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Life Sciences - Plant Sciences | Plant Transposable Elements - Methods and Protocols

Plant Transposable Elements

Methods and Protocols

Series: Methods in Molecular Biology, Vol. 1057

Peterson, Thomas (Ed.)

2013, XV, 324 p. 61 illus., 23 illus. in color.

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  • Details background information and specific experimental protocols on plant transposable elements
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Transposable elements have played a major role in shaping plant genome structure and gene expression.  Transposons not only drive sequence expansion, induce mutations and generate chromosome rearrangements, they also help to shape the epigenetic topology of the eukaryotic genome.  In Plant Transposable Elements: Methods and Protocols, expert researchers in the field detail many of the methods which are now commonly used to study transposons. These methods include computational approaches to study the ancient transposon remnants that comprise the bulk of plant genomes, as well as laboratory techniques to identify recent and ongoing transposition events. 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.

 

Authoritative and practical, Plant Transposable Elements: Methods and Protocols seeks to aid scientists in the further study of transposons by providing essential background information and specific experimental protocols.

Content Level » Professional/practitioner

Keywords » Transposable elements - activation tagging - ancient transposon remnants - chromosome rearrangements - clonal analysis of development - distinguish transposon-based variegation - gene isolation - major Class II (DNA) elements - plant genomes - transposition events - transposon biology - transposon systems

Related subjects » Plant Sciences

Table of contents 

1. Historical Overview of Transposable Element Research

Peter A Peterson

 

2. Distinguishing Variable Phenotypes from Variegation Caused by Transposon Activities

Virginia Walbot

 

3. Using Transposons for Genetic Mosaic Analysis of Plant Development

Philip W. Becraft

 

4. Survey of Natural and Transgenic Gene Markers Used to Monitor Transposon Activity

Lakshminarasimhan Krishnaswamy, Thomas Peterson

 

5. Molecular Biology of Maize Ac/Ds Elements – an Overview

Katina Lazarow, My-Linh Du and Reinhard Kunze

 

6. Gene Tagging with Engineered Ds Elements in Maize

Yubin Li, Gregorio Segal, Qinghua Wang, and Hugo K. Dooner

 

7. Plant Regeneration Methods for Rapid Generation of a Large Scale of Ds Transposant Population in Rice

Yuan Hu Xuan, Jin Huang, Gihwan Yi, Dong-Soo Park, Soo Kwon Park, Moo Young Eun, Doh Won Yun, Gang-Seob Lee, Tae Ho Kim, Chang-deok Han

 

8. Isolation of Sequences Flanking Ac Insertion Sites by Ac Casting

Dafang Wang and Thomas Peterson

 

9. Regulation of the Mutator System of Transposons in Maize

Damon Lisch

 

10. Using MuDR/Mu Transposons in Directed Tagging Strategies 

Virginia Walbot and Julia Qüesta

 

11. Genetic and Molecular Analysis of UniformMu Transposon Insertion Lines

Donald R. McCarty, Masaharu Suzuki, Charles Hunter, Wayne T. Avigne, and Karen E. Koch

 

12. Digestion-Ligation-Amplification (DLA): A Simple Genome Walking Method to Amplify Unknown Sequences Flanking Mutator (Mu) Transposons and Thereby Facilitate Gene Cloning

Sanzhen Liu, An-Ping Hsia, Patrick S. Schnable

 

13. Molecular Genetics and Epigenetics of CACTA Elements

Nina V. Fedoroff

 

14. Activation Tagging Using the Maize En-I Transposon System for the Identification of Abiotic Stress Resistance Genes in Arabidopsis

Amal Harb and Andy Pereira

15. Reverse Genetics in Rice using Tos17

Delphine Mieulet, Anne Diévart, Gaëtan Droc, Nadège Lanau and Emmanuel Guiderdoni

 

16. Identification and Applications of the Petunia Class II Act1/dTph1 Transposable Element System

Tom Gerats , Jan Zethof, and Michiel Vandenbussche

 

17. Transposon Display: A Versatile Method for Transposon Tagging

Michiel Vandenbussche, Jan Zethof, and Tom Gerats

 

18. Massive Indexed Parallel Identification of Transposon Flanking Sequences

Michiel Vandenbussche, Jan Zethof, and Tom Gerats

 

19. Use of Next Generation Sequencing (NGS) Technologies for the Genome-wide Detection of Transposition

Moaine Elbaidouri, Cristian Chaparro and Olivier Panaud

 

20. Overview of Repeat Annotation and de novo Repeat Identification

Ning Jiang

 

21. Computational Methods for Identification of DNA Transposons

Ning Jiang

 

22. TEnest 2.0: Computational Annotation and Visualization of Nested Transposable Elements

Brent A. Kronmiller and Roger P. Wise

 

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