1st Edition

Cap-Analysis Gene Expression (CAGE) The Science of Decoding Genes Transcription

Edited By Piero Carninci Copyright 2010
    ISBN 9789814241342
    266 Pages 19 Color & 31 B/W Illustrations
    Published October 31, 2009 by Jenny Stanford Publishing

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    Sale Price USD $170.00
    USD $170.00
    ISBN 9780429065750
    266 Pages
    Published May 8, 2019 by Jenny Stanford Publishing

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    This book is a guide for users of new technologies, as it includes accurately proven protocols, allowing readers to prepare their samples for experiments. Additionally, it is a guide for the bioinformatics tools that are available for the analysis of the obtained tags, including the design of the software, the sources and the Web. Finally, the book provides examples of the application of these technologies to identify promoters, annotate genomes, identify new RNAs and reconstruct models of transcriptional control. Although examples mainly concern mammalians, the discussion expands to other groups of eukaryotes, where these approaches are complementing genome sequencing.

    Preface v
    Cap Analysis Gene Expression (CAGE)
    Tagging Transcription Starting Sites with CAGE
    The Output of the Genome is Complex
    Mapping 5’ Ends: From ESTs to Tagging Technologies
    Linking Core Promoters to Genomic Elements
    cDNA Ends or the Whole Sequence?
    Identification of Functional Elements in the Genome
    Technology Evolution, Same Lessons?
    Construction of CAGE Libraries
    Stage 1: Synthesis of First-Strand cDNA
    Stage 2: Oxidation/Biotinylation
    Stage 3: Capture-Release
    Stage 4: Single Strand Linker Ligation
    Stage 5: the Second Strand cDNA Synthesis
    Stage 6: Preparing CAGE Tags
    Stage: 7 Amplification of CAGE Tags
    Stage 8: Restriction
    Stage 9: Concatenation
    Transcriptome and Genome Characterization Using Massively Parallel Paired End Tag (PET) Sequencing Analysis
    The Development of Pair end diTag (PET) Analysis
    GIS-PET for Transcriptome Analysis
    ChIP-PET for Whole Genome Mapping of Transcription Factor Binding Sites and Epigenetic Modifications
    ChIA-PET for Whole Genome Identification of Long Range interactions
    New Era of Genome-Wide Gene Expression Analysis
    Tagging Technologies for Genome-Wide Analysis
    Principles of Next Generation Sequencing Technologies
    Genome Analyzer (Illumina/Solexa)
    SOLiD System (Applied Biosystems)
    Advantages of Next Generation Sequencing Technologies over Conventional Sequencing Technology on Tagging Technologies
    From Static Analysis to Dynamic Analysis
    CAGE Method and Next Generation Sequencing Technologies
    Conclusions and Outlook
    Computational Tools to Analyze CAGE
    Introduction to PART II
    Extraction and Quality Control of CAGE Tags
    Using Read Qualities and Read Properties, Pre- and Post-Extraction
    Procedures Before Tag Extraction
    Using QC Values After Tag Extraction
    Origin of Sequence Errors
    Using Sequence Errors to Estimate CAGE Quality
    A Simple CAGE Tag Extraction Method
    Setting CAGE Tags in a Genomic Context
    Mapping Pipelines for Sequence Tag Technologies
    A Mapping Pipeline for CAGE
    Benchmarking with a Sample Dataset
    Using CAGE Data for Quantitative Expression
    High Throughput Expression Platforms
    Comparing CAGE to Other Measures of Gene Expression
    Platform Normalization
    Gene Models and Complex Loci
    Construction of CAGE Promoters and Calculation of Gene Expression Levels
    Comparison of CAGE Expression between Technical Replicates
    Comparison of CAGE Expression from Biological Replicates
    Comparison of CAGE Expression Between Different Time Points Within a Single Time-Course
    Comparison of CAGE Expression Profiling to qRT-PCR Expression Measurements
    Comparison of CAGE Expression Profiling to MicroarrayMeasurements
    Present/Absent Calls
    Databases for CAGE Visualization and Analysis
    Transcription Maps and Activity
    Public Databases
    Genomic View of In-House Data
    For Expression Analyses
    Computational Methods to Identify Transcription Factor Binding Sites Using CAGE Information
    Schema of the Methodology Process
    Initial Links of TF with the Affected Genes
    Correlation of CAGE Tag Counts of Genes and TFs
    Ranking TF!TFBS!TSS/Promoter!GENE Association: The Effective Use of CAGE Tags
    Verification of Results
    Reconstruction of TRNs
    Transcription Regulatory Networks Analysis Using CAGE
    CAGE Data for Network Reconstruction
    Gene Expression Data Complementary to CAGE for Network Reconstruction
    Using Physical Interactions
    TRNs Reconstruction
    Using Pathway Information
    Validation of the Reconstructed Networks
    Gene-Expression Ontologies and Tag-Based Expression Profiling
    Annotating Gene Expression
    Using Ontologies to Integrate Expression Information
    Lessons Learned from Genomic CAGE
    The Classic View on Transcription Start Sites and Core Promoters
    CAGE-Based Views of Transcription Start Sites
    Probing Biological Mechanisms Using CAGE
    Future Challenges in CAGE Analysis
    What are we Measuring?
    How Close to "The Truth" areWe?
    Comparative Genomics and Mammalian Promoter Evolution
    Resources for Comparative Genomic Analysis
    Genome Wide Trends in Mammalian Promoter Evolution
    Promoters Represent an Unusual Genomic Environment
    Integration of Population Genetic Data with Comparative Genomics
    Concluding Remarks
    The Impact of CAGE Data on Understanding Macrophage Transcriptional Biology
    Transcription start site and promoter characteristics revealed by CAGE
    Transcriptional Complexity: Sense-Antisense Transcription and Non-Coding RNA
    Construction of Macrophage Transcriptional Networks
    What does CAGE Data Offer for Traditional Studies of Promoter Regulation?
    Color Index


    Piero Carninci was born in Italy in 1965 and earned his doctorate in biological science at the University of Trieste in 1989. For six months from April 1989, he worked as a research associate at the International Center for Genetic Engineering and Biotechnology and then served as a health assistant in the Italian army. In 1990, he became a researcher at a biotech company called TALENT, after which he moved to RIKEN as a researcher in 1995. Since 2003, he has been working as a senior scientist at the Genome Science Laboratory at the RIKEN Frontier Research Institute and at the RIKEN Genomic Sciences Center.

    "This is a comprehensive introduction to a powerful and important new technique that is transforming our understanding of gene regulation. This volume contains everything you need to know to become an expert in CAGE, from library construction to bioinformatic analysis of the voluminous data sets."
    —Gene E. Robinson, University of Illinois

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