Book
Draft files for the EURASNET book can be found below for download. These are to be discussed at the March meeting.
Chapter 1
Emanuele Buratti, Maurizio Romano and Francisco E. Baralle
- Word file: Structure of RNA, RNA World, role of splicing and alternative splicing history (307 KB)
- Word file: Structure of RNA, RNA World, role of splicing and alternative splicing history – Stamm revision (383 KB)
- Powerpoint file: Chapter 1 figure (1.09 MB)
Chapter 2
- Word file: RNPs, small RNAs, miRNAs (240 KB)
- Word file: RNPs, small RNAs, miRNAs – Stamm revision (539 KB)
- PDF file: Chapter 2 figure (461 KB)
Chapter 3
Antoine Cléry, and Frédéric H.-T. Allain
- Word file: Splicing regulation: a structural biology perspective (370 KB)
- Word file: Splicing regulation: a structural biology perspective – Stamm revision (374 KB)
- PDF file: Chapter 3 figure (515 KB)
See the protein-RNA complex videos that accompany Chapter 3.
Chapter 4
William F. Mueller and Klemens J. Hertel
- Word file: RNA elements involved in splicing (402 KB)
- Word file: RNA elements involved in splicing – Stamm revision (382 KB)
- PDF file: Chapter 4 figure (2.63 MB)
Chapter 5
Patrizia Fabrizio and Reinhard Lührmann
- Word file: The spliceosome in constitutive splicing (259 KB)
- Word file: The spliceosome in constitutive splicing – Stamm revision (269 KB)
- Powerpoint file: Chapter 5 figures (4.13 MB)
Chapter 9
Emanuele Buratti and Francisco E. Baralle
- Word file: Splicing and Disease (446 KB)
- Word file: Splicing and Disease – Stamm revision (443 KB)
- Powerpoint file: Chapter 9 figure (1.15 MB)
Chapter 10
Diana Baralle
- Word file: From bedside to bench: how to analyze a splicing mutation (177 KB)
- Word file: From bedside to bench: how to analyze a splicing mutation – Stamm revision (179 KB)
- Powerpoint file: Chapter 10 figure (97 KB)
- Powerpoint file: Chapter 10 figure – Stamm revision (100 KB)
Chapter 11
Klaus Hartmuth, Maria A. van Santen, Reinhard Lührmann
- Word file: Analysis and purification by ultracentrifugation of spliceosomes assembled in vitro (1.16 MB)
- Word file: Analysis and purification by ultracentrifugation of spliceosomes assembled in vitro – Stamm revision (1.16 MB)
- PDF file: Chapter 11 figure (1.14 MB)
Chapter 13
Claudia Höbartner
- Word file: Synthesis of RNA (659 KB)
- Word file: Synthesis of RNA – Stamm revision (644 KB)
- PDF file: Chapter 13 figure (466 KB)
Chapter 14
Daphne S. Cabianca and Davide Gabellini
- Word file: RNA interference (siRNA, shRNA) (516 KB)
- Word file: RNA interference (siRNA, shRNA) – Stamm revision (524 KB)
Chapter 15
James Stévenin and Cyril F. Bourgeois
- Word file: Expression and purification of splicing proteins (140 KB)
- Word file: Expression and purification of splicing proteins – Stamm revision (519 KB)
- PDF file: Chapter 15 figure (728 KB)
Chapter 17
Natalia N. Singh and Ravindra N. Singh
- Word file: Functional analysis of large exonic sequences through iterative in vivo selection (94 KB)
- Word file: Identification of splicing cis-elements through an ultra-refined antisense microwalk (95 KB)
- Word file: Functional analysis of large exonic sequences through iterative in vivo selection – Stamm revision (455 KB)
- PDF file: Chapter 17 figure (528 KB)
Chapter 17c
Olga Bannikova and Andrea Barta
- Word file: Genomic SELEX to identify RNA targets of plant RNA binding proteins (989 KB)
- Word file: Genomic SELEX to identify RNA targets of plant RNA binding proteins – Stamm revision (996 KB)
Chapter 19
