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Cap Analysis of Gene Expression (CAGE): A Quantitative and Genome-Wide Assay of Transcription Start Sites

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Bioinformatics for Cancer Immunotherapy

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2120))

Abstract

Cap analysis of gene expression (CAGE) is an approach to identify and monitor the activity (transcription initiation frequency) of transcription start sites (TSSs) at single base-pair resolution across the genome. It has been effectively used to identify active promoter and enhancer regions in cancer cells, with potential utility to identify key factors to immunotherapy. Here, we overview a series of CAGE protocols and describe detailed experimental steps of the latest protocol based on the Illumina sequencing platform; both experimental steps (see Subheadings 3.1–3.11) and computational processing steps (see Subheadings 3.12–3.20) are described.

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Authors and Affiliations

  1. Preventive Medicine and Applied Genomics Unit, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan

    Masaki Suimye Morioka & Hideya Kawaji

  2. RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), Yokohama, Kanagawa, Japan

    Hideya Kawaji & Masayoshi Itoh

  3. Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan

    Hideya Kawaji

  4. Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan

    Hiromi Nishiyori-Sueki, Mitsuyoshi Murata, Miki Kojima-Ishiyama & Piero Carninci

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  1. Masaki Suimye Morioka
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  2. Hideya Kawaji
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  3. Hiromi Nishiyori-Sueki
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  4. Mitsuyoshi Murata
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  5. Miki Kojima-Ishiyama
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Correspondence to Masayoshi Itoh .

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    Sebastian Boegel

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Morioka, M.S. et al. (2020). Cap Analysis of Gene Expression (CAGE): A Quantitative and Genome-Wide Assay of Transcription Start Sites. In: Boegel, S. (eds) Bioinformatics for Cancer Immunotherapy. Methods in Molecular Biology, vol 2120. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0327-7_20

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  • DOI: https://doi.org/10.1007/978-1-0716-0327-7_20

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