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Analysis of Poly(A) Site Choice Using a Java-Based Clustering Algorithm

  • Patrick E. Thomas
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1255)

Abstract

Modern high-throughput DNA sequencing has the potential to generate large volumes of data for analysis by investigators—including poly(A) site data. Here I describe a computational method to compare poly(A) site choice differences between two large data sets based on the relative abundance and position of tags within each reference sequence to which they are aligned. This method provides rapid quantification and visualization of differences and similarities in poly(A) site choice between the two datasets.

Key words

Alternative polyadenylation Java Next generation sequencing PAT-seq 

Notes

Acknowledgements

This work was supported by the National Science Foundation (award MCB-0313472 to Drs. Arthur G. Hunt and Q. Quinn Li, and an RET supplement to award IOS-0817818).

References

  1. 1.
    Mueller AA, Cheung TH, Rando TA (2013) All’s well that ends well: alternative polyadenylation and its implications for stem cell biology. Curr Opin Cell Biol 25(2):222–232. doi: 10.1016/j.ceb.2012.12.008 PubMedCentralPubMedCrossRefGoogle Scholar
  2. 2.
    Elkon R, Ugalde AP, Agami R (2013) Alternative cleavage and polyadenylation: extent, regulation and function. Nat Rev Genet 14(7):496–506. doi: 10.1038/nrg3482 PubMedCrossRefGoogle Scholar
  3. 3.
    Shi Y (2012) Alternative polyadenylation: new insights from global analyses. RNA 18(12):2105–2117. doi: 10.1261/rna.035899.112 PubMedCentralPubMedCrossRefGoogle Scholar
  4. 4.
    Xing D, Li QQ (2011) Alternative polyadenylation and gene expression regulation in plants. Wiley Interdiscip Rev RNA 2(3):445–458. doi: 10.1002/wrna.59 PubMedCrossRefGoogle Scholar
  5. 5.
    Hunt AG (2008) Messenger RNA 3′ end formation in plants. Curr Top Microbiol Immunol 326:151–177PubMedGoogle Scholar
  6. 6.
    Thomas PE, Wu X, Liu M, Gaffney B, Ji G, Li QQ, Hunt AG (2012) Genome-wide control of polyadenylation site choice by CPSF30 in Arabidopsis. Plant Cell 24(11):4376–4388. doi: 10.1105/tpc.112.096107 PubMedCentralPubMedCrossRefGoogle Scholar
  7. 7.
    Sherstnev A, Duc C, Cole C, Zacharaki V, Hornyik C, Ozsolak F, Milos PM, Barton GJ, Simpson GG (2012) Direct sequencing of Arabidopsis thaliana RNA reveals patterns of cleavage and polyadenylation. Nat Struct Mol Biol 19(8):845–852. doi: 10.1038/nsmb.2345 PubMedCentralPubMedCrossRefGoogle Scholar
  8. 8.
    Wu X, Liu M, Downie B, Liang C, Ji G, Li QQ, Hunt AG (2011) Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation. Proc Natl Acad Sci U S A 108(30):12533–12538. doi: 10.1073/pnas.1019732108 PubMedCentralPubMedCrossRefGoogle Scholar
  9. 9.
    Ma L, Pati PK, Liu M, Li QQ, Hunt AG (2013) High throughput characterizations of poly(A) site choice in plants. Methods 67(1):74–83. doi: 10.1016/j.ymeth.2013.06.037 PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.Department of Plant and Soil SciencesUniversity of KentuckyLexingtonUSA
  2. 2.Franklin-Simpson High SchoolFranklinUSA

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