Skip to main content
Book cover

Polyadenylation in Plants pp 3–11Cite as

Computational Analysis of Plant Polyadenylation Signals

Part of the Methods in Molecular Biology book series (MIMB,volume 1255)

Abstract

Messenger RNA polyadenylation in eukaryotes marks the end of a transcript, and the process is associated with transcription termination. Increasing evidence reveals the potential of gene expression regulation through alternative polyadenylation. The site of poly(A) addition is defined by poly(A) signals reside in the transcribed pre-mRNA. To gain further insight into poly(A) signals and their functions in defining alternative polyadenylation sites that lie within different genomic regions, SignalSleuth2 was developed to extract and analyze cis-elements from a set of data with known poly(A) sites. After obtaining the sequences surrounding the poly(A) sites, exhaustive search of short sequence motifs in specified range of nucleotide sequences are performed, variable motif sizes and rank the detected motifs based on their occurrence frequencies are tallied. It also has new functions including Position-Specific Scoring Matrix (PSSM) scores calculation and multiple scanning modes. This program is powerful in revealing underline sequence motifs surrounding any target regions in a given dataset.

Key words

  • Polyadenylation signal
  • Pattern recognition
  • Alternative polyadenylation
  • Cis-elements

This is a preview of subscription content, access via your institution.

Protocol
USD   49.95
Price excludes VAT (USA)
  • DOI: 10.1007/978-1-4939-2175-1_1
  • Chapter length: 9 pages
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
eBook
USD   89.00
Price excludes VAT (USA)
  • ISBN: 978-1-4939-2175-1
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
Softcover Book
USD   119.00
Price excludes VAT (USA)
Hardcover Book
USD   169.99
Price excludes VAT (USA)
Learn about institutional subscriptions
Fig. 1
Fig. 2

Springer Nature is developing a new tool to find and evaluate Protocols. Learn more

References

  1. Hu J, Lutz CS, Wilusz J, Tian B (2005) Bioinformatic identification of candidate cis-regulatory elements involved in human mRNA polyadenylation. RNA 11(10):1485–1493

    CAS  PubMed Central  PubMed  CrossRef  Google Scholar 

  2. Bartel DP (2009) MicroRNAs: target recognition and regulatory functions. Cell 136(2):215–233. doi:10.1016/j.cell.2009.01.002

    CAS  PubMed Central  PubMed  CrossRef  Google Scholar 

  3. Wickens M, Bernstein DS, Kimble J, Parker R (2002) A PUF family portrait: 3′ UTR regulation as a way of life. Trends Genet 18(3):150–157

    CAS  PubMed  CrossRef  Google Scholar 

  4. Holec SLH, Kuhn K, Alioua M, Borner T, Gagliardi D (2006) Relaxed transcription in Arabidopsis mitochondria is counterbalanced by RNA stability control mediated by polyadenylation and polynucleotide phosphorylase. Mol Cell Biol 26:2869–2876

    CAS  PubMed Central  PubMed  CrossRef  Google Scholar 

  5. Hammell CMGS, Zenklusen D, Heath CV, Stutz F, Moore C, Cole CN (2002) Coupling of termination, 3′ processing, and mRNA export. Mol Cell Biol 22:6441–6457

    CAS  PubMed Central  PubMed  CrossRef  Google Scholar 

  6. Buratowski S (2005) Connections between mRNA 3′ end processing and transcription termination. Curr Opin Cell Biol 17:257–261

    CAS  PubMed  CrossRef  Google Scholar 

  7. Moor CH, Meijer H, Lissenden S (2005) Mechanisms of translational control by the 3′ UTR in development and differentiation. Semin Cell Dev Biol 16(1):49–58. doi:10.1016/j.semcdb.2004.11.007

    PubMed  CrossRef  Google Scholar 

  8. Beaudoing E, Freier S, Wyatt JR, Claverie JM, Gautheret D (2000) Patterns of variant polyadenylation signal usage in human genes. Genome Res 10(7):1001–1010

    CAS  PubMed Central  PubMed  CrossRef  Google Scholar 

  9. Legendre M, Gautheret D (2003) Sequence determinants in human polyadenylation site selection. BMC Genomics 4(1):7

    PubMed Central  PubMed  CrossRef  Google Scholar 

  10. Liu H, Han H, Li J, Wong L (2003) An in-silico method for prediction of polyadenylation signals in human sequences. Genome Inform 14:84–93

