What are natural antisense transcripts good for?

Biochemical Society Transactions

Volumn 38, Issue 4, 2010, Pages 1144-1149

  Werner, Andreas ^a   Swan, Daniel ^a  

^a NEWCASTLE UNIVERSITY   (United Kingdom)

Author keywords

Endogenous short interfering RNA; Monoallelic gene expression; Natural antisense transcript; Non protein coding RNA; Random imprinting; Transcriptional silencing

Indexed keywords

NATURAL ANTISENSE TRANSCRIPT; SMALL INTERFERING RNA; UNCLASSIFIED DRUG; UNTRANSLATED RNA;

EUKARYOTE; GENE CONTROL; GENE EXPRESSION; GENETIC ASSOCIATION; NONHUMAN; POSTTRANSCRIPTIONAL GENE SILENCING; PRIORITY JOURNAL; REVIEW; RNA SEQUENCE; ZEBRA FISH;

ANIMALS; GENOME; HUMANS; MODELS, BIOLOGICAL; PROMOTER REGIONS, GENETIC; RNA INTERFERENCE; RNA, ANTISENSE; RNA, MESSENGER; TRANSCRIPTION, GENETIC;

EUKARYOTA;

EID: 77955941659     PISSN: 03005127     EISSN: 14708752     Source Type: Journal    
DOI: 10.1042/BST0381144     Document Type: Review

References (61)

