8. Identification and Expression Profiling of Small RNA Populations Using High-Throughput Sequencing

  1. Dr. Matthias Harbers3,4 and
  2. Prof. Dr. Günter Kahl5,6,7
  1. Javier Armisen1,
  2. W. Robert Shaw2 and
  3. Eric A. Miska1

Published Online: 23 JAN 2012

DOI: 10.1002/9783527644582.ch8

Tag-Based Next Generation Sequencing

Tag-Based Next Generation Sequencing

How to Cite

Armisen, J., Shaw, W. R. and Miska, E. A. (2011) Identification and Expression Profiling of Small RNA Populations Using High-Throughput Sequencing, in Tag-Based Next Generation Sequencing (eds M. Harbers and G. Kahl), Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany. doi: 10.1002/9783527644582.ch8

Editor Information

  1. 3

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

  2. 4

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

  3. 5

    Mohrmühlgasse 3, 63500 Seligenstadt, Germany

  4. 6

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

  5. 7

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

Author Information

  1. 1

    Wellcome Trust/Cancer Research UK, Gurdon Institute, University of Cambridge, The Henry Wellcome Building of Cancer and Developmental Biology, Tennis Court Road, Cambridge CB2 1QN, UK

  2. 2

    Imperial College London, Department of Life Sciences, London SW7 2AZ, UK

Publication History

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

ISBN Information

Print ISBN: 9783527328192

Online ISBN: 9783527644582

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Keywords:

  • expression profiling;
  • small RNA populations;
  • high-throughput sequencing (HTS);
  • methods;
  • troubleshooting;
  • applications

Summary

Small RNAs are noncoding regulatory RNAs of short length (18–31 nucleotides long) with important roles in gene expression. Since the first identified endogenous small regulatory RNAs in the early 1990s, many functional small RNAs have been identified in diverse organisms using conventional techniques such as genetics, molecular cloning, and predictions from bioinformatics. However, in recent years, and with the implementation of new high-throughput sequencing technologies, also called next-generation sequencing (NGS) technologies, the number of novel small RNAs identified has increased drastically, from a few hundred to hundred of thousands, opening up a new dimension in our attempts to understand gene regulation and altering the landscape of functional RNA molecules indefinitely. In this chapter, we provide a brief summary of three major classes of small RNAs and the NGS technologies used to investigate these classes. We present a generalized method to prepare small RNA libraries suitable for all NGS technologies, and we explain the advantages and disadvantages of the use of NGS to identify and monitor small RNAs populations.