Books  Animal & General Biology  Genetics 

Alternative Pre-mRNA Splicing: Theory and Protocols

Handbook / Manual

Edited By: Stefan Stamm, Chris Smith and Reinhard Luhrmann

John Wiley & Sons

Paperback | Jan 2012 | #194506 | ISBN-13: 9783527326068
Availability: Usually dispatched within 5 days Details
NHBS Price: £85.00 $104/€96 approx

About this book

All eukaryotic messenger RNAs are derived from precursors, the pre-mRNAs, by an extensive series of nuclear modifi cations. Most notably, the removal of introns and the joining of the remaining exons in the process of pre-mRNA splicing is essential to generate mRNAs that are suitable templates for translation. The vast majority of human pre-mRNAs undergo alternative splicing, in which different RNA parts are either included or omitted in the mature mRNA. This process allows individual genes to generate multiple proteins and makes alternative pre-mRNA splicing a central element in gene regulation. Although pre-mRNA splicing occurs with high fidelity, an increasing number of diseases have been linked to defects that lead to mis-spliced mRNAs.

This book was written for graduate and medical students, as well as clinicians and postdoctoral researchers. It describes the theory of alternative pre-mRNA splicing in twelve introductory chapters and then introduces protocols and their theoretical background relevant for experimental research. These 43 practical chapters cover: Basic methods, Detection of splicing events, Analysis of alternative pre-mRNA splicing in vitro and in vivo, Manipulation of splicing events, and Bioinformatic analysis of alternative splicing. A theoretical introduction and practical guide for molecular biologists, geneticists,clinicians and every researcher interested in alternative splicing.


- Splicing in the RNA World
- RNPs, small RNAs, miRNAs
- RNA Elements Involved in Splicing
- A Structural Biology Perspective of Proteins Involved in Splicing Regulation
- The Spliceosome in Constitutive Splicing
- The Use of Saccharomyces cerevisiae to Study the Mechanism of pre-mRNA Splicing
- Challenges in Plant Alternative Splicing
- Alternative Splice Site Selection
- Integration of Splicing with Nuclear and Cellular Events
- Splicing and Disease
- From Bedside to Bench: How to Analyze a Splicing Mutation
- Analysis of Splicing Problems

- Ultracentrifugation in the Analysis and Purification by of Spliceosomes Assembled in Vitro
- Chemical Synthesis of RNA
- RNA Interference (siRNA, ShRNA)
- Expression and Purification of Splicing Proteins
- Detection of RNA-Protein Complexes By Electrophoretic Mobility Shift Assay
- Functional Analysis of large Exonic Sequences through Iterative in Vivo Selection
- Identification of Splicing cis-Elements through an Ultra-Refined Antisense Microwalk
- Genomic SELEX to Identify RNA Targets of Plant RNA Binding Proteins

- Quantification of Alternative Splice Variants
- High-Throughput Analysis of Alternative Splicing by RT-PCR
- Monitoring Changes in Plant Alternative Splicing Events
- Array Analysis
- The CLIP Method to Study Protein-RNA Interactions in Intact Cells and Tissues
- RNA: Protein Crosslinking and Immunoprecipitation in Yeast (CLIP)
- Identification of Proteins Bound to RNA
- Single Cell Detection of Splicing Events with Fluorescent Splicing Reporters

- The Preparation of HeLa Cell Nuclear Extracts
- In Vitro Splicing Assays
- Assembly of Spliceosomes in Vitro
- Analysis of Site-Specific RNA-Protein Interactions
- Immunoprecipitation and Pull-Down of Nuclear Proteins
- Analysis of Protein (RNA) Complexes by (Quantitative) Mass Spec Analysis

- Fast cloning of splicing reporter minigenes
- In Vivo Splicing Assays
- Coupled Promoter Splicing Systems
- Stable Cell Lines With Splicing Reporters
- Splicing Factor ChIP and ChRIP: Detection of Splicing and Splicing Factors at Genes by Chromatin Immunoprecipitation
- Yeast Genetics to Investigate the Function of Core Pre-mRNA Splicing Factors
- Analysis of HIV-1 RNA Splicing
- In Vivo Analysis of Plant Intron Splicing
- Modificaton State-Specific Antibodies
- Analysis of Alternative Splicing in Drosophila Genetic Mosaics

- Antisense Derivatives of U7 Small Nuclear RNA as Modulators of Pre-mRNA Splicing
- Screening for Alternative Splicing Modulators
- Use of Oligonucleotides to Change Splicing
- Changing Signals to the Spliceosome

- Overview of Splicing Relevant Databases
- High Throughput Sequencing
- Identification of Splicing Factor Target Genes by High Throughput Sequencing
- Bioinformatic Analysis of Splicing Events
- Analysis of Pre-mRNA Secondary Structures and Alternative Splicing
- Structure Prediction for Alternatively Spliced Proteins
- Comparative Genomics Methods for the Prediction of Small RNA Binding Sites

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Stefan Stamm is Associate Professor in the Department for Molecular and Cellular Biochemistry at the University of Kentucky. He studied Biochemistry in Hannover (Germany) and did the practical work for his PhD as well as postdoctoral work at the Cold Spring Harbor Laboratory, NY. His research focuses on mechanisms and regulation of alternative splicing, with the aim to apply the fi ndings to the Prader-Willi Syndrome and Spinal Muscular Atrophy.

Chris Smith is Professor of RNA Molecular Biology in the Department of Biochemistry at the University of Cambridge. His PhD research in Biochemistry was carried out at the University of London, followed by postdoctoral research at Harvard Medical School. His research interests encompass the mechanisms, regulation and function of alternative splicing.

Reinhard Luhrmann is Director at the Max Planck Institute for Biophysical Chemistry in Gottingen where he is head of the Department of Cellular Biochemistry. He is an Honorary Professor at the University of Gottingen. He has studied chemistry at the University of Munster where he also received his PhD. He worked as a postdoctoral fellow at the Max Planck Institute for Molecular Genetics in Berlin. His research focuses on the structure and mechanism of the spliceosome.

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