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Computational Analysis of Plant Polyadenylation Signals

  • Xiaohui Wu
  • Guoli Ji
  • Qingshun Quinn LiEmail author
Protocol
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 

Notes

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).

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.Department of AutomationXiamen UniversityXiamenChina
  2. 2.Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and EcologyXiamen UniversityXiamenChina
  3. 3.Department of BiologyMiami UniversityOxfordUSA
  4. 4.Rice Research InstituteFujian Academy of Agricultural SciencesFujianChina

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