Sequence analysis of mRNA polyadenylation signals of rice genes

Chinese Science Bulletin

Volumn 51, Issue 9, 2006, Pages 1069-1077

  Lu, Ying ^a,b   Gao, Chenxi ^a,b,c   Han, Bin ^a,c  

^a Chinese Academy of Sciences   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c INSTITUTE OF PLANT PHYSIOLOGY AND ECOLOGY   (China)

Author keywords

cDNA; Expressed sequences tags; Polyadenylation signals; Rice; RNA processing; U rich downstream elements

Indexed keywords

EUKARYOTA;

EID: 33748933233     PISSN: 10016538     EISSN: 18619541     Source Type: Journal    
DOI: 10.1007/s11434-006-1069-5     Document Type: Article

References (31)

1. Moore C L, Sharp P A. Accurate cleavage and polyadenylation of exogenous RNA substrate. Cell, 1985, 41: 845-855
2. Wichkens M. How the message got its tail addition of poly(A) in the nucleus. Trends Biochem Sci, 1990, 15: 277-281
3. Edwalds-Gilbert G, Veraldi K L, Milcarek C. Alternative poly(A) site selection in complex transcription units: Means to an end? Nucleic Acids Res, 1997, 25: 2547-2561
4. MacDonald C C, Redondo J L. Reexamining the polyadenylation signal: Were we wrong about AAUAAA? Mol Cell Endocrinol, 2002, 190: 1-8
5. Zarudnaya M I, Kolomiets I M, Potyahaylo A L, et al. Downstream elements of mammalian pre-mRNA polyadenylation signals: Primary, secondary and higher-order structures. Nucleic Acids Res, 2003, 31: 1375-1386
6. Proudfoot N. Poly(A) signals. Cell, 1991, 64: 671-674
7. Colgan D F, Manley J L. Mechanism and regulation of mRNA polyadenylation. Genes, 1997, 11:2755-2766
8. Graber J H, Cantor C R. Mohr S C, et al. In silico detection of control signals: mRNA 3′-end-processing sequences in diverse species. Proc Natl Acad Sci USA, 1999, 96: 14055-14060
9. Hunt A G Messenger RNA 3′ end formation in plants. Annu Rev Plant Physiol Plant Mol Biol, 1994, 45: 47-60
10. Loke J C, Stahlberg E A, Strenski D G, et al. Compilation of mRNA polyadenylation signals in Arabidopsis revealed a new signal element and potential secondary structures. Plant Physiol, 2005, 138: 1457-1468
11. Wu L, Ueda T, Messing J. The formation of mRNA 3′-ends in plants. Plant J, 1995, 8: 323-329
12. An G, Mitra A, Choi H K, et al. Functional analysis of the 3′ control region of the potato wound-inducible proteinase inhibitor II gene. Plant Cell, 1989, 1: 115-122
13. Chou Z F, Chen F, Wilusz J. Sequence and position requirements for uridylate-rich downstream elements of polyadenylation signals. Nucleic Acids Res, 1994, 22: 2525-2531
14. Chen F, MacDonald C C, Wilusz J. Cleavage site determinants in the mammalian polyadenylation signal. Nucleic Acids Res, 1995, 23:2614-2620
15. Beyer K, Dandekar T, Keller W. RNA ligands selected by cleavage stimulation factor contain distinct sequence motifs that function as downstream elements in 3′-end processing of pre-mRNA. J Biol Chem, 1997, 272: 26769-26779
16. Kikuchi S, Satoh K, Nagata T, et al. Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science, 2003, 301:376-379
17. Beaudoing E, Freier S, Wyatt J R, et al. Patterns of variant polyadenylation signal usage in human genes. Genome Res, 2000, 10: 1001-1010
18. Beaudoing E, Gautheret D. Identification of alternate polyadenylation sites and analysis of their tissue distribution using EST data. Genome Res, 2001, 11: 1520-1526
19. Tian B, Hu J, Zhang H, et al. A large-scale analysis of mRNA polyadenylation of human and mouse genes. Nucleic Acids Res, 2005, 33:201-212
20. Altschul S F, Madden T L, Schaffer A A, et al. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs, Nucleic Acids Res, 1997, 25: 3389-3402
21. Marino-Ramirez L, Spouge J L, Kanga G C, et al. Statistical analysis of over-represented words in human promoter sequences. Nucleic Acids Res, 2004, 32: 949-958
22. Schbath S. An efficient statistic to detect over- and under-represented words in DNA sequences. J Comput Biol, 1997, 4: 189-192
23. Sheets M D, Ogg S C, Wickens M P. Point mutations in AAUAAA and the poly (A) addition site: Effects on the accuracy and efficiency of cleavage and polyadenylation in vitro. Nucleic Acids Res, 1990, 18: 5799-5805
24. Li Q, Hunt A G A near-upstream element in a plant polyadenylation signal consists of more than six nucleotides. Plant Mol Biol, 1995, 28:927-934
25. Wu L, Ueda T, Messing J. 3′-end processing of the maize 27 kDa zein mRNA. Plant J, 1993, 4: 535-544
26. Andrews E M, DiMaio D. Hierarchy of polyadenylation site usage by bovine papillomavirus in transformed mouse cells. J Virol, 1993, 67: 7705-7710
27. Aranda A, Perez-Ortin J E, Moore C, ct al. Transcription termination downstream of the Saccharomyces cerevisiae FBP1 [changed from FPB1] poly(A) site does not depend on efficient 3′end processing. RNA, 1998,4: 870
28. Chen J S, Nordstrom J L. Bipartite structure of the downstream element of the mouse beta globin (major) poly(A) signal. Nucleic Acids Res, 1992, 20:2565-2572
29. Wahle E. 3′-end cleavage and polyadenylation of mRNA precursors. Biochim Biophys Acta, 1995, 1261: 183-194
30. Brown P H, Tiley L S, Cullen B R. Effect of RNA secondary structure on polyadenylation site selection. Genes Dev, 1991, 5: 1277-1284
31. Ahmed Y F, Gilmartin G M, Hanly S M, et al. The HTLV-I Rex response clement mediates a novel form of mRNA polyadenylation. Cell, 1991, 64:727-737