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

By Stefan Stamm, Chris Smith, Reinhard Lührmann

The booklet includes significant components: The first one offers a quick theoretical
introduction that offers a quick 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 other splicing.
Contents
1 Splicing within the RNA World
2 RNPs, Small RNAs, and miRNAs
3 RNA components taken with Splicing
4 A Structural Biology standpoint of Proteins fascinated about 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: how one can research 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 through Electrophoretic Mobility Shift Assay
18 practical research of huge Exonic Sequences via Iterative In Vivo Selection
19 id of Splicing cis-Elements via an Ultra-Refined Antisense Microwalk
20 Genomic SELEX to spot RNA objectives of Plant RNA-Binding Proteins
21 Quantification of different Splice Variants
22 High-Throughput research of different Splicing by means of RT-PCR
23 tracking adjustments in Plant replacement Splicing Events
24 Array Analysis
25 The CLIP approach to learn Protein–RNA Interactions in Intact Cells and Tissues
26 RNA–Protein Crosslinking and Immunoprecipitation (CLIP) in Schizosaccharomyces pombe
27 identity of Proteins guaranteed to RNA
28 Single-Cell Detection of Splicing occasions with Fluorescent Splicing Reporters
29 The coaching of HeLa mobile 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 means of (Quantitative) Mass Spectrometric Analysis
35 quickly Cloning of Splicing Reporter Minigenes
36 In Vivo research of Splicing Assays
37 Coupled Promoter Splicing Systems
38 strong telephone traces with Splicing Reporters
39 Splicing issue ChIP and ChRIP: Detection ofSplicing and Splicing elements at
Genes via Chromatin Immunoprecipitation
40 Yeast Genetics to enquire the functionality of middle 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 different Splicing in Drosophila Genetic Mosaics
45 Antisense Derivatives of U7 Small Nuclear RNA as Modulators of Pre-mRNA Splicing
46 Screening for substitute Splicing Modulators
47 Use of Oligonucleotides to alter Splicing
48 altering signs to the Spliceosome
49 review of Splicing correct Databases
50 research of RNA Transcripts via High-Throughput RNA Sequencing
51 id of Splicing issue goal Genes by means of High-Throughput Sequencing
52 Bioinformatic research of Splicing Events
53 research of Pre-mRNA Secondary constructions and substitute Splicing
54 constitution Prediction for then again Spliced Proteins
55 Comparative Genomics equipment for the Prediction of Small RNA-Binding websites

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

Example text

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. Mol. , 14, 683–690. D. (2007) prp8 mutations that cause human retinitis pigmentosa lead to a U5 snRNP maturation defect in yeast.

2009) Small RNAs derived from snoRNAs. RNA, 15, 1233–1240. , and Stamm, S. (2010) The snoRNA MBII-52 (SNORD 115) is processed into smaller RNAs and regulates alternative splicing. Hum. Mol. , 19, 1153–1164. Kishore, S. and Stamm, S. (2006) The snoRNA HBII-52 regulates alternative splicing of the serotonin receptor 2C. Science, 311, 230–232. R. A. (1979) 29 30 31 32 33 34 35 36 37 38 39 40 41 42 Antibodies to small nuclear RNAs complexed with proteins are produced by patients with systemic lupus erythematosus.

The mRNAs are generated by processing from their pre-mRNAs precursor molecules. Pre-mRNAs are the first product of gene transcription performed by RNA polymerase II, and are processed while their synthesis is still ongoing (see Chapter 9 Neugebauer). In this case, there are sequences that are removed from the pre-mRNA, which are referred to as “introns” (for intragenic or intervening sequence), while the sequences that are joined and exported to the cytoplasm are referred to as “exons” (for expressed or exported sequence) [32].

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