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Polyadenylation in Plants

Methods and Protocols

  • Book
  • © 2015

Overview

Editors:
  1. Arthur G. Hunt

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

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  2. Qingshun Quinn Li

    1. 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, China

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts
  • Includes supplementary material: sn.pub/extras

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

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Table of contents (18 protocols)

  1. Front Matter

    Pages i-ix
    Download chapter PDF

  2. Bioinformatics Studies of Plant Polyadenylation

    1. Front Matter

      Pages 1-1
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    2. Computational Analysis of Plant Polyadenylation Signals

      • Xiaohui Wu, Guoli Ji, Qingshun Quinn Li
      Pages 3-11

    3. Prediction of Plant mRNA Polyadenylation Sites

      • Xiaohui Wu, Guoli Ji, Qingshun Quinn Li
      Pages 13-23

    4. Extraction of Poly(A) Sites from Large-Scale RNA-seq Data

      • Min Dong, Guoli Ji, Qingshun Quinn Li, Chun Liang
      Pages 25-37

    5. Poly(A)-Tag Deep Sequencing Data Processing to Extract Poly(A) Sites

      • Xiaohui Wu, Guoli Ji, Qingshun Quinn Li
      Pages 39-48

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

      • Patrick E. Thomas
      Pages 49-56

    7. RADPRE: A Computational Program for Identification of Differential mRNA Processing Including Alternative Polyadenylation

      • Denghui Xing, Qingshun Quinn Li
      Pages 57-66

  3. Biochemistry of Polyadenylation in Plants

    1. Front Matter

      Pages 67-67
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    2. Characterization of Plant Polyadenylation Complexes by Using Tandem Affinity Purification

      • Hongwei Zhao, Xinfu Ye, Qingshun Quinn Li
      Pages 69-78

    3. In Vitro Analysis of Cleavage and Polyadenylation in Arabidopsis

      • Hongwei Zhao, Qingshun Quinn Li
      Pages 79-89

    4. Production, Purification, and Assay of Recombinant Proteins for In Vitro Biochemical Analyses of the Plant Polyadenylation Complex

      • Stephen A. Bell, Balasubrahmanyam Addepalli
      Pages 91-115

    5. Detection of Disulfide Linkage by Chemical Derivatization and Mass Spectrometry

      • Balasubrahmanyam Addepalli
      Pages 117-126

    6. Transient Expression Using Agroinfiltration to Study Polyadenylation in Plants

      • Carol Von Lanken, Arthur G. Hunt
      Pages 127-133

    7. A 3′ RACE Protocol to Confirm Polyadenylation Sites

      • Liuyin Ma, Arthur G. Hunt
      Pages 135-144

  4. Genome-Scale Study of Polyadenylation in Plants

    1. Front Matter

      Pages 145-145
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    2. Phage Display Library Screening for Identification of Interacting Protein Partners

      • Balasubrahmanyam Addepalli, Suryadevara Rao, Arthur G. Hunt
      Pages 147-158

    3. Genome-Wide Determination of Poly(A) Site Choice in Plants

      • Pratap Kumar Pati, Liuyin Ma, Arthur G. Hunt
      Pages 159-174

    4. DNA/RNA Hybrid Primer Mediated Poly(A) Tag Library Construction for Illumina Sequencing

      • Man Liu, Xiaohui Wu, Qingshun Quinn Li
      Pages 175-184

    5. Poly(A) Tag Library Construction from 10 ng Total RNA

      • Jingyi Cao, Qingshun Quinn Li
      Pages 185-194
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Keywords

About this book

This volume presents the most recent studies on mRNA polyadenylation in plants. Chapters are divided into three sections covering recent development of the use of bioinformatics tools in the field. numerous molecular, biochemical, and methods used to characterize polyadenylation sites on a genome-wide scale. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Some are specific for plant research, but most can be adopted for research in other organisms.

Authoritative and practical, Polyadenylation in Plants: Methods and Protocols provides scientists with a wide range of methods to study mRNA 3’-end formation in plants.

Editors and Affiliations

  • Department of Plant and Soil Sciences, University of Kentucky, Lexington, USA

    Arthur G. Hunt

  • 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, China

    Qingshun Quinn Li

Bibliographic Information

  • Book Title: Polyadenylation in Plants

  • Book Subtitle: Methods and Protocols

  • Editors: Arthur G. Hunt, Qingshun Quinn Li

  • Series Title: Methods in Molecular Biology

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

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media New York 2015

  • Hardcover ISBN: 978-1-4939-2174-4Published: 09 December 2014

  • Softcover ISBN: 978-1-4939-4668-6Published: 22 September 2016

  • eBook ISBN: 978-1-4939-2175-1Published: 08 December 2014

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: IX, 225

  • Number of Illustrations: 11 b/w illustrations, 23 illustrations in colour

  • Topics: Plant Sciences, Plant Genetics and Genomics, Gene Function

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