Promoter architecture of mouse olfactory receptor genes

  1. Piero Carninci1,15
  1. 1RIKEN Yokohama Institute, Omics Science Center, Yokohama, Kanagawa 230-0045, Japan;
  2. 2International School for Advanced Studies, Sector of Neurobiology, Trieste 34136, Italy;
  3. 3The Giovanni Armenise–Harvard Foundation Laboratory, Sector of Neurobiology, International School for Advanced Studies, Trieste 34136, Italy;
  4. 4University of Bergen, Bergen Center for Computational Science–Computational Biology Unit and Sars Centre for Marine Molecular Biology Bergen, 5008, Norway;
  5. 5The Rockefeller University, New York, New York 10065, USA;
  6. 6Cluster in Biomedicine, Trieste 34149, Italy;
  7. 7Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Roslin EH25 9RG, United Kingdom;
  8. 8Italian Institute of Technology–International School for Advanced Studies Unit, Trieste 34136, Italy;
  9. 9Max Planck Institute of Biophysics, Frankfurt 60438, Germany

    1. ↵14 These authors contributed equally to this work.

    • ↵Present addresses: 10Department of Physiology and Biophysics and the Institute for Computational Biomedicine, Weill Cornell Medical College of Cornell University, New York, NY 10065, USA;

    • ↵11 Center for Integrative Genomics, Lausanne University, Lausanne CH-1015, Switzerland;

    • ↵12 RIKEN Yokohama Institute, Omics Science Center, Yokohama, Kanagawa 230-0045, Japan;

    • ↵13 Reta Lila Weston Institute, UCL Institute of Neurology, London WC1N 1PJ, UK.

    Abstract

    Odorous chemicals are detected by the mouse main olfactory epithelium (MOE) by about 1100 types of olfactory receptors (OR) expressed by olfactory sensory neurons (OSNs). Each mature OSN is thought to express only one allele of a single OR gene. Major impediments to understand the transcriptional control of OR gene expression are the lack of a proper characterization of OR transcription start sites (TSSs) and promoters, and of regulatory transcripts at OR loci. We have applied the nanoCAGE technology to profile the transcriptome and the active promoters in the MOE. nanoCAGE analysis revealed the map and architecture of promoters for 87.5% of the mouse OR genes, as well as the expression of many novel noncoding RNAs including antisense transcripts. We identified candidate transcription factors for OR gene expression and among them confirmed by chromatin immunoprecipitation the binding of TBP, EBF1 (OLF1), and MEF2A to OR promoters. Finally, we showed that a short genomic fragment flanking the major TSS of the OR gene Olfr160 (M72) can drive OSN-specific expression in transgenic mice.

    Footnotes

    • ↵15 Corresponding authors.

      E-mail Boris.Lenhard{at}bccs.uib.no.

      E-mail gustinci{at}sissa.it.

      E-mail carninci{at}riken.jp.

    • [Supplemental material is available for this article.]

    • Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.126201.111.

    • Received May 12, 2011.
    • Accepted November 30, 2011.

    Freely available online through the Genome Research Open Access option.

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    1. Published in Advance December 22, 2011, doi: 10.1101/gr.126201.111 Genome Res. 22: 486-497 Copyright © 2012 by Cold Spring Harbor Laboratory Press

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