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

By Stefan Stamm, Chris Smith, Reinhard Lührmann

The e-book contains significant components: The first one presents a short 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 excited about Splicing
4 A Structural Biology viewpoint of Proteins concerned with 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 substitute Splicing
8 substitute Splice website Selection
9 Integration of Splicing with Nuclear and mobile Events
10 Splicing and Disease
11 From Bedside to Bench: how you 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 useful research of enormous 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 other Splice Variants
22 High-Throughput research of different Splicing by way of RT-PCR
23 tracking adjustments in Plant substitute Splicing Events
24 Array Analysis
25 The CLIP approach to research Protein–RNA Interactions in Intact Cells and Tissues
26 RNA–Protein Crosslinking and Immunoprecipitation (CLIP) in Schizosaccharomyces pombe
27 id of Proteins certain to RNA
28 Single-Cell Detection of Splicing occasions with Fluorescent Splicing Reporters
29 The training 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 via (Quantitative) Mass Spectrometric Analysis
35 quickly Cloning of Splicing Reporter Minigenes
36 In Vivo research of Splicing Assays
37 Coupled Promoter Splicing Systems
38 solid telephone strains with Splicing Reporters
39 Splicing issue ChIP and ChRIP: Detection ofSplicing and Splicing elements at
Genes through 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 replacement Splicing Modulators
47 Use of Oligonucleotides to alter Splicing
48 altering signs to the Spliceosome
49 evaluate of Splicing correct Databases
50 research of RNA Transcripts through High-Throughput RNA Sequencing
51 identity of Splicing issue objective Genes through 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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F. Møllers Alle, Bldg 1130 8000 Aarhus C Denmark Michele Liney Scottish Crop Research Institute Genetics Programme Dundee DD2 5DA UK Imke Listerman Max Planck Institute of Molecular Cell Biology and Genetics Pfotenhauerstraße 108 01307 Dresden Germany Miriam Llorian University of Cambridge Department of Biochemistry Tennis Court Road Cambridge CB2 1QW UK Isabel C. López-Mejía Institut de Génétique Moléculaire de Montpellier UMR 5535 CNRS 1919 route de Mende 34293 Montpellier Cedex 5 France Japan Science and Technology Agency (JST) Precursory Research for Embryonic Science and Technology (PRESTO) Kawaguchi, Saitama Japan and Branislav Kusenda Medical University of Vienna Max F.

Cell, 136, 599–602. E. et al. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447, 799–816. R. (2010) Most ‘dark matter’ transcripts are associated with known genes. , 8 (5), e1000371. S. (2008) The eukaryotic genome as an RNA machine. Science, 319, 1787–1789. , and Montanini, B. (2009) Eukaryotic snoRNAs: a paradigm for gene expression flexibility. Genomics, 94, 83–88. P. (2007) Non-coding RNAs: lessons from the small nuclear and small nucleolar RNAs.

KGaA. 1 Overview of different cellular small RNPs. RNP Small RNA Function Reference(s) snRNP scaRNP snoRNP Telomerase miRNP/RISC miRNP/RISC RISC piRNP RITS RNase P SRP 7SK RNP tiRNP snRNA scaRNA snoRNA snoRNA, TER miRNA snoRNA-derived miRNAs siRNA piRNA siRNA (rasiRNAs) RNase P RNA 7SL RNA 7SK RNA tiRNA Splicing, major components of the spliceosome snRNA modification rRNA processing, pre-polysomes Telomere length regulation Sequence-specific gene silencing Sequence-specific gene silencing RNA interference Gene silencing, gametogenesis, transposon silencing Heterochromatin formation t-RNA maturation, transcription of tRNAs, rRNAs, snRNAs Transport of nascent proteins to the ER for further processing Regulation of transcription elongation Regulation of transcription initiation [31] [9] [9] [8] [19] [10] [13] [17,25] [18] [5–7] [26,27] [28,29] [32] In eukaryotic cells, noncoding RNA-containing RNPs are required for mRNA maturation, as well as for transcription and translation.

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