Alternative pre-mRNA Splicing (Theory and Protocols)

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Автор: Stefan Stamm, Chris Smith, and Reinhard Luhrmann (Editors)

Название: Alternative pre-mRNA Splicing (Theory and Protocols)

Издательство: Wiley-Blackwell

Год: 2012

Формат: pdf

Размер: 12.3Mb

Страниц:620

Язык:английский

The book consists of two major parts: The first one provides a brief theoretical

introduction that gives a short overview of alternative splicing and cites key papers in the field for more in-depth information. The second part is a collection of experimental protocols that are used in the field of alternative splicing.

Contents

1 Splicing in the RNA World

2 RNPs, Small RNAs, and miRNAs

3 RNA Elements Involved in Splicing

4 A Structural Biology Perspective of Proteins Involved in Splicing Regulation

5 The Spliceosome in Constitutive Splicing

6 The Use of Saccharomyces cerevisiae to Study the Mechanism of pre-mRNA Splicing

7 Challenges in Plant Alternative Splicing

8 Alternative Splice Site Selection

9 Integration of Splicing with Nuclear and Cellular Events

10 Splicing and Disease

11 From Bedside to Bench: How to Analyze a Splicing Mutation

12 Analysis of Common Splicing Problems

13 Ultracentrifugation in the Analysis and Purification of Spliceosomes Assembled In Vitro

14 Chemical Synthesis of RNA

15 RNA Interference (siRNA, shRNA)

16 Expression and Purification of Splicing Proteins

17 Detection of RNA–Protein Complexes by Electrophoretic Mobility Shift Assay

18 Functional Analysis of Large Exonic Sequences Through Iterative In Vivo Selection

19 Identification of Splicing cis-Elements Through an Ultra-Refined Antisense Microwalk

20 Genomic SELEX to Identify RNA Targets of Plant RNA-Binding Proteins

21 Quantification of Alternative Splice Variants

22 High-Throughput Analysis of Alternative Splicing by RT-PCR

23 Monitoring Changes in Plant Alternative Splicing Events

24 Array Analysis

25 The CLIP Method to Study Protein–RNA Interactions in Intact Cells and Tissues

26 RNA–Protein Crosslinking and Immunoprecipitation (CLIP) in Schizosaccharomyces pombe

27 Identification of Proteins Bound to RNA

28 Single-Cell Detection of Splicing Events with Fluorescent Splicing Reporters

29 The Preparation of HeLa Cell Nuclear Extracts

30 In Vitro Splicing Assays

31 Assembly and Isolation of Spliceosomal Complexes In Vitro

32 Analysis of Site-Specific RNA–Protein Interactions

33 Immunoprecipitation and Pull-Down of Nuclear Proteins

34 Analysis of Protein (-RNA) Complexes by (Quantitative) Mass Spectrometric Analysis

35 Fast Cloning of Splicing Reporter Minigenes

36 In Vivo Analysis of Splicing Assays

37 Coupled Promoter Splicing Systems

38 Stable Cell Lines with Splicing Reporters

39 Splicing Factor ChIP and ChRIP: Detection ofSplicing and Splicing Factors at

Genes by Chromatin Immunoprecipitation

40 Yeast Genetics to Investigate the Function of Core Pre-mRNA Splicing Factors

41 Analysis of HIV-1 RNA Splicing

42 In Vivo Analysis of Plant Intron Splicing

43 Modification State-Specific Antibodies

44 Analysis of Alternative Splicing in Drosophila Genetic Mosaics

45 Antisense Derivatives of U7 Small Nuclear RNA as Modulators of Pre-mRNA Splicing

46 Screening for Alternative Splicing Modulators

47 Use of Oligonucleotides to Change Splicing

48 Changing Signals to the Spliceosome

49 Overview of Splicing Relevant Databases

50 Analysis of RNA Transcripts by High-Throughput RNA Sequencing

51 Identification of Splicing Factor Target Genes by High-Throughput Sequencing

52 Bioinformatic Analysis of Splicing Events

53 Analysis of Pre-mRNA Secondary Structures and Alternative Splicing

54 Structure Prediction for Alternatively Spliced Proteins

55 Comparative Genomics Methods for the Prediction of Small RNA-Binding Sites