R. G. 2005. Transcript analysis of Escherichia coli K-12 insertion element IS5. FEMS Microbiol. Lett. 244:397-401.
58. 58. Scherer, S. W., J. Cheung, J. R. MacDonald, L. R. Osborne, K. Nakabayashi, J. A. Herbrick, A. R. Carson, L. Parker-Katiraee, J. Skaug, R. Khaja, J. Zhang, A. K. Hudek, M. Li, M. Haddad, G. E. Duggan, B. A. Fernandez, E. Kanematsu, S. Gentles, C. C. Christopoulos, S. Choufani, D. Kwasnicka, X. H. Zheng, Z. Lai, D. Nusskern, Q. Zhang, Z. Gu, F. Lu, S. Zeesman, M. J. Nowaczyk, I. Teshima, D. Chitayat, C. Shuman, R. Weksberg, E. H. Zackai, T. A. Grebe, S. R. Cox, S. J. Kirkpatrick, N. Rahman, J. M. Friedman, H. H. Heng, P. G. Pelicci, F. Lo-Coco, E. Belloni, L. G. Shaffer, B. Pober, C. C. Morton, J. F. Gusella, G. A. Bruns, B. R. Korf, B. J. Quade, A. H. Ligon, H. Ferguson, A. W. Higgins, N. T. Leach, S. R. Herrick, E. Lemyre, C. G. Farra, H. G. Kim, A. M. Summers, K. W. Gripp, W. Roberts, P. Szatmari, E. J. Winsor, K. H. Grzeschik, A. Teebi, B. A. Minassian, J. Kere, L. Armengol, M. A. Pujana, X. Estivill, M. D. Wilson, B. F. Koop, S. Tosi, G. E. Moore, A. P. Boright, E. Zlotorynski, B. Kerem, P. M. Kroisel, E. Petek, D. G. Oscier, S. J. Mould, H. Dohner, K. Dohner, J. M. Rommens, J. B. Vincent, J. C. Venter, P. W. Li, R. J. Mural, M. D. Adams, and L. C. Tsui. 2003. Human chromosome 7: DNA sequence and biology. Science 300:767-772. (Pubitemid 36532105)
59. Schnetz, K., and B. Rak. 1992. IS5: a mobile enhancer of transcription in Escherichia coli. Proc. Natl. Acad. Sci. USA 89:1244-1248.
60. 60. Schoner, B., and M. Kahn. 1981. The nucleotide sequence of IS5 from Escherichia coli. Gene 14:165-174. (Pubitemid 11021731)
61. Silverman, T. A., M. Noguchi, and B. Safer. 1992. Role of sequences within the first intron in the regulation of expression of eukaryotic initiation factor 2 alpha. J. Biol. Chem. 267:9738-9742.
62. 62. Stolc, V., Z. Gauhar, C. Mason, G. Halasz, M. F. van Batenburg, S. A. Rifkin, S. Hua, T. Herreman, W. Tongprasit, P. E. Barbano, H. J. Bussemaker, and K. P. White. 2004. A gene expression map for the euchromatic genome of Drosophila melanogaster. Science 306:655-660. (Pubitemid 39440907)
63. Su, A. I., T. Wiltshire, S. Batalov, H. Lapp, K. A. Ching, D. Block, J. Zhang, R. Soden, M. Hayakawa, G. Kreiman, M. P. Cooke, J. R. Walker, and J. B. Hogenesch. 2004. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl. Acad. Sci. USA 101:6062-6067.
64. Sweeney, R., Q. Fan, and M. C. Yao. 1996. Antisense ribosomes: rRNA as a vehicle for antisense RNAs. Proc. Natl. Acad. Sci. USA 93:8518-8523.
65. Tiong, S. Y., and D. Nash. 1990. Genetic analysis of the adenosine3 (Gart) region of the second chromosome of Drosophila melanogaster. Genetics 124:889-897.
66. Vanhée-Brossollet, C., and C. Vaquero. 1998. Do natural antisense transcripts make sense in eukaryotes? Gene 211:1-9.
67. 67. Veeramachaneni, V., W. Makalowski, M. Galdzicki, R. Sood, and I. Makalowska. 2004. Mammalian overlapping genes: the comparative perspective. Genome Res. 14:280-286. (Pubitemid 38219841)
68. Wang, Q., and G. G. Carmichael. 2004. Effects of length and location on the cellular response to double-stranded RNA. Microbiol. Mol. Biol. Rev. 68: 432-452.
69. Williams, B. A., C. H. Slamovits, N. J. Patron, N. M. Fast, and P. J. Keeling. 2005. A high frequency of overlapping gene expression in compacted eukaryotic genomes. Proc. Natl. Acad. Sci. USA 102:10936-10941.
70. 70. Wutz, A., O. W. Smrzka, N. Schweifer, K. Schellander, E. F. Wagner, and D. P. Barlow. 1997. Imprinted expression of the Igf2r gene depends on an intronic CpG island. Nature 389:745-749. (Pubitemid 27458963)
71. Yelin, R., D. Dahary, R. Sorek, E. Y. Levanon, O. Goldstein, A. Shoshan, A. Diber, S. Biton, Y. Tamir, R. Khosravi, S. Nemzer, E. Pinner, S. Walach, J. Bernstein, K. Savitsky, and G. Rotman. 2003. Widespread occurrence of antisense transcription in the human genome. Nat. Biotechnol. 21:379-386.
72. Yu, P., D. Ma, and M. Xu. 2005. Nested genes in the human genome. Genomics 86:414-422.
73. Zarzov, P., C. Mazzoni, and C. Mann. 1996. The SLT2(MPK1) MAP kinase is activated during periods of polarized cell growth in yeast. EMBO J. 15:83-91.
74. Zweifel, E., J. Smith, D. Romero, T. H. Giddings, Jr., M. Winey, J. Honts, J. Dahlseid, B. Schneider, and E. S. Cole. 2009. Nested genes CDA12 and CDA13 encode proteins associated with membrane trafficking in the ciliate Tetrahymena thermophila. Eukaryot. Cell 8:899-912.