1. Mattick, J.S. (2001) Non-coding RNAs: the architects of eukaryotic complexity. EMBO Rep. 2, 986-991
2. Carninci, P., Yasuda, J. and Hayashizaki, Y. (2008) Multifaceted mammalian transcriptome. Curr. Opin. Cell Biol. 20, 274-280
3. Kapranov, P., Willingham, A.T. and Gingeras, T.R. (2007) Genome-wide transcription and the implications for genomic organization. Nat. Rev. 8, 413-423
4. Mercer, T.R., Dinger, M.E. and Mattick, J.S. (2009) Long non-coding RNAs: insights into functions. Nat. Rev. 10, 155-159
5. Carthew, R.W. and Sontheimer, E.J. (2009) Origins and mechanisms of miRNAs and siRNAs. Cell 136, 642-655
6. Seto, A.G., Kingston, R.E. and Lau, N.C. (2007) The coming of age for Piwi proteins. Mol. Cell 26, 603-609
7. Ding, S.W. and Voinnet, O. (2007) Antiviral immunity directed by small RNAs. Cell 130, 413-426
8. Okamura, K. and Lai, E.C. (2008) Endogenous small interfering RNAs in animals. Nat. Rev. Mol. Cell Biol. 9, 673-678
9. Lau, N.C., Seto, A.G., Kim, J., Kuramochi-Miyagawa, S., Nakano, T., Bartel, D.P. and Kingston, R.E. (2006) Characterization of the piRNA complex from rat testes. Science 313, 363-367 (Pubitemid 44480963)
10. Vagin, V.V., Sigova, A., Li, C., Seitz, H., Gvozdev, V. and Zamore, P.D. (2006) A distinct small RNA pathway silences selfish genetic elements in the germline. Science 313, 320-324 (Pubitemid 44480950)
11. Aravin, A.A., Sachidanandam, R., Bourc'his, D., Schaefer, C., Pezic, D., Toth, K.F., Bestor, T. and Hannon, G.J. (2008) A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice. Mol. Cell 31, 785-799
12. Carninci, P., Kasukawa, T., Katayama, S., Gough, J., Frith, M.C., Maeda, N., Oyama, R., Ravasi, T., Lenhard, B., Wells, C. et al. (2005) The transcriptional landscape of the mammalian genome. Science 309, 1559-1563
13. Kapranov, P., Cheng, J., Dike, S., Nix, D.A., Duttagupta, R., Willingham, A.T., Stadler, P.F., Hertel, J., Hackermuller, J., Hofacker, I.L. et al. (2007) RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316, 1484-1488
14. Seila, A.C., Calabrese, J.M., Levine, S.S., Yeo, G.W., Rahl, P.B., Flynn, R.A., Young, R.A. and Sharp, P.A. (2008) Divergent transcription from active promoters. Science 322, 1849-1851
15. Jacquier, A. (2009) The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs. Nat. Rev. 10, 833-844
16. Taft, R.J., Glazov, E.A., Cloonan, N., Simons, C., Stephen, S., Faulkner, G.J., Lassmann, T., Forrest, A.R., Grimmond, S.M., Schroder, K. et al. (2009) Tiny RNAs associated with transcription start sites in animals. Nat. Genet. 41, 572-578
17. Saiz, L. and Vilar, J.M. (2006) DNA looping: the consequences and its control. Curr. Opin. Struct. Biol. 16, 344-350
18. Ponting, C.P., Oliver, P.L. and Reik, W. (2009) Evolution and functions of long noncoding RNAs. Cell 136, 629-641
19. Rinn, J.L., Kertesz, M., Wang, J.K., Squazzo, S.L., Xu, X., Brugmann, S.A., Goodnough, L.H., Helms, J.A., Farnham, P.J., Segal, E. and Chang, H.Y. (2007) Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129, 1311-1323 (Pubitemid 46962090)
20. Guttman, M., Amit, I., Garber, M., French, C., Lin, M.F., Feldser, D., Huarte, M., Zuk, O., Carey, B.W., Cassady, J.P. et al. (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458, 223-227
21. Khalil, A.M., Guttman, M., Huarte, M., Garber, M., Raj, A., Rivea Morales, D., Thomas, K., Presser, A., Bernstein, B.E., van Oudenaarden, A. et al. (2009) Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc. Natl. Acad. Sci. U.S.A. 106, 11667-11672
22. Beiter, T., Reich, E., Williams, R.W. and Simon, P. (2008) Antisense transcription: a critical look in both directions. Cell. Mol. Life Sci. 66, 94-112
23. Chen, J., Sun, M., Kent, W.J., Huang, X., Xie, H., Wang, W., Zhou, G., Shi, R.Z. and Rowley, J.D. (2004) Over 20% of human transcripts might form sense-antisense pairs. Nucleic Acids Res. 32, 4812-4820
