A large-scale analysis of mRNA polyadenylation of human and mouse genes

Nucleic Acids Research

Volumn 33, Issue 1, 2005, Pages 201-212

  Tian, Bin ^b   Hu, Jun ^b   Zhang, Haibo ^a   Lutz, Carol S ^b  

^a NEW JERSEY INSTITUTE OF TECHNOLOGY   (United States)

^b RUTGERS NEW JERSEY MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CIS ACTING ELEMENT; MESSENGER RNA; NUCLEOTIDE; POLYADENYLATED RNA;

ARTICLE; CELL METABOLISM; EUKARYOTE; GENE EXPRESSION REGULATION; GENE LOCATION; GENETIC TRANSCRIPTION; GENOME; HUMAN; MAMMAL; MOUSE; NONHUMAN; ORTHOLOGY; POLYADENYLATION; PRIORITY JOURNAL; REGULATORY MECHANISM; RNA METABOLISM; STATISTICAL SIGNIFICANCE; ANIMAL; CHEMISTRY; GENETICS; METABOLISM;

ANIMALS; GENOME; GENOME, HUMAN; HUMANS; MICE; POLYADENYLATION; RNA, MESSENGER;

EID: 13744254695     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gki158     Document Type: Article

References (46)

1. Lewis,J.D., Gunderson,S.I. and Mattaj,I.W. (1995) The influence of 5′ and 3′ end structures on pre-mRNA metabolism. J. Cell. Sci. Suppl., 19, 13-19.
2. Jacobson,A. and Peltz,S.W. (1996) Interrelationships of the pathways of mRNA decay and translation in eukaryotic cells. Annu. Rev. Biochem., 65, 693-739.
3. Wickens,M., Anderson,P. and Jackson,R.J. (1997) Life and death in the cytoplasm: messages from the 3′ end. Curr. Opin. Genet. Dev., 7, 220-232.
4. Maniatis,T. and Reed,R. (2002) An extensive network of coupling among gene expression machines. Nature, 416, 499-506.
5. Proudfoot,N. (2004) New perspectives on connecting messenger RNA 3′ end formation to transcription. Curr. Opin. Cell. Biol., 16, 272-278.
6. Neugebauer,K.M. (2002) On the importance of being co-transcriptional. J. Cell. Sci., 115, 3865-3871.
7. Calvo,O. and Manley,J.L. (2003) Strange bedfellows: polyadenylation factors at the promoter. Genes Dev., 17, 1321-1327.
8. Wahle,E. and Kuhn,U. (1997) The mechanism of 3′ cleavage and polyadenylation of eukaryotic pre-mRNA. Prog. Nucleic Acid Res. Mol. Biol., 57, 41-71.
9. Keller,W. and Minvielle-Sebastia,L. (1997) A comparison of mammalian and yeast pre-mRNA 3′-end processing. Curr. Opin. Cell. Biol., 9, 329-336.
10. Colgan,D.F. and Manley,J.L. (1997) Mechanism and regulation of mRNA polyadenylation. Genes Dev., 11, 2755-2766.
11. Edmonds,M. (2002) A history of poly A sequences: from formation to factors to function. Prog. Nucleic Acid Res. Mol. Biol. 71, 285-389.
12. Zhao,J., Hyman,L. and Moore,C. (1999) Formation of mRNA 3′ ends in eukaryotes: mechanism, regulation, and interrelationships with other steps in mRNA synthesis. Microbiol. Mol. Biol. Rev., 63 405-445.
13. Brown,C.E. and Sachs,A.B. (1998) Poly(A) tail length control in Saccharomyces cerevisiae occurs by message-specific deadenylation. Mol. Cell. Biol., 18, 6548-6559.
14. Beaudoing,E. and Gautheret,D. (2001) Identification of alternate polyadenylation sites and analysis of their tissue distribution using EST data. Genome Res., 11, 1520-1526.
15. Pauws,E., van Kampen,A.H., van de Graaf,S.A., de Vijlder,J.J. and Ris-Stalpers,C. (2001) Heterogeneity in polyadenylation cleavage sites in mammalian mRNA sequences: implications for SAGE analysis. Nucleic Acids Res., 29, 1690-1694.
16. Beaudoing,E., Freier,S., Wyatt,J.R., Claverie,J.M. and Gautheret,D. (2000) Patterns of variant polyadenylation signal usage in human genes. Genome Res., 10, 1001-1010.
17. Edwalds-Gilbert,G., Veraldi,K.L. and Milcarek,C. (1997) Alternative poly(A) site selection in complex transcription units: means to an end? Nucleic Acids Res., 25, 2547-2561.
18. Takagaki,Y., Seipelt,R.L., Peterson,M.L. and Manley,J.L. (1996) The polyadenylation factor CstF-64 regulates alternative processing of IgM heavy chain pre-mRNA during B cell differentiation. Cell, 87, 941-952.
19. Graber,J.H., Cantor,C.R., Mohr,S.C. and Smith,T.F. (1999) In silico detection of control signals: mRNA 3′ -end-processing sequences in diverse species. Proc. Natl Acad. Sci. USA, 96, 14055-14060.
20. MacDonald,C.C. and Redondo,J.L. (2002) Reexamining the polyadenylation signal: were we wrong about AAUAAA? Mol. Cell. Endocrinol., 190, 1-8.
21. Zarudnaya,M.I., Kolomiets,I.M., Potyahaylo,A.L. and Hovorun,D.M. (2003) Downstream elements of mammalian pre-mRNA polyadenylation signals: primary, secondary and higher-order structures. Nucleic Acids Res., 31, 1375-1386.
