Identification of mRNA Polyadenylation Sites in Genomes Using cDNA Sequences, Expressed Sequence Tags, and Trace

  • Ju Youn Lee
  • Ji Yeon Park
  • Bin Tian
Part of the Methods In Molecular Biology™ book series (MIMB, volume 419)


Polyadenylation of nascent transcripts is an essential step for most mRNAs in eukaryotic cells. It is directly involved in the termination of transcription and is coupled with other steps of pre-mRNA processing. Recent studies have shown that transcript variants resulting from alternative polyadenylation are widespread for human and mouse genes, contributing to the complexity of mRNA pool in the cell. In addition to 3′-most exons, alternative polyadenylation sites (or poly(A) sites) can be located in internal exons and introns. Identification of poly(A) sites in genomes is critical for understanding the occurrence and significance of alternative polyadenylation events. Bioinformatic methods using cDNA sequences, Expressed Sequence Tags (ESTs), and Trace offer a sensitive and systematic approach to detect poly(A) sites in genomes. Various criteria can be employed to enhance the specificity of the detection, including identifying sequences derived from internal priming of mRNA and polyadenylated RNAs during degradation.

Key Words

Polyadenylation EST Trace genome intron exon 3′-UTR internal priming 



We thank Carol S. Lutz and members of B.T. laboratory for helpful discussions. This work was supported by The Foundation of the University of Medicine and Dentistry of New Jersey.


