Ebook: Alternative pre-mRNA Splicing: Theory and Protocols
- Year: 2012
- Publisher: Wiley-Blackwell
- Language: English
- pdf
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
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.
Website: www.wiley-vch.de/home/splicingContent:
Chapter 1 Splicing in the RNA World (pages 1–12): Emanuele Buratti, Maurizio Romano and Francisco E. Baralle
Chapter 2 RNPs, Small RNAs, and miRNAs (pages 13–19): Michaela Beitzinger and Gunter Meister
Chapter 3 RNA Elements Involved in Splicing (pages 21–31): William F. Mueller and Klemens J. Hertel
Chapter 4 A Structural Biology Perspective of Proteins Involved in Splicing Regulation (pages 33–48): Antoine Clery and Frederic H.?T. Allain
Chapter 5 The Spliceosome in Constitutive Splicing (pages 49–64): Patrizia Fabrizio and Prof. Dr. Reinhard Luhrmann
Chapter 6 The Use of Saccharomyces cerevisiae to Study the Mechanism of pre?mRNA Splicing (pages 65–77): Brian C. Rymond
Chapter 7 Challenges in Plant Alternative Splicing (pages 79–91): Andrea Barta, Yamile Marquez and John W. S. Brown
Chapter 8 Alternative Splice Site Selection (pages 93–107): Miguel B. Coelho and Prof. Dr. Christopher W. J. Smith
Chapter 9 Integration of Splicing with Nuclear and Cellular Events (pages 109–117): Aparna K. Sapra and Karla Neugebauer
Chapter 10 Splicing and Disease (pages 119–128): Emanuele Buratti and Francisco E. Baralle
Chapter 11 From Bedside to Bench: How to Analyze a Splicing Mutation (pages 129–138): Marco Baralle and Diana Baralle
Chapter 12 Analysis of Common Splicing Problems (pages 146–145): Prof. Dr. Stefan Stamm
Chapter 13 Ultracentrifugation in the Analysis and Purification of Spliceosomes Assembled In Vitro (pages 147–153): Klaus Hartmuth, Maria A. van Santen and Prof. Dr. Reinhard Luhrmann
Chapter 14 Chemical Synthesis of RNA (pages 154–162): Claudia Hobartner
Chapter 15 RNA Interference (siRNA, shRNA) (pages 164–173): Daphne S. Cabianca and Davide Gabellini
Chapter 16 Expression and Purification of Splicing Proteins (pages 174–180): James Stevenin and Cyril F. Bourgeois
Chapter 17 Detection of RNA–Protein Complexes by Electrophoretic Mobility Shift Assay (pages 182–198): Manli Shen and Michael G. Fried
Chapter 18 Functional Analysis of Large Exonic Sequences Through Iterative In Vivo Selection (pages 200–209): Ravindra N. Singh and Natalia N. Singh
Chapter 19 Identification of Splicing cis?Elements Through an Ultra?Refined Antisense Microwalk (pages 210–217): Natalia N. Singh, Joonbae Seo and Ravindra N. Singh
Chapter 20 Genomic SELEX to Identify RNA Targets of Plant RNA?Binding Proteins (pages 218–226): Olga Bannikova, Maria Kalyna and Andrea Barta
Chapter 21 Quantification of Alternative Splice Variants (pages 227–236): Miriam Llorian and Prof. Dr. Christopher W. J. Smith
Chapter 22 High?Throughput Analysis of Alternative Splicing by RT?PCR (pages 238–246): Roscoe Klinck, Benoit Chabot and Sherif Abou Elela
Chapter 23 Monitoring Changes in Plant Alternative Splicing Events (pages 248–259): Craig G. Simpson, Naeem Hasan Syed, Sujatha Manthri, John D. Fuller, Monika Maronova, Branislav Kusenda, Maria Kalyna, Andrea Barta and John W.S. Brown
Chapter 24 Array Analysis (pages 260–267): Pierre de la Grange
Chapter 25 The CLIP Method to Study Protein–RNA Interactions in Intact Cells and Tissues (pages 268–278): James Tollervey and Jernej Ule
Chapter 26 RNA–Protein Crosslinking and Immunoprecipitation (CLIP) in Schizosaccharomyces pombe (pages 280–288): Branislav Kusenda and Andrea Barta
Chapter 27 Identification of Proteins Bound to RNA (pages 290–297): Emanuele Buratti
Chapter 28 Single?Cell Detection of Splicing Events with Fluorescent Splicing Reporters (pages 298–309): Hidehito Kuroyanagi, Akihide Takeuchi, Takayuki Nojima and Masatoshi Hagiwara
