Evidence for a preferential targeting of 3′-UTRs by cis-encoded natural antisense transcripts

Nucleic Acids Research

Volumn 33, Issue 17, 2005, Pages 5533-5543

  Sun, Miao ^c   Hurst, Laurence D ^a   Carmichael, Gordon G ^b   Chen, Jianjun ^c  

^a University of Bath   (United Kingdom)

^b UNIVERSITY OF CONNECTICUT HEALTH CENTER   (United States)

^c UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY RNA; MESSENGER RNA; RNA;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; CONTROLLED STUDY; EUKARYOTE; GENE CLUSTER; GENE EXPRESSION; GENE FUNCTION; GENE TARGETING; GENETIC CODE; GENETIC CONSERVATION; HUMAN; HUMAN GENOME; MAMMALIAN GENETICS; MOUSE; NONHUMAN; POSTTRANSCRIPTIONAL GENE SILENCING; PRIORITY JOURNAL; PROBABILITY; SIMULATION; TRANSCRIPTION REGULATION; ANIMAL; BASE PAIRING; BINDING SITE; BIOLOGICAL MODEL; BIOSYNTHESIS; GENE EXPRESSION REGULATION; GENETICS; GENOMICS; MOLECULAR EVOLUTION;

EUKARYOTA; MAMMALIA;

3' UNTRANSLATED REGIONS; 5' UNTRANSLATED REGIONS; ANIMALS; BASE PAIRING; BINDING SITES; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION; GENOMICS; HUMANS; MICE; MODELS, GENETIC; RNA; RNA, ANTISENSE;

EID: 26944454054     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki852     Document Type: Article

References (46)

