Bioinformatics

Get Alternative pre-mRNA Splicing: Theory and Protocols PDF

By Stefan Stamm, Chris Smith, Reinhard Lührmann

The booklet involves significant elements: The first one presents a quick theoretical
introduction that provides a brief assessment of other splicing and cites key papers within the field for extra in-depth info. the second one half is a set 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 fascinated by Splicing
4 A Structural Biology viewpoint of Proteins focused on Splicing Regulation
5 The Spliceosome in Constitutive Splicing
6 using Saccharomyces cerevisiae to review the Mechanism of pre-mRNA Splicing
7 demanding situations in Plant replacement Splicing
8 replacement 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 study 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 practical research of enormous 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 goals of Plant RNA-Binding Proteins
21 Quantification of other Splice Variants
22 High-Throughput research of other Splicing by means of RT-PCR
23 tracking adjustments in Plant replacement Splicing Events
24 Array Analysis
25 The CLIP technique to research Protein–RNA Interactions in Intact Cells and Tissues
26 RNA–Protein Crosslinking and Immunoprecipitation (CLIP) in Schizosaccharomyces pombe
27 identity of Proteins certain to RNA
28 Single-Cell Detection of Splicing occasions with Fluorescent Splicing Reporters
29 The education 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 speedy Cloning of Splicing Reporter Minigenes
36 In Vivo research of Splicing Assays
37 Coupled Promoter Splicing Systems
38 sturdy cellphone strains 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 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 indications to the Spliceosome
49 review of Splicing proper Databases
50 research of RNA Transcripts via High-Throughput RNA Sequencing
51 identity of Splicing issue goal Genes by way of High-Throughput Sequencing
52 Bioinformatic research of Splicing Events
53 research of Pre-mRNA Secondary buildings and substitute Splicing
54 constitution Prediction for on the other hand 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

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. Proc. Natl Acad. Sci. USA, 76, 5495–5499. , and Satoh, M. (2003) Henry Kunkel, Stephanie Smith, clinical immunology, and split genes. Lupus, 12, 213–217. A. (1980) Are snRNPs involved in splicing?

A. (2008) A structural 16 17 18 19 20 21 22 23 24 25 26 27 understanding of the dynamic ribosome machine. Nat. Rev. Mol. , 9, 242–253. L. (2007) Protein-free spliceosomal snRNAs catalyze a reaction that resembles the first step of splicing. RNA, 13, 2300–2311. , and Rossmanith, W. (2008) RNase P without RNA: identification and functional reconstitution of the human mitochondrial tRNA processing enzyme. Cell, 135, 462–474. E. (1998) The origin of life – a review of facts and speculations. Trends Biochem.

Umultowska 89 61-614 Poznan Poland Emanuele Buratti International Centre of Genetic Engineering and Biotechnology (ICGEB) Department of Molecular Pathology Padriciano 99 34012 Trieste Italy Daphne S. Cabianca San Raffaele Scientific Institute Division of Regenerative Medicine Via Olgettina 58 20132 Milan Italy and Università Vita-Salute San Raffaele Via Olgettina 58 20132 Milan Italy Antoine Cléry ETH Zürich Institute for Molecular Biology and Biophysics Schafmattstr. 20, HPK G18 8093 Zurich Switzerland Alan Cochrane University of Toronto Department of Molecular Genetics 1 King’s College Circle Toronto, Ontario Canada M5S-1A8 Miguel B.

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