Chapter 29 The Preparation of HeLa Cell Nuclear Extracts (pages 311–319): Klaus Hartmuth, Maria A. van Santen, Tanja Rosel, Berthold Kastner and Prof. Dr. Reinhard Luhrmann
Chapter 30 In Vitro Splicing Assays (pages 320–329): Akila Mayeda and Adrian R. Krainer
Chapter 31 Assembly and Isolation of Spliceosomal Complexes In Vitro (pages 330–340): Klaus Hartmuth, Maria A. van Santen, Peter Odenwalder and Prof. Dr. Reinhard Luhrmann
Chapter 32 Analysis of Site?Specific RNA–Protein Interactions (pages 342–356): Nathalie Marmier?Gourrier, Audrey Vautrin, Christiane Branlant and Isabelle Behm?Ansmant
Chapter 33 Immunoprecipitation and Pull?Down of Nuclear Proteins (pages 358–364): Natalya Benderska, Chiranthani Sumanasekera and Prof. Dr. Stefan Stamm
Chapter 34 Analysis of Protein (?RNA) Complexes by (Quantitative) Mass Spectrometric Analysis (pages 366–379): Carla Schmidt and Henning Urlaub
Chapter 35 Fast Cloning of Splicing Reporter Minigenes (pages 381–391): Zhaiyi Zhang, Amit Khanna and Prof. Dr. Stefan Stamm
Chapter 36 In Vivo Analysis of Splicing Assays (pages 392–399): Isabel C. Lopez?Mejia and Jamal Tazi
Chapter 37 Coupled Promoter Splicing Systems (pages 400–407): Manuel J. Mu?noz, Manuel de la Mata and Alberto R. Kornblihtt
Chapter 38 Stable Cell Lines with Splicing Reporters (pages 408–414): Christian Kroun Damgaard, Soren Lykke?Andersen and Jorgen Kjems
Chapter 39 Splicing Factor ChIP and ChRIP: Detection of Splicing and Splicing Factors at Genes by Chromatin Immunoprecipitation (pages 416–427): Aparna K. Sapra, Fernando Carrillo Oesterreich, Marta Pabis, Imke Listerman, Nicole Bardehle and Karla M. Neugebauer
Chapter 40 Yeast Genetics to Investigate the Function of Core Pre?mRNA Splicing Factors (pages 428–436): Raymond T. O. Keefe and Jean D. Beggs
Chapter 41 Analysis of HIV?1 RNA Splicing (pages 438–448): Simon Duffy and Alan Cochrane
Chapter 42 In Vivo Analysis of Plant Intron Splicing (pages 450–462): Craig G. Simpson, Michele Liney, Diane Davidson, Dominika Lewandowska, Maria Kalyna, Sean Chapman, Andrea Barta and John W. S. Brown
Chapter 43 Modification State?Specific Antibodies (pages 464–473): Jordan B. Fishman, Olga Kelemen and Eric A. Berg
Chapter 44 Analysis of Alternative Splicing in Drosophila Genetic Mosaics (pages 474–479): Shihuang Su, Diana O'Day, Shanzhi Wang and William Mattox
Chapter 45 Antisense Derivatives of U7 Small Nuclear RNA as Modulators of Pre?mRNA Splicing (pages 481–494): Kathrin Meyer and Daniel Schumperli
Chapter 46 Screening for Alternative Splicing Modulators (pages 496–508): Peter Stoilov
Chapter 47 Use of Oligonucleotides to Change Splicing (pages 510–520): Annemieke Aartsma?Rus and Judith C. T. van Deutekom
Chapter 48 Changing Signals to the Spliceosome (pages 522–534): Denise R. Cooper and Niketa A. Patel
Chapter 49 Overview of Splicing Relevant Databases (pages 535–543): Pierre de la Grange
Chapter 50 Analysis of RNA Transcripts by High?Throughput RNA Sequencing (pages 544–554): Paolo Ribeca, Vincent Lacroix, Michael Sammeth and Roderic Guigo
Chapter 51 Identification of Splicing Factor Target Genes by High?Throughput Sequencing (pages 556–564): Chaolin Zhang and Michael Q. Zhang
Chapter 52 Bioinformatic Analysis of Splicing Events (pages 566–573): Zhaiyi Zhang and Prof. Dr. Stefan Stamm
Chapter 53 Analysis of Pre?mRNA Secondary Structures and Alternative Splicing (pages 574–580): Michael Hiller
Chapter 54 Structure Prediction for Alternatively Spliced Proteins (pages 582–591): Lukasz Kozlowski, Jerzy Orlowski and Janusz M. Bujnicki
Chapter 55 Comparative Genomics Methods for the Prediction of Small RNA?Binding Sites (pages 592–601): Rym Kachouri?Lafond and Mihaela Zavolan
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
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.
