Computational Analysis Of Plant Polyadenylation Signals -- Prediction of Plant mRNA Polyadenylation Sites -- Extraction of poly(A) Sites from Large-scale RNA-seq Data -- Poly(A)-tag Deep Sequencing Data Processing To Extract poly(A) Sites -- Analysis of poly(A) Site Choice Using A Java-Based Clustering Algorithm -- RADPRE: a Computational Program for Identification of Differential mRNA Processing Including Alternative Polyadenylation -- Characterization Of Plant Polyadenylation Complexes By Using Tandem Affinity Purification -- In vitro Analysis Of Cleavage And Polyadenylation In Arabidopsis -- Production, Purification, and Assay of Recombinant Proteins for in vitro Biochemical Analyses of the Plant Polyadenylation Complex -- Detection of Disulfide Linkage By Chemical Derivatization And Mass Spectrometry -- Transient Expression Using Agroinfiltration To Study Polyadenylation In Plants -- A 3' RACE Protocol To Confirm Polyadenylation Sites -- Phage Display Library Screening for Identification of Interacting Protein Partners -- Genome-wide Determination Of Poly(A) Site Choice In Plants -- DNA/RNA Hybrid Primer Mediated Poly(A) Tag Library Construction for Illumina Sequencing -- Poly(A) Tag Library Construction from 10 ng Total RNA -- Genome-Wide Analysis Of Distribution of RNA Polymerase II isoforms using ChIP-seq.

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.