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Occupancy of tissue-specific cis-regulatory modules by Otx2 and TLE/Groucho for embryonic head specification

Author

Listed:
  • Yuuri Yasuoka

    (Graduate School of Science, University of Tokyo
    Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University)

  • Yutaka Suzuki

    (Graduate School of Frontier Sciences, University of Tokyo
    Graduate School of Frontier Sciences, University of Tokyo)

  • Shuji Takahashi

    (Komaba Organization for Educational Excellence, College of Arts and Sciences, University of Tokyo
    Present address: Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashihiroshima, Hiroshima 739-8526, Japan)

  • Haruka Someya

    (Graduate School of Science and Engineering, Tokyo Metropolitan University)

  • Norihiro Sudou

    (Graduate School of Science, University of Tokyo
    Present address: Department of Anatomy, School of Medicine, Tokyo Women’s Medical University, 8-1 Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan)

  • Yoshikazu Haramoto

    (Komaba Organization for Educational Excellence, College of Arts and Sciences, University of Tokyo
    Research Center for Stem Cell Engineering (SCRC), National Institute of Advanced Industrial Science and Technology (AIST))

  • Ken W. Cho

    (Developmental Biology Center, University of California)

  • Makoto Asashima

    (Research Center for Stem Cell Engineering (SCRC), National Institute of Advanced Industrial Science and Technology (AIST)
    Graduate School of Arts and Sciences, University of Tokyo)

  • Sumio Sugano

    (Graduate School of Frontier Sciences, University of Tokyo
    Graduate School of Frontier Sciences, University of Tokyo)

  • Masanori Taira

    (Graduate School of Science, University of Tokyo)

Abstract

Head specification by the head-selector gene, orthodenticle (otx), is highly conserved among bilaterian lineages. However, the molecular mechanisms by which Otx and other transcription factors (TFs) interact with the genome to direct head formation are largely unknown. Here we employ ChIP-seq and RNA-seq approaches in Xenopus tropicalis gastrulae and find that occupancy of the corepressor, TLE/Groucho, is a better indicator of tissue-specific cis-regulatory modules (CRMs) than the coactivator p300, during early embryonic stages. On the basis of TLE binding and comprehensive CRM profiling, we define two distinct types of Otx2- and TLE-occupied CRMs. Using these devices, Otx2 and other head organizer TFs (for example, Lim1/Lhx1 (activator) or Goosecoid (repressor)) are able to upregulate or downregulate a large battery of target genes in the head organizer. An underlying principle is that Otx marks target genes for head specification to be regulated positively or negatively by partner TFs through specific types of CRMs.

Suggested Citation

  • Yuuri Yasuoka & Yutaka Suzuki & Shuji Takahashi & Haruka Someya & Norihiro Sudou & Yoshikazu Haramoto & Ken W. Cho & Makoto Asashima & Sumio Sugano & Masanori Taira, 2014. "Occupancy of tissue-specific cis-regulatory modules by Otx2 and TLE/Groucho for embryonic head specification," Nature Communications, Nature, vol. 5(1), pages 1-14, September.
    • Handle: RePEc:nat:natcom:v:5:y:2014:i:1:d:10.1038_ncomms5322
    DOI: 10.1038/ncomms5322
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