Website: www.wiley-vch.de/home/splicingContent:
Chapter 1 Splicing in the RNA World (pages 1–12): Emanuele Buratti, Maurizio Romano and Francisco E. Baralle
Chapter 2 RNPs, Small RNAs, and miRNAs (pages 13–19): Michaela Beitzinger and Gunter Meister
Chapter 3 RNA Elements Involved in Splicing (pages 21–31): William F. Mueller and Klemens J. Hertel
Chapter 4 A Structural Biology Perspective of Proteins Involved in Splicing Regulation (pages 33–48): Antoine Clery and Frederic H.?T. Allain
Chapter 5 The Spliceosome in Constitutive Splicing (pages 49–64): Patrizia Fabrizio and Prof. Dr. Reinhard Luhrmann
Chapter 6 The Use of Saccharomyces cerevisiae to Study the Mechanism of pre?mRNA Splicing (pages 65–77): Brian C. Rymond
Chapter 7 Challenges in Plant Alternative Splicing (pages 79–91): Andrea Barta, Yamile Marquez and John W. S. Brown
Chapter 8 Alternative Splice Site Selection (pages 93–107): Miguel B. Coelho and Prof. Dr. Christopher W. J. Smith
Chapter 9 Integration of Splicing with Nuclear and Cellular Events (pages 109–117): Aparna K. Sapra and Karla Neugebauer
Chapter 10 Splicing and Disease (pages 119–128): Emanuele Buratti and Francisco E. Baralle
Chapter 11 From Bedside to Bench: How to Analyze a Splicing Mutation (pages 129–138): Marco Baralle and Diana Baralle
Chapter 12 Analysis of Common Splicing Problems (pages 146–145): Prof. Dr. Stefan Stamm
Chapter 13 Ultracentrifugation in the Analysis and Purification of Spliceosomes Assembled In Vitro (pages 147–153): Klaus Hartmuth, Maria A. van Santen and Prof. Dr. Reinhard Luhrmann
Chapter 14 Chemical Synthesis of RNA (pages 154–162): Claudia Hobartner
Chapter 15 RNA Interference (siRNA, shRNA) (pages 164–173): Daphne S. Cabianca and Davide Gabellini
Chapter 16 Expression and Purification of Splicing Proteins (pages 174–180): James Stevenin and Cyril F. Bourgeois
Chapter 17 Detection of RNA–Protein Complexes by Electrophoretic Mobility Shift Assay (pages 182–198): Manli Shen and Michael G. Fried
Chapter 18 Functional Analysis of Large Exonic Sequences Through Iterative In Vivo Selection (pages 200–209): Ravindra N. Singh and Natalia N. Singh
Chapter 19 Identification of Splicing cis?Elements Through an Ultra?Refined Antisense Microwalk (pages 210–217): Natalia N. Singh, Joonbae Seo and Ravindra N. Singh
Chapter 20 Genomic SELEX to Identify RNA Targets of Plant RNA?Binding Proteins (pages 218–226): Olga Bannikova, Maria Kalyna and Andrea Barta
Chapter 21 Quantification of Alternative Splice Variants (pages 227–236): Miriam Llorian and Prof. Dr. Christopher W. J. Smith
Chapter 22 High?Throughput Analysis of Alternative Splicing by RT?PCR (pages 238–246): Roscoe Klinck, Benoit Chabot and Sherif Abou Elela
Chapter 23 Monitoring Changes in Plant Alternative Splicing Events (pages 248–259): Craig G. Simpson, Naeem Hasan Syed, Sujatha Manthri, John D. Fuller, Monika Maronova, Branislav Kusenda, Maria Kalyna, Andrea Barta and John W.S. Brown
Chapter 24 Array Analysis (pages 260–267): Pierre de la Grange
Chapter 25 The CLIP Method to Study Protein–RNA Interactions in Intact Cells and Tissues (pages 268–278): James Tollervey and Jernej Ule
Chapter 26 RNA–Protein Crosslinking and Immunoprecipitation (CLIP) in Schizosaccharomyces pombe (pages 280–288): Branislav Kusenda and Andrea Barta
Chapter 27 Identification of Proteins Bound to RNA (pages 290–297): Emanuele Buratti
Chapter 28 Single?Cell Detection of Splicing Events with Fluorescent Splicing Reporters (pages 298–309): Hidehito Kuroyanagi, Akihide Takeuchi, Takayuki Nojima and Masatoshi Hagiwara
Chapter 29 The Preparation of HeLa Cell Nuclear Extracts (pages 311–319): Klaus Hartmuth, Maria A. van Santen, Tanja Rosel, Berthold Kastner and Prof. Dr. Reinhard Luhrmann