Roscoe Klinck, Benoit Chabot and Sherif Abou Elela
- Word file: High-throughput analysis of alternative splicing by RT-PCR (252 KB)
- Word file: High-throughput analysis of alternative splicing by RT-PCR – Stamm revision (252 KB)
Chapter 19b
Craig G. Simpson, Naeem Hasan Syed, Sujatha Manthri, John D. Fuller, Monika Maronova, Branislav Kusenda, Maria Kalyna, Andrea Barta and John W.S. Brown
- Word file: Monitoring changes in plant alternative splicing events (1.97 MB)
- Word file: Monitoring changes in plant alternative splicing events – Stamm revision (1.95 MB)
- PDF file: Chapter 19b figure (200 KB)
Chapter 20
Pierre de la Grange
- Word file: Array analysis (72 KB)
- Word file: Array analysis – Stamm revision (61.5 KB)
- Powerpoint file: Chapter 20 figure (673 KB)
Chapter 21
Paolo Ribeca, Vincent Lacroix, Michael Sammeth and Roderic Guigó
- Word file: High throughput RNA sequencing (374 KB)
- Word file: High throughput RNA sequencing – Stamm revision (382 KB)
Chapter 22
James Tollervey and Jernej Ule
- Word file: CLIP method to study protein-RNA interactions in intact cells and tissues (135 KB)
- Word file: CLIP method to study protein-RNA interactions in intact cells and tissues – Stamm revision (131 KB)
Chapter 22b
Branislav Kusenda and Andrea Barta
- PDF file: RNA: Protein Crosslinking and Immunoprecipitation in vivo (CLIP) (744 KB)
- Word file: RNA: Protein Crosslinking and Immunoprecipitation in vivo (CLIP) - Stamm revision (532 KB)
Chapter 23
Emanuele Buratti
- Word file: Identification of proteins bound to RNA (132 KB)
- Word file: Identification of proteins bound to RNA – Stamm revision (691 KB)
- Powerpoint file: Chapter 23 figure (757 KB)
Chapter 24
Hidehito Kuroyanagi, Akihide Takeuchi, Takayuki Nojima and Masatoshi Hagiwara
- PDF file: Single cell detection of splicing events with fluorescent splicing reporters (150 KB)
- Word file: Single cell detection of splicing events with fluorescent splicing reporters – Stamm revision (179 KB)
- PDF file: Chapter 24 figure (178 KB)
Chapter 27
Klaus Hartmuth, Maria A. van Santen, Peter Odenwälder, Reinhard Lührmann
- Word file: The assembly of spliceosomes in vitro (138 KB)
- Word file: The assembly of spliceosomes in vitro – Stamm revision (140 KB)
- PDF file: Chapter 27 figure (1.86 MB)
Chapter 31
Zhaiyi Zhang, Amit Khanna and Stefan Stamm
- Word file: Fast cloning of splicing reporter minigenes (122 KB)
- Word file: Construction of reporter minigenes (90 KB)
Chapter 32
Isabel Cristina López Mejía and Jamal Tazi
- Word file: Ex vivo analysis of splicing assays (116 KB)
- Word file: Ex vivo analysis of splicing assays – Stamm revision (103 KB)
- Powerpoint file: Chapter 32 figure (407 KB)
Chapter 33
Manuel J. Muñoz, Manuel de la Mata and Alberto R. Kornblihtt
- Word file: Coupled promoter splicing systems (89 KB)
- Word file: Coupled promoter splicing systems – Stamm revision (657 KB)
- Powerpoint file: Chapter 33 figure (323 KB)
Chapter 34
Raymond T. O’Keefe and Jean D. Beggs
- Word file: Yeast genetics to investigate the function of core pre-mRNA splicing factors (429 KB)
- Word file: Yeast genetics to investigate the function of core pre-mRNA splicing factors – Stamm revision (405 KB)
- Powerpoint file: Chapter 34 figure (156 KB)
Chapter 35
Simon Duffy and Alan Cochrane
- Word file: Analysis of HIV-1 RNA Splicing (312 KB)
- Word file: Analysis of HIV-1 RNA Splicing – Stamm revision (316 KB)
- PDF file: Chapter 35 figure (121 KB)
Chapter 36