22. Natalizio,B.J., Muniz,L.C., Arhin,G.K., Wilusz,J. and Lutz,C.S. (2002) Upstream elements present in the 3′-untranslated region of collagen genes influence the processing efficiency of overlapping polyadenylation signals. J. Biol. Chem., 277, 42733-42740.
23. Chen,F. and Wilusz,J. (1998) Auxiliary downstream elements are required for efficient polyadenylation of mammalian pre-mRNAs. Nucleic Acids Res., 26, 2891-2898.
24. Arhin,G.K., Boots,M., Bagga,P.S., Milcarek,C. and Wilusz,J. (2002) Downstream sequence elements with different affinities for the hnRNP H/H′ protein influence the processing efficiency of mammalian polyadenylation signals. Nucleic Acids Res., 30, 1842-1850.
25. Schek,N., Cooke,C. and Alwine,J.C. (1992) Definition of the upstream efficiency element of the simian virus 40 late polyadenylation signal by using in vitro analyses. Mol. Cell. Biol., 12 5386-5393.
26. Gilmartin,G.M., Fleming,E.S., Oetjen,J. and Graveley,B.R. (1995) CPSF recognition of an HIV-1 mRNA 3′-processing enhancer: multiple sequence contacts involved in poly(A) site definition. Genes Dev., 9, 72-83.
27. Moreira,A., Takagaki,Y., Brackenridge,S., Wollerton,M., Manley,J.L. and Proudfoot,N.J. (1998) The upstream sequence element of the C2 complement poly(A) signal activates mRNA 3′ end formation by two distinct mechanisms. Genes Dev., 12, 2522-2534.
28. Legendre,M. and Gautheret,D. (2003) Sequence determinants in human polyadenylation site selection. BMC Genomics, 4, 7.
29. Tabaska,J.E. and Zhang,M.Q. (1999) Detection of polyadenylation signals in human DNA sequences. Gene, 231, 77-86.
30. Zhang,H. (2003) Alignment of BLAST high-scoring segment pairs based on the longest increasing subsequence algorithm. Bioinformatics 19, 1391-1396.
31. Burset,M., Seledtsov,I.A. and Solovyev,V.V. (2001) SpliceDB: database of canonical and non-canonical mammalian splice sites. Nucleic Acids Res., 29, 255-259.
32. Kent,W.J. (2002) BLAT - the BLAST-like alignment tool. Genome Res., 12, 656-664.
33. Kan,Z., Gish,W., Rouchka,E., Glasscock,J. and States,D. (2000) UTR reconstruction and analysis using genomically aligned EST sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol., 8, 218-227.
34. Benjamini,Y. and Hochberg,Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B, 57, 289-300.
35. Venables,W.N. and Ripley,B.D. (2002) Modern Applied Statistics with S. Springer, New York, NY.
36. Chen,F., MacDonald,C.C. and Wilusz,J. (1995) Cleavage site determinants in the mammalian polyadenylation signal. Nucleic Acids Res., 23, 2614-2620.
37. Frischmeyer,P.A., van Hoof,A., O'Donnell,K., Guerrerio,A.L., Parker,R. and Dietz,H.C. (2002) An mRNA surveillance mechanism that eliminates transcripts lacking termination codons. Science, 295 2258-2261.
38. Wilusz,J. and Shenk,T. (1988) A 64 kD nuclear protein binds to RNA segments that include the AAUAAA polyadenylation motif. Cell 52, 221-228.
39. Fairbrother,W.G., Yeh,R.F., Sharp,P.A. and Burge,C.B. (2002) Predictive identification of exonic splicing enhancers in human genes. Science, 297, 1007-1013.
40. Sheets,M.D., Ogg,S.C. and Wickens,M.P. (1990) 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., 18, 5799-5805.
41. Shaw,G. and Kamen,R. (1986) A conserved AU sequence from the 3′ untranslated region of GM-CSF mRNA mediates selective mRNA degradation. Cell, 46, 659-667.
42. Chen,C.Y. and Shyu,A.B. (1995) AU-rich elements: characterization and importance in mRNA degradation. Trends Biochem. Sci., 20, 465-470.
43. Ford,L.P., Watson,J., Keene,J.D. and Wilusz,J. (1999) ELAV proteins stabilize deadenylated intermediates in a novel in vitro mRNA deadenylation/degradation system. Genes Dev., 13, 188-201.
44. Fan,X.C. and Steitz,J.A. (1998) Overexpression of HuR, a nuclear-cytoplasmic shuttling protein, increases the in vivo stability of ARE-containing mRNAs. EMBO J., 17, 3448-3460.
45. Peng,S.S., Chen,C.Y., Xu,N. and Shyu,A.B. (1998) RNA stabilization by the AU-rich element binding protein, HuR, an ELAV protein. EMBO J., 17, 3461-3470.
46. Loflin,P., Chen,C.Y. and Shyu,A.B. (1999) Unraveling a cytoplasmic role for hnRNP D in the in vivo mRNA destabilization directed by the AU-rich element. Genes Dev., 13, 1884-1897.