24. Yelin, R., Dahary, D., Sorek, R., Levanon, E.Y., Goldstein, O., Shoshan, A., Diber, A., Biton, S., Tamir, Y., Khosravi, R. et al. (2003) Widespread occurrence of antisense transcription in the human genome. Nat. Biotechnol. 21, 379-386
25. Okazaki, Y., Furuno, M., Kasukawa, T., Adachi, J., Bono, H., Kondo, S., Nikaido, I., Osato, N., Saito, R., Suzuki, H. et al. (2002) Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420, 563-573
26. Katayama, S., Tomaru, Y., Kasukawa, T., Waki, K., Nakanishi, M., Nakamura, M., Nishida, H., Yap, C.C., Suzuki, M., Kawai, J. et al. (2005) Antisense transcription in the mammalian transcriptome. Science 309, 1564-1566
27. Zhang, Y., Liu, X.S., Liu, Q.R. and Wei, L. (2006) Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species. Nucleic Acids Res. 34, 3465-3475
28. Dahary, D., Elroy-Stein, O. and Sorek, R. (2005) Naturally occurring antisense: transcriptional leakage or real overlap? Genome Res. 15, 364-368
29. Kiyosawa, H., Yamanaka, I., Osato, N., Kondo, S. and Hayashizaki, Y. (2003) Antisense transcripts with FANTOM2 clone set and their implications for gene regulation. Genome Res. 13, 1324-1334
30. Werner, A. and Berdal, A. (2005) Natural antisense transcripts: sound or silence? Physiol. Genomics 23, 125-131 (Pubitemid 44437972)
31. Faghihi, M.A., Modarresi, F., Khalil, A.M., Wood, D.E., Sahagan, B.G., Morgan, T.E., Finch, C.E., St Laurent, III, G., Kenny, P.J. and Wahlestedt, C. (2008) Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feed-forward regulation of beta-secretase. Nat. Med. 14, 723-730
32. Uchida, T., Rossignol, F., Matthay, M.A., Mounier, R., Couette, S., Clottes, E. and Clerici, C. (2004) Prolonged hypoxia differentially regulates hypoxia-inducible factor (HIF)-1α and HIF-2α expression in lung epithelial cells: implication of natural antisense HIF-1α. J. Biol. Chem. 279, 14871-14878
33. Faghihi, M.A. and Wahlestedt, C. (2009) Regulatory roles of natural antisense transcripts. Nat. Rev. Mol. Cell Biol. 10, 637-643
34. He, Y., Vogelstein, B., Velculescu, V.E., Papadopoulos, N. and Kinzler, K.W. (2008) The antisense transcriptomes of human cells. Science 322, 1855-1857
35. Werner, A., Schmutzler, G., Carlile, M., Miles, C.G. and Peters, H. (2007) Expression profiling of antisense transcripts on DNA arrays. Physiol. Genomics 28, 294-300 (Pubitemid 46708769)
36. Ge, X., Rubinstein, W.S., Jung, Y.C. and Wu, Q. (2008) Genome-wide analysis of antisense transcription with Affymetrix exon array. BMC Genomics 9, 27
37. Oeder, S., Mages, J., Flicek, P. and Lang, R. (2007) Uncovering information on expression of natural antisense transcripts in Affymetrix MOE430 datasets. BMC Genomics 8, 200
38. Carlile, M., Swan, D., Jackson, K., Preston-Fayers, K., Ballester, B., Flicek, P. and Werner, A. (2009) Strand selective generation of endo-siRNAs from the Na/phosphate transporter gene Slc34a1 in murine tissues. Nucleic Acids Res. 37, 2274-2282
39. Okada, Y., Tashiro, C., Numata, K., Watanabe, K., Nakaoka, H., Yamamoto, N., Okubo, K., Ikeda, R., Saito, R., Kanai, A. et al. (2008) Comparative expression analysis uncovers novel features of endogenous antisense transcription. Hum. Mol. Genet. 17, 1631-1640
40. Petit, S., Meary, F., Pibouin, L., Jeanny, J.C., Fernandes, I., Poliard, A., Hotton, D., Berdal, A. and Babajko, S. (2009) Autoregulatory loop of Msx1 expression involving its antisense transcripts. J. Cell Physiol. 220, 303-310
41. Wang, Q. and Carmichael, G.G. (2004) Effects of length and location on the cellular response to double-stranded RNA. Microbiol. Mol. Biol. Rev. 68, 432-452
42. Neeman, Y., Dahary, D., Levanon, E.Y., Sorek, R. and Eisenberg, E. (2005) Is there any sense in antisense editing? Trends Genet. 21, 544-547
