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.
Brief Historical Perspective on Transcriptional Regulation. Preparation of CAGE Libraries: An Enabling Experimental Protocol. Ditags and PET-Technologies for Transcript Identification and Review Use of Ditags with Emphasis on Gene Identification. From Sequencing Output to CAGE Tags: A Chapter on the Extraction of CAGE Tags from the Raw Output of the Sequencing Machine. Using CAGE Data for Quantitative Expression. Compare CAGE Expression to Microarrays and qPCR. Identification of Isoforms. Promoter Analysis Databases. Construction and Tutorial of the CAGE Analysis Viewer and Genome Viewer. Transcriptional Network Analysis Using CAGE. Biological Examples of Alternative TSS/Promoters. Challenges in CAGE Analysis.
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