Aparna K. Sapra, Fernando Carrillo Oesterreich, Marta Pabis, Imke Listerman, Nicole Bardehle and Karla M. Neugebauer
- PDF file: Splicing Factor ChIP and ChRIP: Detection of splicing and splicing factors at genes by chromatin immunoprecipitation (3.6 MB)
- Word file: Splicing Factor ChIP and ChRIP: Detection of splicing and splicing factors at genes by chromatin immunoprecipitation – Stamm revision (134 KB)
Chapter 37
Craig G. Simpson, Michele Liney, Diane Davidson, Dominika Lewandowska, Maria Kalyna, Sean Chapman, Andrea Barta and John W.S. Brown
- Word file: In vivo analysis of plant intron splicing (1.26 MB)
- Word file: In vivo analysis of plant intron splicing – Stamm revision (1.28 MB)
Chapter 38
Christian Kroun Damgaard, Søren Lykke-Andersen and Jørgen Kjems
- Word file: Stable cell lines with splicing reporters (497 KB)
- Word file: Stable cell lines with splicing reporters – Stamm revision (468 KB)
Chapter 39
Shihuang Su, Diana O’Day, Shanzhi Wang and William Mattox
- Word file: Analysis of alternative splicing in Drosophila genetic mosaics (102 KB)
- Word file: Analysis of alternative splicing in Drosophila genetic mosaics – Stamm revision (127 KB)
- Powerpoint file: Chapter 39 figure (1.4 MB)
Chapter 40
Kathrin Meyer and Daniel Schümperli
- Word file: Antisense derivatives of U7 small nuclear RNA as modulators of pre-mRNA splicing (854 KB)
- Word file: Antisense derivatives of U7 small nuclear RNA as modulators of pre-mRNA splicing – Stamm revision (848 KB)
Chapter 41
Peter Stoilov
- Word file: Screening for alternative splicing modulators (89 KB)
- Word file: Screening for alternative splicing modulators – Stamm revision (101 KB)
- PDF file: Chapter 41 figure (576 KB)
Chapter 42
Annemieke Aartsma-Rus and Judith C.T. van Deutekom
- Word file: Use of oligonucleotides to change splicing (122 KB)
- Word file: Use of oligonucleotides to change splicing – Stamm revision (179 KB)
- Powerpoint file: Chapter 42 figure (453 KB)
Chapter 43
Denise Cooper
- Word file: Changing signals to the spliceosome (219 KB)
- Word file: Changing signals to the spliceosome – Stamm revision (303 KB)
- Powerpoint file: Chapter 43 figure (92 KB)
Chapter 44
Pierre de la Grange
- Word file: Overview of splicing relevant databases (66KB)
- Word file: Overview of splicing relevant databases – Stamm revision (147 KB)
- Powerpoint file: Chapter 44 figure (644 KB)
- Excel file: Chapter 44 table 1 (36 KB)
Chapter 45
Chaolin Zhang and Michael Q. Zhang
- Word file: Analysis of splicing variants by high-throughput sequencing (100 KB)
- Word file: Analysis of splicing variants by high-throughput sequencing – Stamm revision (143 KB)
- Powerpoint file: Chapter 45 figure (532 KB)
Chapter 48
Michael Hiller
- Word file: Analysis of pre-mRNA secondary structures and alternative splicing (167 KB)
- Word file: Analysis of pre-mRNA secondary structures and alternative splicing – Stamm revision (354 KB)
- PDF file: chapter 48 figure (224 KB)
Chapter 49
Lukasz Kozlowski, Jerzy Orlowski, Janusz M. Bujnicki
- Word file: Structure prediction of alternatively spliced proteins (657 KB)
- Word file: Structure prediction of alternatively spliced proteins – Stamm revision (662 KB)
- PDF file: Chapter 49 figure (137 KB)
Chapter 50
Rym Kachouri-Lafond and Mihaela Zavolan
- Word file: Comparative genomics methods for the prediction of small RNA binding sites (139 KB)
- Word file: Comparative genomics methods for the prediction of small RNA binding sites – Stamm revision (209 KB)
- PDF file: Chapter 50 figure (44 KB)
