Polyadenylation in Plants: Methods and Protocols

ISBN-13: 9781493921744 / Angielski / Twarda / 2014 / 225 str.

Arthur G. Hunt; Qingshun Quinn Li

Opis

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.

Spis treści

Part I: Bioinformatics Studies of Plant Polyadenylation

1. Computational Analysis Of Plant Polyadenylation Signals

Xiaohui Wu, Guoli Ji,  and Qingshun Quinn Li

2. Prediction of Plant mRNA Polyadenylation Sites

Xiaohui Wu, Guoli Ji,  and Qingshun Quinn Li

 3. Extraction of poly(A) Sites from Large-scale RNA-seq Data Min Dong, Guoli Ji, Qingshun Q. Li,  and Chun Liang

4. Poly(A)-tag Deep Sequencing Data Processing To Extract poly(A) Sites

Xiaohui Wu, Guoli Ji,  and Qingshun Quinn Li

5. Analysis of poly(A) Site Choice Using A Java-Based Clustering Algorithm

Patrick E. Thomas

6. RADPRE: a Computational Program for Identification of Differential mRNA Processing Including Alternative Polyadenylation

Denghui Xing  and Qingshun Quinn Li 

Part II: Biochemistry of Polyadenylation in Plants

7. Characterization Of Plant Polyadenylation Complexes By Using Tandem Affinity Purification

Hongwei Zhao，Xinfu Ye, and Qingshun Quinn Li

8. In vitro Analysis Of Cleavage And Polyadenylation In Arabidopsis

Hongwei Zhao and Qingshun Quinn Li

9. Production, Purification, and Assay of Recombinant Proteins for in vitro Biochemical Analyses of the Plant Polyadenylation Complex

Stephen A. Bell and Balasubrahmanyam Addepalli

10. Detection of Disulfide Linkage By Chemical Derivatization And Mass Spectrometry

Balasubrahmanyam Addepalli

11. Transient Expression Using Agroinfiltration To Study Polyadenylation In Plants

Carol Von Lanken and Arthur G. Hunt

12. A 3’ RACE Protocol To Confirm Polyadenylation Sites

Liuyin Ma and Arthur G. Hunt

Part III: Genome-Scale Study of Polyadeylation in Plants

13. Phage Display Library Screening for Identification of Interacting Protein Partners

Balasubrahmanyam Addepalli, Suryadevara Rao, and Arthur G. Hunt

14. Genome-wide Determination Of Poly(A) Site Choice In Plants

Pratap Kumar Pati, Liuyin Ma, and Arthur G. Hunt

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

Man Liu, Xiaohui Wu, and Qingshun Quinn Li

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

Jingyi Cao and Qingshun Q. Li

 17. A Rapid, Simple, and Inexpensive Method for the Preparation of Strand-specific RNA-Seq Libraries

Arthur G. Hunt

18. Genome-Wide Analysis Of Distribution of RNA Polymerase II isoforms using ChIP-seq

Laura de Lorenzo