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

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

Summary

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 
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Notes

Acknowledgments

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.

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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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