43. Carlile, M., Nalbant, P., Preston-Fayers, K., McHaffie, G.S. and Werner, A. (2008) Processing of naturally occurring sense/antisense transcripts of the vertebrate Slc34a gene into short RNAs. Physiol. Genomics 34, 95-100
44. Tam, O.H., Aravin, A.A., Stein, P., Girard, A., Murchison, E.P., Cheloufi, S., Hodges, E., Anger, M., Sachidanandam, R., Schultz, R.M. and Hannon, G.J. (2008) Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Nature 453, 534-538
45. Watanabe, T., Totoki, Y., Toyoda, A., Kaneda, M., Kuramochi-Miyagawa, S., Obata, Y., Chiba, H., Kohara, Y., Kono, T., Nakano, T. et al. (2008) Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes. Nature 453, 539-543
46. Ro, S., Park, C., Young, D., Sanders, K.M. and Yan, W. (2007) Tissue-dependent paired expression of miRNAs. Nucleic Acids Res. 35, 5944-5953
47. Wei, J.X., Yang, J., Sun, J.F., Jia, L.T., Zhang, Y., Zhang, H.Z., Li, X., Meng, Y.L., Yao, L.B. and Yang, A.G. (2009) Both strands of siRNA have potential to guide posttranscriptional gene silencing in mammalian cells. PLoS One 4, e5382
48. Werner, A., Carlile, M. and Swan, D. (2009) What do natural antisense transcripts regulate? RNA Biol. 6, 43-48
49. Morris, K.V., Santoso, S., Turner, A.M., Pastori, C. and Hawkins, P.G. (2008) Bidirectional transcription directs both transcriptional gene activation and suppression in human cells. PLoS Genet. 4, e1000258
50. Matzke, M.A. and Birchler, J.A. (2005) RNAi-mediated pathways in the nucleus. Nat. Rev. 6, 24-35
51. Tufarelli, C., Stanley, J.A., Garrick, D., Sharpe, J.A., Ayyub, H., Wood, W.G. and Higgs, D.R. (2003) Transcription of antisense RNA leading to gene silencing and methylation as a novel cause of human genetic disease. Nat. Genet. 34, 157-165
52. Yu, W., Gius, D., Onyango, P., Muldoon-Jacobs, K., Karp, J., Feinberg, A.P. and Cui, H. (2008) Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA. Nature 451, 202-206
53. Janowski, B.A., Huffman, K.E., Schwartz, J.C., Ram, R., Hardy, D., Shames, D.S., Minna, J.D. and Corey, D.R. (2005) Inhibiting gene expression at transcription start sites in chromosomal DNA with antigene RNAs. Nat. Chem. Biol. 1, 216-222
54. Morris, K.V., Chan, S.W., Jacobsen, S.E. and Looney, D.J. (2004) Small interfering RNA-induced transcriptional gene silencing in human cells. Science 305, 1289-1292
55. Kim, D.H., Villeneuve, L.M., Morris, K.V. and Rossi, J.J. (2006) Argonaute-1 directs siRNA-mediated transcriptional gene silencing in human cells. Nat. Struct. Mol. Biol. 13, 793-797
56. Janowski, B.A., Younger, S.T., Hardy, D.B., Ram, R., Huffman, K.E. and Corey, D.R. (2007) Activating gene expression in mammalian cells with promoter-targeted duplex RNAs. Nat. Chem. Biol. 3, 166-173
57. Li, L.C., Okino, S.T., Zhao, H., Pookot, D., Place, R.F., Urakami, S., Enokida, H. and Dahiya, R. (2006) Small dsRNAs induce transcriptional activation in human cells. Proc. Natl. Acad. Sci. U.S.A. 103, 17337-17342
58. Schwartz, J.C., Younger, S.T., Nguyen, N.B., Hardy, D.B., Monia, B.P., Corey, D.R. and Janowski, B.A. (2008) Antisense transcripts are targets for activating small RNAs. Nat. Struct. Mol. Biol. 15, 842-848
59. Huang, V., Qin, Y., Wang, J., Wang, X., Place, R.F., Lin, G., Lue, T.F. and Li, L.C. RNAa is conserved in mammalian cells. PLoS One 5, e8848
60. Kawamata, T., Seitz, H. and Tomari, Y. (2009) Structural determinants of miRNAs for RISC loading and slicer-independent unwinding. Nat. Struct. Mol. Biol. 16, 953-960
61. Gonzalez-Gonzalez, E., Lopez-Casas, P.P. and del Mazo, J. (2008) The expression patterns of genes involved in the RNAi pathways are tissue-dependent and differ in the germ and somatic cells of mouse testis. Biochim. Biophys. Acta 1779, 306-311