Chapter 30 In Vitro Splicing Assays (pages 320–329): Akila Mayeda and Adrian R. Krainer
Chapter 31 Assembly and Isolation of Spliceosomal Complexes In Vitro (pages 330–340): Klaus Hartmuth, Maria A. van Santen, Peter Odenwalder and Prof. Dr. Reinhard Luhrmann
Chapter 32 Analysis of Site?Specific RNA–Protein Interactions (pages 342–356): Nathalie Marmier?Gourrier, Audrey Vautrin, Christiane Branlant and Isabelle Behm?Ansmant
Chapter 33 Immunoprecipitation and Pull?Down of Nuclear Proteins (pages 358–364): Natalya Benderska, Chiranthani Sumanasekera and Prof. Dr. Stefan Stamm
Chapter 34 Analysis of Protein (?RNA) Complexes by (Quantitative) Mass Spectrometric Analysis (pages 366–379): Carla Schmidt and Henning Urlaub
Chapter 35 Fast Cloning of Splicing Reporter Minigenes (pages 381–391): Zhaiyi Zhang, Amit Khanna and Prof. Dr. Stefan Stamm
Chapter 36 In Vivo Analysis of Splicing Assays (pages 392–399): Isabel C. Lopez?Mejia and Jamal Tazi
Chapter 37 Coupled Promoter Splicing Systems (pages 400–407): Manuel J. Mu?noz, Manuel de la Mata and Alberto R. Kornblihtt
Chapter 38 Stable Cell Lines with Splicing Reporters (pages 408–414): Christian Kroun Damgaard, Soren Lykke?Andersen and Jorgen Kjems
Chapter 39 Splicing Factor ChIP and ChRIP: Detection of Splicing and Splicing Factors at Genes by Chromatin Immunoprecipitation (pages 416–427): Aparna K. Sapra, Fernando Carrillo Oesterreich, Marta Pabis, Imke Listerman, Nicole Bardehle and Karla M. Neugebauer
Chapter 40 Yeast Genetics to Investigate the Function of Core Pre?mRNA Splicing Factors (pages 428–436): Raymond T. O. Keefe and Jean D. Beggs
Chapter 41 Analysis of HIV?1 RNA Splicing (pages 438–448): Simon Duffy and Alan Cochrane
Chapter 42 In Vivo Analysis of Plant Intron Splicing (pages 450–462): Craig G. Simpson, Michele Liney, Diane Davidson, Dominika Lewandowska, Maria Kalyna, Sean Chapman, Andrea Barta and John W. S. Brown
Chapter 43 Modification State?Specific Antibodies (pages 464–473): Jordan B. Fishman, Olga Kelemen and Eric A. Berg
Chapter 44 Analysis of Alternative Splicing in Drosophila Genetic Mosaics (pages 474–479): Shihuang Su, Diana O'Day, Shanzhi Wang and William Mattox
Chapter 45 Antisense Derivatives of U7 Small Nuclear RNA as Modulators of Pre?mRNA Splicing (pages 481–494): Kathrin Meyer and Daniel Schumperli
Chapter 46 Screening for Alternative Splicing Modulators (pages 496–508): Peter Stoilov
Chapter 47 Use of Oligonucleotides to Change Splicing (pages 510–520): Annemieke Aartsma?Rus and Judith C. T. van Deutekom
Chapter 48 Changing Signals to the Spliceosome (pages 522–534): Denise R. Cooper and Niketa A. Patel
Chapter 49 Overview of Splicing Relevant Databases (pages 535–543): Pierre de la Grange
Chapter 50 Analysis of RNA Transcripts by High?Throughput RNA Sequencing (pages 544–554): Paolo Ribeca, Vincent Lacroix, Michael Sammeth and Roderic Guigo
Chapter 51 Identification of Splicing Factor Target Genes by High?Throughput Sequencing (pages 556–564): Chaolin Zhang and Michael Q. Zhang
Chapter 52 Bioinformatic Analysis of Splicing Events (pages 566–573): Zhaiyi Zhang and Prof. Dr. Stefan Stamm
Chapter 53 Analysis of Pre?mRNA Secondary Structures and Alternative Splicing (pages 574–580): Michael Hiller
Chapter 54 Structure Prediction for Alternatively Spliced Proteins (pages 582–591): Lukasz Kozlowski, Jerzy Orlowski and Janusz M. Bujnicki
Chapter 55 Comparative Genomics Methods for the Prediction of Small RNA?Binding Sites (pages 592–601): Rym Kachouri?Lafond and Mihaela Zavolan
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