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Two independent transcription initiation codes overlap on vertebrate core promoters

Author

Listed:
  • Vanja Haberle

    (University of Bergen, Thormøhlensgate 53A, N-5008 Bergen, Norway
    Institute of Clinical Sciences and MRC Clinical Sciences Center, Faculty of Medicine, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK)

  • Nan Li

    (School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK)

  • Yavor Hadzhiev

    (School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK)

  • Charles Plessy

    (RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
    RIKEN Center for Life Science Technologies, RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan)

  • Christopher Previti

    (Computational Biology Unit, Uni Computing, Uni Research AS, University of Bergen, Thormøhlensgate 55, N-5008 Bergen, Norway
    Present addresses: German Cancer Research Center (DKFZ), Genomics & Proteomics Core Facility (GPCF), Im Neuenheimer Feld 580/TP3, Heidelberg 69120, Germany (C.Pr.); Broegelmann Research Laboratory, The Gade Institute, University of Bergen, The Laboratory Building, Haukeland University Hospital, N-5021 Bergen, Norway (C.N.); Acquifer AG, Sophienstraße 136, 76135 Karlsruhe, Germany (J.G.); Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA (X.D.); Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland (A.A.).)

  • Chirag Nepal

    (Computational Biology Unit, Uni Computing, Uni Research AS, University of Bergen, Thormøhlensgate 55, N-5008 Bergen, Norway
    Present addresses: German Cancer Research Center (DKFZ), Genomics & Proteomics Core Facility (GPCF), Im Neuenheimer Feld 580/TP3, Heidelberg 69120, Germany (C.Pr.); Broegelmann Research Laboratory, The Gade Institute, University of Bergen, The Laboratory Building, Haukeland University Hospital, N-5021 Bergen, Norway (C.N.); Acquifer AG, Sophienstraße 136, 76135 Karlsruhe, Germany (J.G.); Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA (X.D.); Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland (A.A.).)

  • Jochen Gehrig

    (School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
    Present addresses: German Cancer Research Center (DKFZ), Genomics & Proteomics Core Facility (GPCF), Im Neuenheimer Feld 580/TP3, Heidelberg 69120, Germany (C.Pr.); Broegelmann Research Laboratory, The Gade Institute, University of Bergen, The Laboratory Building, Haukeland University Hospital, N-5021 Bergen, Norway (C.N.); Acquifer AG, Sophienstraße 136, 76135 Karlsruhe, Germany (J.G.); Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA (X.D.); Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland (A.A.).)

  • Xianjun Dong

    (Computational Biology Unit, Uni Computing, Uni Research AS, University of Bergen, Thormøhlensgate 55, N-5008 Bergen, Norway
    Present addresses: German Cancer Research Center (DKFZ), Genomics & Proteomics Core Facility (GPCF), Im Neuenheimer Feld 580/TP3, Heidelberg 69120, Germany (C.Pr.); Broegelmann Research Laboratory, The Gade Institute, University of Bergen, The Laboratory Building, Haukeland University Hospital, N-5021 Bergen, Norway (C.N.); Acquifer AG, Sophienstraße 136, 76135 Karlsruhe, Germany (J.G.); Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA (X.D.); Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland (A.A.).)

  • Altuna Akalin

    (Computational Biology Unit, Uni Computing, Uni Research AS, University of Bergen, Thormøhlensgate 55, N-5008 Bergen, Norway
    Present addresses: German Cancer Research Center (DKFZ), Genomics & Proteomics Core Facility (GPCF), Im Neuenheimer Feld 580/TP3, Heidelberg 69120, Germany (C.Pr.); Broegelmann Research Laboratory, The Gade Institute, University of Bergen, The Laboratory Building, Haukeland University Hospital, N-5021 Bergen, Norway (C.N.); Acquifer AG, Sophienstraße 136, 76135 Karlsruhe, Germany (J.G.); Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA (X.D.); Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland (A.A.).)

  • Ana Maria Suzuki

    (RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
    RIKEN Center for Life Science Technologies, RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan)

  • Wilfred F. J. van IJcken

    (Erasmus Medical Center, Center for Biomics, Room Ee679b, Dr Molewaterplein 50, 3015 GE Rotterdam, The Netherlands)

  • Olivier Armant

    (Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Postfach 3640, 76021 Karlsruhe, Germany)

  • Marco Ferg

    (Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Postfach 3640, 76021 Karlsruhe, Germany)

  • Uwe Strähle

    (Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Postfach 3640, 76021 Karlsruhe, Germany)

  • Piero Carninci

    (RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
    RIKEN Center for Life Science Technologies, RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan)

  • Ferenc Müller

    (School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK)

  • Boris Lenhard

    (Institute of Clinical Sciences and MRC Clinical Sciences Center, Faculty of Medicine, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
    University of Bergen, Thormøhlensgate 55, N-5008 Bergen, Norway)

Abstract

The transcription start sites used during the maternal to zygotic transition in zebrafish are mapped, revealing that the transition is characterized by a switch between two different sequence signs to guide transcription initiation, which often co-exist in core promoters.

Suggested Citation

  • Vanja Haberle & Nan Li & Yavor Hadzhiev & Charles Plessy & Christopher Previti & Chirag Nepal & Jochen Gehrig & Xianjun Dong & Altuna Akalin & Ana Maria Suzuki & Wilfred F. J. van IJcken & Olivier Arm, 2014. "Two independent transcription initiation codes overlap on vertebrate core promoters," Nature, Nature, vol. 507(7492), pages 381-385, March.
    • Handle: RePEc:nat:nature:v:507:y:2014:i:7492:d:10.1038_nature12974
    DOI: 10.1038/nature12974
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    Citations

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    Cited by:

    1. Ruiyan Hou & Chung-Chau Hon & Yuanhua Huang, 2023. "CamoTSS: analysis of alternative transcription start sites for cellular phenotypes and regulatory patterns from 5' scRNA-seq data," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    2. Meijiang Gao & Marina Veil & Marcus Rosenblatt & Aileen Julia Riesle & Anna Gebhard & Helge Hass & Lenka Buryanova & Lev Y. Yampolsky & Björn Grüning & Sergey V. Ulianov & Jens Timmer & Daria Onichtch, 2022. "Pluripotency factors determine gene expression repertoire at zygotic genome activation," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
    3. Chirag Nepal & Jesper B. Andersen, 2023. "Alternative promoters in CpG depleted regions are prevalently associated with epigenetic misregulation of liver cancer transcriptomes," Nature Communications, Nature, vol. 14(1), pages 1-14, December.

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