3. Definition of Promotome–Transcriptome Architecture Using CAGEscan

  1. Dr. Matthias Harbers2,3 and
  2. Prof. Dr. Günter Kahl4,5,6
  1. Nicolas Bertin1,
  2. Charles Plessy1,
  3. Piero Carninci1 and
  4. Dr. Matthias Harbers2,3

Published Online: 23 JAN 2012

DOI: 10.1002/9783527644582.ch3

Tag-Based Next Generation Sequencing

Tag-Based Next Generation Sequencing

How to Cite

Bertin, N., Plessy, C., Carninci, P. and Harbers, M. (2011) Definition of Promotome–Transcriptome Architecture Using CAGEscan, in Tag-Based Next Generation Sequencing (eds M. Harbers and G. Kahl), Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany. doi: 10.1002/9783527644582.ch3

Editor Information

  1. 2

    4-2-6 Nishihara, Kashiwa-Shi, Chiba 277-0885, Japan

  2. 3

    DNAFORM Inc., Leading Venture Plaza 2, 75-1 Ono-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0046, Japan

  3. 4

    Mohrmühlgasse 3, 63500 Seligenstadt, Germany

  4. 5

    University of Frankfurt am Main Biocenter, Max-von-Lauestraße 9, 60439 Frankfurt am Main, Germany

  5. 6

    Frankfurt Biotechnology Innovation Center (FIZ), GenXPro Ltd, Altenhöferallee 3, 60438 Frankfurt am Main, Germany

Author Information

  1. 1

    RIKEN Yokohama Institute, Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan

  2. 2

    4-2-6 Nishihara, Kashiwa-Shi, Chiba 277-0885, Japan

  3. 3

    DNAFORM Inc., Leading Venture Plaza 2, 75-1 Ono-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0046, Japan

Publication History

  1. Published Online: 23 JAN 2012
  2. Published Print: 14 DEC 2011

ISBN Information

Print ISBN: 9783527328192

Online ISBN: 9783527644582



  • promotome–transcriptome architecture;
  • CAGEscan;
  • methods;
  • applications


In this chapter, we describe CAGEscan – a novel approach that, like its parent method cap analysis gene expression (CAGE), allows for the selective capture and sequencing of the very 5′ end of capped transcripts on a genome-wide scale. The CAGEscan technology, however, goes beyond the classic CAGE approach and allows for selectively capturing of capped transcripts from orders of magnitude smaller amount of starting total RNA and allows for the paired sequencing of the very 5′ end segment of transcripts together with a randomly primed associated downstream exon segment. CAGEscan differs from its parent CAGE technology in two respects. (i) The selection of capped transcripts is driven by molecular biology rather than by biochemical principles, which allows for a drastic reduction in the number of steps required to produce a library of tags for sequencing, enabling the analysis of samples containing only minute amounts of total RNA. This extends the applicability of CAGE-like analysis to novel frontiers such as the analysis of subcellular and subnuclear transcriptomes or the analysis of samples for which only limited quantities of RNA can be obtained (e.g., selectively captured ex vivo cells such as specific neurons or immune cell subpopulations, ex vivo tumor cells as well as their neighboring noncarcinogenic counterparts, etc.). (ii) By allowing the paired-end sequencing of both the 5′ end and a random downstream transcript segment, CAGEscan alleviates one of the main limitations of CAGE-like technologies and associates each transcriptional start site (TSS) to a downstream exon, thus directly linking the promotome (the entire collection of proximal promoter regions derived from the precise positioning of TSS) to the transcriptome (the entire collection of transcripts). Additionally, CAGEscan offers a better characterization of the functions of promoters and deciphering the architecture of complex loci composed of interlaced sense and antisense coding and noncoding transcripts. In the final section of the chapter we also detail how CAGEscan delineates the structure of orphan promoters for which no current transcript models exists.