Polyadenylation in Plants

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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.

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InhaltsangabePart I: Bioinformatics Studies of Plant Polyadenylation1. Computational Analysis Of Plant Polyadenylation SignalsXiaohui Wu, Guoli Ji,  and Qingshun Quinn Li  2. Prediction of Plant mRNA Polyadenylation SitesXiaohui 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 AlgorithmPatrick E. Thomas 6. RADPRE: a Computational Program for Identification of Differential mRNA Processing Including Alternative PolyadenylationDenghui Xing  and Qingshun Quinn Li Part II: Biochemistry of Polyadenylation in Plants7. Characterization Of Plant Polyadenylation Complexes By Using Tandem Affinity PurificationHongwei Zhao,Xinfu Ye, and Qingshun Quinn Li 8. In vitro Analysis Of Cleavage And Polyadenylation In ArabidopsisHongwei Zhao and Qingshun Quinn Li 9. Production, Purification, and Assay of Recombinant Proteins for in vitro Biochemical Analyses of the Plant Polyadenylation ComplexStephen A. Bell and Balasubrahmanyam Addepalli 10. Detection of Disulfide Linkage By Chemical Derivatization And Mass SpectrometryBalasubrahmanyam Addepalli 11. Transient Expression Using Agroinfiltration To Study Polyadenylation In PlantsCarol Von Lanken and Arthur G. Hunt 12. A 3' RACE Protocol To Confirm Polyadenylation SitesLiuyin Ma and Arthur G. Hunt Part III: Genome-Scale Study of Polyadeylation in Plants13. Phage Display Library Screening for Identification of Interacting Protein PartnersBalasubrahmanyam Addepalli, Suryadevara Rao, and Arthur G. Hunt 14. Genome-wide Determination Of Poly(A) Site Choice In PlantsPratap 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 RNAJingyi Cao and Qingshun Q. Li 17. A Rapid, Simple, and Inexpensive Method for the Preparation of Strand-specific RNA-Seq LibrariesArthur G. Hunt18. Genome-Wide Analysis Of Distribution of RNA Polymerase II isoforms using ChIP-seq Laura de Lorenzo 

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