Alternative pre-mRNA Splicing: Theory and Protocols by Stefan Stamm, Chris Smith, Reinhard Lührmann PDF

By Stefan Stamm, Chris Smith, Reinhard Lührmann

ISBN-10: 3527326065

ISBN-13: 9783527326068

ISBN-10: 3527636773

ISBN-13: 9783527636778

The ebook contains significant components: The first one presents a short theoretical
introduction that offers a brief review of different splicing and cites key papers within the field for extra in-depth info. the second one half is a suite of experimental protocols which are utilized in the field of different splicing.
1 Splicing within the RNA World
2 RNPs, Small RNAs, and miRNAs
3 RNA components fascinated by Splicing
4 A Structural Biology point of view of Proteins taken with Splicing Regulation
5 The Spliceosome in Constitutive Splicing
6 using Saccharomyces cerevisiae to check the Mechanism of pre-mRNA Splicing
7 demanding situations in Plant substitute Splicing
8 substitute Splice web site Selection
9 Integration of Splicing with Nuclear and mobile Events
10 Splicing and Disease
11 From Bedside to Bench: the way to examine a Splicing Mutation
12 research of universal Splicing Problems
13 Ultracentrifugation within the research 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 via Electrophoretic Mobility Shift Assay
18 sensible research of huge Exonic Sequences via Iterative In Vivo Selection
19 identity of Splicing cis-Elements via an Ultra-Refined Antisense Microwalk
20 Genomic SELEX to spot RNA ambitions of Plant RNA-Binding Proteins
21 Quantification of different Splice Variants
22 High-Throughput research of other Splicing by way of RT-PCR
23 tracking alterations in Plant substitute Splicing Events
24 Array Analysis
25 The CLIP strategy to learn Protein–RNA Interactions in Intact Cells and Tissues
26 RNA–Protein Crosslinking and Immunoprecipitation (CLIP) in Schizosaccharomyces pombe
27 id of Proteins sure to RNA
28 Single-Cell Detection of Splicing occasions with Fluorescent Splicing Reporters
29 The guidance of HeLa phone Nuclear Extracts
30 In Vitro Splicing Assays
31 meeting and Isolation of Spliceosomal Complexes In Vitro
32 research of Site-Specific RNA–Protein Interactions
33 Immunoprecipitation and Pull-Down of Nuclear Proteins
34 research of Protein (-RNA) Complexes by way of (Quantitative) Mass Spectrometric Analysis
35 quick Cloning of Splicing Reporter Minigenes
36 In Vivo research of Splicing Assays
37 Coupled Promoter Splicing Systems
38 strong phone strains with Splicing Reporters
39 Splicing issue ChIP and ChRIP: Detection ofSplicing and Splicing components at
Genes by way of Chromatin Immunoprecipitation
40 Yeast Genetics to enquire the functionality of center Pre-mRNA Splicing Factors
41 research of HIV-1 RNA Splicing
42 In Vivo research of Plant Intron Splicing
43 amendment State-Specific Antibodies
44 research of other Splicing in Drosophila Genetic Mosaics
45 Antisense Derivatives of U7 Small Nuclear RNA as Modulators of Pre-mRNA Splicing
46 Screening for replacement Splicing Modulators
47 Use of Oligonucleotides to alter Splicing
48 altering signs to the Spliceosome
49 assessment of Splicing correct Databases
50 research of RNA Transcripts through High-Throughput RNA Sequencing
51 id of Splicing issue goal Genes via High-Throughput Sequencing
52 Bioinformatic research of Splicing Events
53 research of Pre-mRNA Secondary buildings and replacement Splicing
54 constitution Prediction for then again Spliced Proteins
55 Comparative Genomics tools for the Prediction of Small RNA-Binding websites

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Additional info for Alternative pre-mRNA Splicing: Theory and Protocols

Example text

RNA secondary structures are locally confined, which is in contrast to the extended double-stranded DNA helix. As RNAs do not form a long-range double-stranded structure, the short RNA helices themselves can interact with each other to form what is known as the “tertiary structure” [10]. The rules that exactly define the final outcome of these folding processes, and the various factors that influence them, remain the subject of many active studies. In contrast to proteins, it is currently not possible to predict in vivo RNA tertiary structures accurately [10] (see Chapter 54 Bujnicki for structure prediction of splicing proteins).

J. Biol. , 276, 22648–22654. , and Konig, H. (2001) Regulation of alternative pre-mRNA splicing by the ERK MAP-kinase pathway. , 20, 4194–4203. M. R. (2001) Alternative splicing of the Drosophila Dscam pre-mRNA is both temporally and spatially regulated. Genetics, 159, 599–608. A. (1999) The RNA Modification Database: 1999 update. , 27, 196–197. B. and Westhof, E. (2001) Geometric nomenclature and classification of RNA base pairs. RNA, 7, 499–512. Brion, P. and Westhof, E. (1997) Hierarchy and dynamics of RNA folding.

J. (2005) From birth to death: the complex lives of eukaryotic mRNAs. Science, 309, 1514–1518. , and Dreyfuss, G. (2009) RNA and disease. Cell, 136, 777–793. Jeanteur, P. (2006) Alternative Splicing and Disease, Springer. , and Stamm, S. (2009) Alternative splicing and disease. Biochim. Biophys. Acta, 1792, 14–26. T. et al. 4 (RP11). Mol. Cell, 8, 375–381. M. (2008) Disease mechanism for 12 43 44 45 46 j 1 Splicing in the RNA World retinitis pigmentosa (RP11) caused by missense mutations in the splicing factor gene PRPF31.

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Alternative pre-mRNA Splicing: Theory and Protocols by Stefan Stamm, Chris Smith, Reinhard Lührmann

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