Cap-Analysis Gene Expression (CAGE): The Science of Decoding Genes Transcription, 1st Edition (Hardback) book cover

Cap-Analysis Gene Expression (CAGE)

The Science of Decoding Genes Transcription, 1st Edition

Edited by Piero Carninci

Jenny Stanford Publishing

266 pages | 19 Color Illus. | 31 B/W Illus.

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pub: 2009-10-31
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Description

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.

Reviews

"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

Table of Contents

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

Introduction

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

Introduction

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

Perspective

New Era of Genome-Wide Gene Expression Analysis

Introduction

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

Overview

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

Replication

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

Discussion

Databases for CAGE Visualization and Analysis

Introduction

Transcription Maps and Activity

Public Databases

Genomic View of In-House Data

For Expression Analyses

Discussion

Computational Methods to Identify Transcription Factor Binding Sites Using CAGE Information

Introduction

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

Methodology

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

Introduction

Annotating Gene Expression

Using Ontologies to Integrate Expression Information

Lessons Learned from Genomic CAGE

Introduction

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

Introduction

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

Introduction

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?

Conclusion

Color Index

Index

About the Editor

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.

Subject Categories

BISAC Subject Codes/Headings:
MAT029000
MATHEMATICS / Probability & Statistics / General
SCI010000
SCIENCE / Biotechnology
SCI029000
SCIENCE / Life Sciences / Genetics & Genomics
SCI086000
SCIENCE / Life Sciences / General