    CAS  PubMed  Google Scholar 

  11. Akhtar MN, Bukhari SA, Fazal Z, Qamar R, Shahmuradov I (2010) POLYAR, a new computer program for prediction of poly(A) sites in human sequences. BMC Genomics 11(1):646

    PubMed Central  PubMed  CrossRef  Google Scholar 

  12. Cheng Y, Miura RM, Tian B (2006) Prediction of mRNA polyadenylation sites by support vector machine. Bioinformatics 22(19):2320–2325

    CAS  PubMed  CrossRef  Google Scholar 

  13. Thomas-Chollier M, Sand O, Turatsinze JV, Janky R, Defrance M, Vervisch E, Brohee S, van Helden J (2008) RSAT: regulatory sequence analysis tools. Nucleic Acids Res 36(Web Server):W119–W127. doi:10.1093/nar/gkn304

    CAS  PubMed Central  PubMed  CrossRef  Google Scholar 

  14. Crooks GE, Hon G, Chandonia JM, Brenner SE (2004) WebLogo: a sequence logo generator. Genome Res 14(6):1188–1190. doi:10.1101/gr.849004

    CAS  PubMed Central  PubMed  CrossRef  Google Scholar 

  15. Ji G, Zheng J, Shen Y, Wu X, Jiang R, Lin Y, Loke JC, Davis KM, Reese GJ, Li QQ (2007) Predictive modeling of plant messenger RNA polyadenylation sites. BMC Bioinform 8(43):43

    CrossRef  Google Scholar 

  16. Loke JC, Stahlberg EA, Strenski DG, Haas BJ, Wood PC, Li QQ (2005) Compilation of mRNA polyadenylation signals in Arabidopsis revealed a new signal element and potential secondary structures. Plant Physiol 138(3):1457–1468

    CAS  PubMed Central  PubMed  CrossRef  Google Scholar 

  17. Shen Y, Ji G, Haas BJ, Wu X, Zheng J, Reese GJ, Li QQ (2008) Genome level analysis of rice mRNA 3′-end processing signals and alternative polyadenylation. Nucleic Acids Res 36(9):3150–3161

    CAS  PubMed Central  PubMed  CrossRef  Google Scholar 

  18. Shen Y, Liu Y, Liu L, Liang C, Li QQ (2008) Unique features of nuclear mRNA poly(A) signals and alternative polyadenylation in Chlamydomonas reinhardtii. Genetics 179(1):167–176

    CAS  PubMed Central  PubMed  CrossRef  Google Scholar 

Download references

Acknowledgement

Funding supports for this work were from the National Natural Science Foundation of China (Nos. 61174161 and 61304141), the Natural Science Foundation of Fujian Province of China (No. 2012J01154), the specialized Research Fund for the Doctoral Program of Higher Education of China (Nos. 20130121130004 and 20120121120038), and the Fundamental Research Funds for the Central Universities in China (Xiamen University: No. 2013121025), Xiamen Shuangbai Talent Plan (to QQL), and US National Science Foundation (grant nos. IOS–0817829 and IOS-1353354 to QQL).

Author information

Authors and Affiliations

  1. Department of Automation, Xiamen University, Xiamen, Fujian, 361005, China

    Xiaohui Wu & Guoli Ji

  2. Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China

    Qingshun Quinn Li

  3. Department of Biology, Miami University, 390 Pearson, Oxford, OH, 45056, USA

    Qingshun Quinn Li

  4. Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China

    Qingshun Quinn Li

Authors
  1. Xiaohui Wu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Guoli Ji
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Qingshun Quinn Li
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Qingshun Quinn Li .

Editor information

Editors and Affiliations

  1. Department of Plant and Soil Sciences, University of Kentucky, Lexington, Kentucky, USA

    Arthur G. Hunt

  2. Department of Biology, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Miami University, Oxford, OH, USA and Xiamen University, Xiamen, Fujian, Fujian, China

    Qingshun Quinn Li

Rights and permissions

Reprints and Permissions

Copyright information

© 2015 Springer Science+Business Media New York

About this protocol

Cite this protocol

Wu, X., Ji, G., Li, Q.Q. (2015). Computational Analysis of Plant Polyadenylation Signals. In: Hunt, A., Li, Q. (eds) Polyadenylation in Plants. Methods in Molecular Biology, vol 1255. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2175-1_1

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-2175-1_1

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-2174-4

  • Online ISBN: 978-1-4939-2175-1

  • eBook Packages: Springer Protocols