1. Waterston,A.H., Lindblad-Toh,K., Birney,E., Rogers,J., Abril,J.F., Agarwal,P., Agarwala,R., Ainscough,R.. Alexandersson,M., An,P. et al. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature, 420, 520-562.
2. International Human Genome Sequencing Consortium (2004), Finishing the euchromatic sequence of the human genome. Nature, 431, 931-945.
3. Levinen,M. and Tjian,R. (2003) Transcription regulation and animal diversity. Nature, 424, 147-151.
4. Mattick,J.S. (2001) Non-coding RNAs: The architects of eukaryotic complexity. EMBO Rep., 2, 986-991.
5. Mattick,J.S. (2004) RNA regulation: A new genetics? Nature Rev Genet. 5, 316-323.
6. Mattick,J.S. (2005) What makes a human? Scientist, 19, 32-33.
7. Kumar,M. and Carmichael,G,G. (1998) Antisense RNA: Function and fate of duplex RNA in cells of higher eukaryotes. Microbiol. Mol. Biol. Rev., 62, 1415-1434.
8. Vanhee-Brossollet,C. and Vaquero,C. (1998) Do natural antisense transcripts make sense in eukaryotes? Gene, 211, 1-9.
9. Lavorgna,G., Dahary,D., Lehner,B., Sorek,R., Sanderson,C.M. and Casari,G. (2004) In search of antisense. Trends Biochem Sci., 29, 88-94.
10. Lehner,B., Williams,G., Campbell,R.D. and Sanderson,C.M. (2002) Antisense transcripts in the human genome. Trends Genet., 18, 63-65.
11. Shendure,J. and Church,G.M. (2002) Computational discovery of sense-antisense transcription in the human and mouse genomes. Genome Biol., 3, RESEARCH0044.
12. Kiyosawa,H., Yamanaka,I., Osato,N., Kondo,S. and Hayashizaki,Y,; RIKEN GER Group: GSL Members. (2003) Antisense transcripts with FANTOM2 clone set and their implications for gene regulation. Genome Res., 13, 1324-1334.
13. 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.
14. 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.
15. Chen,J., Sun,M., Hurst,L.D., Carmichael,G.G. and Rowley,J.D. (2005) Genome-wide analysis of coordinate expression and evolution of human cis-encoded sense-antisense transcripts. Trends Genet., 21, 326-329.
16. Chen,J., Sun,M., Hurst,L.D., Carmichael,G.G. and Rowley,J.D. (2005) Human antisense genes have unusually short introns: Evidence for selection for rapid transcription. Trends Genet., 21, 203-207.
17. Cheng,J., Kapranov,P., Drenkow,J., Dike,S., Brubaker,S., Patel,S., Long,J., Stern,D., Tammana,H., Helt,G. et al. (2005) Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science, 308, 1149-1154.
18. Mignone,F., Gissi,C., Liuni,S. and Pesole,G. (2002) Untranslated regions of mRNAs. Genome Biol., 3, REVIEWS0004.
19. Pesole,G., Liuni,S., Grillo,G. and Saccone,C. (1998) UTRdb: A specialized database of 5′- and 3′-untranslated regions of eukaryotic mRNAs. Nucleic Acids Res., 26, 192-195.
20. Wilkie,G.S., Dickson,K.S. and Gray,N.K. (2003) Regulation of mRNA translation by 5′- and 3′-UTR-binding factors. Trends Biochem Sci., 28, 182-188.
21. Veeramachaneni,V., Makalowski,W., Galdzicki,M., Sood,R. and Makalowska,J. (2004) Mammalian overlapping genes: The comparative perspective. Genome Res., 14, 280-286.
22. Schuler,G.D., Boguski,M.S., Stewart,E.A., Stein,L.D., Gyapay,G., Rice,K., White,R.E., Rodriguez-Tome,P., Aggarwal,A., Bajorek,E. et al. (1996) A gene map of the human genome. Science, 274, 540-546.
23. Lipman,D.J. (1997) Making (anti)sense of non-coding sequence conservation. Nucleic Acids Res., 25, 3580-3583.
24. Adachi,N. and Lieber,M.R. (2002) Bidirectional gene organization: A common architectural feature of the human genome. Cell, 109, 807-809.
25. Trinklein,N.D., Aldred,S.F., Hartman,S.J., Schroeder,D.I., Otillar,R.P. and Myers,R.M. (2004) An abundance of bidirectional promoters in the human genome. Genome Res., 14, 62-66.
26. Velculescu,V.E., Zhang,L., Vogelstein,B. and Kinzler,K.W. (1995) Serial analysis of gene expression. Science, 270, 484-487.
27. Lercher,M.J., Urrutia,A.O. and Hurst,L.D. (2002) Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nature Genet., 31, 180-183.
28. Suzuki,Y., Yamashita,R., Nakai,K. and Sugano,S. (2002) DBTSS: Database of human transcriptional start sites and full-length cDNAs. Nucleic Acids Res., 30, 328-331.
29. Mironov,A.A., Fickett,J.W. and Gelfand,M.S. (1999) Frequent alternative splicing of human genes. Genome Res., 9, 1288-1293.
30. Mignone,F., Grillo,G., Licciulli,F., Iacono,M., Liuni,S., Kersey,P.J., Duarte,J., Saccone,C. and Pesole,G. (2005) UTRdb and UTRsite: A collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. Nucleic Acids Res., 33, D141-D146.
31. Eddy,S.R. (2001) Non-coding RNA genes and the modern RNA world. Nature Rev. Genet., 2, 919-929.
32. Eddy,S.R. (2002) Computational genomics of noncoding RNA genes. Cell, 109, 137-140.
33. Storz,G. (2002) An expanding universe of noncoding RNAs. Science, 296, 1260-1263.
34. Duret,L., Dorkeld,F. and Gautier,C. (1993) Strong conservation of non-coding sequences during vertebrates evolution: Potential involvement in post-transcriptional regulation of gene expression. Nucleic Acids Res., 21, 2315-2322.
35. Duret,L. and Bucher,P. (1997) Searching for regulatory elements in human noncoding sequences. Curr. Opin. Struct. Biol., 7, 399-406.
36. Ashburner,M., Ball,C.A., Blake,J.A., Botstein,D., Butler,H., Cherry,J.M., Davis,A.P., Dolinski,K., Dwight,S.S., Eppig,J.T. et al. (2000) Gene ontology: Tool for the unification of biology. Nature Genet., 25, 25-29.
37. Conne,B., Stutz,A. and Vassalli,J.D. (2000) The 3′ untranslated region of messenger RNA: A molecular 'hotspot' for pathology? Nature Med. 6, 637-641.
38. Bartel,D.P. (2004) MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell, 116, 281-297.
39. Bartel,D.P. and Chen,C.Z. (2004) Micromanagers of gene expression: The potentially widespread influence of metazoan microRNAs. Nature Rev. Genet., 5, 396-400.
40. Ambros,V. (2003) MicroRNA pathways in flies and worms: Growth, death, fat, stress, and timing. Cell, 113, 673-676.
41. Ambros,V. (2004) The functions of animal microRNAs. Nature, 431, 350-355.
42. Lewis,B.P., Burge,C.B. and Bartel,D.P. (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell, 120, 15-20.
43. Lim,L.P., Lau,N.C., Garrett-Engele,P., Grimson,A., Schelter,J.M., Castle,J., Bartel,D.P., Linsley,P.S. and Johnson,J.M. (2005) Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature, 433, 769-773.
44. DeCerbo,J. and Carmichael,G.G. (2005) Retention and repression: Fates of hyperedited RNAs in the nucleus. Curr. Opin. Cell. Biol., 17, 302-308.
45. Kiyosawa,H., Mise,N., Iwase,S., Hayashizaki,Y. and Abe,K. (2005) Disclosing hidden transcripts: Mouse natural sense-antisense transcripts tend to be poly(A) negative and nuclear localized. Genome Res., 15, 463-474.
46. Grzybowska,E.A., Wilczynska,A. and Siedlecki,J.A. (2001) Regulatory functions of 3′UTRs. Biochem. Biophys. Res. Commun., 288, 291-295.