  1. 1.
    Edmonds, M. (2002) A history of poly A sequences: from formation to factors to function. Prog Nucleic Acid Res Mol Biol, 71, 285–389.CrossRefPubMedGoogle Scholar
  2. 2.
    Marzluff, W.F. (2005) Metazoan replication-dependent histone mRNAs: a distinct set of RNA polymerase II transcripts. Curr Opin Cell Biol, 17, 274–280.CrossRefPubMedGoogle Scholar
  3. 3.
    Mangus, D.A., Evans, M.C. and Jacobson, A. (2003) Poly(A)-binding proteins: multifunctional scaffolds for the post-transcriptional control of gene expression. Genome Biol, 4, 223.CrossRefPubMedGoogle Scholar
  4. 4.
    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.CrossRefPubMedGoogle Scholar
  5. 5.
    Colgan, D.F. and Manley, J.L. (1997) Mechanism and regulation of mRNA polyadenylation. Genes Dev, 11, 2755–2766.CrossRefPubMedGoogle Scholar
  6. 6.
    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.PubMedGoogle Scholar
  7. 7.
    Minvielle-Sebastia, L. and Keller, W. (1999) mRNA polyadenylation and its coupling to other RNA processing reactions and to transcription. Curr Opin Cell Biol, 11, 352–357.CrossRefPubMedGoogle Scholar
  8. 8.
    Proudfoot, N. (2004) New perspectives on connecting messenger RNA 3″ end formation to transcription. Curr Opin Cell Biol, 16, 272–278.CrossRefPubMedGoogle Scholar
  9. 9.
    Tian, B., Hu, J., Zhang, H. and Lutz, C.S. (2005) A large-scale analysis of mRNA polyadenylation of human and mouse genes. Nucleic Acids Res, 33, 201–212.CrossRefPubMedGoogle Scholar
  10. 10.
    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.CrossRefPubMedGoogle Scholar
  11. 11.
    Chen, F., MacDonald, C.C. and Wilusz, J. (1995) Cleavage site determinants in the mammalian polyadenylation signal. Nucleic Acids Res, 23, 2614–2620.CrossRefPubMedGoogle Scholar
  12. 12.
    Yan, J. and Marr, T.G. (2005) Computational analysis of 3′-ends of ESTs shows four classes of alternative polyadenylation in human, mouse, and rat. Genome Res, 15, 369–375.CrossRefPubMedGoogle Scholar
  13. 13.
    Zhang, H., Lee, J.Y. and Tian, B. (2005) Biased alternative polyadenylation in human tissues. Genome Biol, 6, R100.CrossRefPubMedGoogle Scholar
  14. 14.
    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.CrossRefPubMedGoogle Scholar
  15. 15.
    Houseley, J., LaCava, J. and Tollervey, D. (2006) RNA-quality control by the exosome. Nat Rev Mol Cell Biol, 7, 529–539.CrossRefPubMedGoogle Scholar
  16. 16.
    West, S., Gromak, N., Norbury, C.J. and Proudfoot, N.J. (2006) Adenylation and exosome-mediated degradation of cotranscriptionally cleaved pre-messenger RNA in human cells. Mol Cell, 21, 437–443.CrossRefPubMedGoogle Scholar
  17. 17.
    Hall-Pogar, T., Zhang, H., Tian, B. and Lutz, C.S. (2005) Alternative polyadenylation of cyclooxygenase-2. Nucleic Acids Res, 33, 2565–2579.CrossRefPubMedGoogle Scholar
  18. 18.
    Pan, Z., Zhang, H., Hague, L.K., Lee, J.Y., Lutz, C.S. and Tian, B. (2006) An intronic polyadenylation site in human and mouse CstF-77 genes suggests an evolutionarily conserved regulatory mechanism. Gene, 366, 325–334.CrossRefPubMedGoogle Scholar
  19. 19.
    Gautheret, D., Poirot, O., Lopez, F., Audic, S. and Claverie, J.M. (1998) Alternate polyadenylation in human mRNAs: a large-scale analysis by EST clustering. Genome Res, 8, 524–530.PubMedGoogle Scholar
  20. 20.
    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.CrossRefPubMedGoogle Scholar
  21. 21.
    Iseli, C., Stevenson, B.J., de Souza, S.J., Samaia, H.B., Camargo, A.A., Buetow, K.H., Strausberg, R.L., Simpson, A.J., Bucher, P. and Jongeneel, C.V. (2002) Long-range heterogeneity at the 3′ ends of human mRNAs. Genome Res, 12, 1068–1074.PubMedGoogle Scholar
  22. 22.
    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.CrossRefPubMedGoogle Scholar
  23. 23.
    Chen, J., Sun, M., Lee, S., Zhou, G., Rowley, J.D. and Wang, S.M. (2002) Identifying novel transcripts and novel genes in the human genome by using novel SAGE tags. Proc Natl Acad Sci USA, 99, 12257–12262.CrossRefPubMedGoogle Scholar
  24. 24.
    Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) Basic local alignment search tool. J Mol Biol, 215, 403–410.PubMedGoogle Scholar
  25. 25.
    Kent, W.J. (2002) BLAT–the BLAST-like alignment tool. Genome Res, 12, 656–664.PubMedGoogle Scholar
  26. 26.
    Florea, L., Hartzell, G., Zhang, Z., Rubin, G.M. and Miller, W. (1998) A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res, 8, 967–974.PubMedGoogle Scholar
  27. 27.
    Wheelan, S.J., Church, D.M. and Ostell, J.M. (2001) Spidey: a tool for mRNA-to-genomic alignments. Genome Res, 11, 1952–1957.PubMedGoogle Scholar
  28. 28.
    Wheeler, D.L., Barrett, T., Benson, D.A., Bryant, S.H., Canese, K., Chetvernin, V., Church, D.M., DiCuccio, M., Edgar, R., Federhen, S., et al. (2006) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res, 34, D173–D180.CrossRefPubMedGoogle Scholar
  29. 29.
    Venkataraman, K., Brown, K.M. and Gilmartin, G.M. (2005) Analysis of a noncanonical poly(A) site reveals a tripartite mechanism for vertebrate poly(A) site recognition. Genes Dev, 19, 1315–1327.CrossRefPubMedGoogle Scholar
  30. 30.
    Hu, J., Lutz, C.S., Wilusz, J. and Tian, B. (2005) Bioinformatic identification of candidate cis-regulatory elements involved in human mRNA polyadenylation. RNA, 11, 1485–1493.CrossRefPubMedGoogle Scholar
  31. 31.
    Cheng, Y., Miura, R.M. and Tian, B. (2006) Prediction of mRNA polyadenylation sites by support vector machine. Bioinformatics, 22, 2320–2335CrossRefPubMedGoogle Scholar
  32. 32.
    Tabaska, J.E. and Zhang, M.Q. (1999) Detection of polyadenylation signals in human DNA sequences. Gene, 231, 77–86.CrossRefPubMedGoogle Scholar

Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • Ju Youn Lee
    • 1
  • Ji Yeon Park
    • 1
  • Bin Tian
  1. 1.Department of Biochemistry and Molecular Biology, New Jersey Medical SchoolUniversity of Medicine and Dentistry of New JerseyNewarkUSA

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