1. Chromosomes and Gene Expression
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Regulation of alternative polyadenylation by Nkx2-5 and Xrn2 during mouse heart development

  1. Keisuke Nimura  Is a corresponding author
  2. Masamichi Yamamoto
  3. Makiko Takeichi
  4. Kotaro Saga
  5. Katsuyoshi Takaoka
  6. Norihiko Kawamura
  7. Hirohisa Nitta
  8. Hiromichi Nagano
  9. Saki Ishino
  10. Tatsuya Tanaka
  11. Robert J Schwartz
  12. Hiroyuki Aburatani
  13. Yasufumi Kaneda
  1. Osaka University Graduate School of Medicine, Japan
  2. Kyoto University Graduate School of Medicine, Japan
  3. Osaka University, Japan
  4. University of Houston, United States
  5. The University of Tokyo, Japan
Research Article
  • Cited 5
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Cite this article as: eLife 2016;5:e16030 doi: 10.7554/eLife.16030

Abstract

Transcription factors organize gene expression profiles by regulating promoter activity. However, the role of transcription factors after transcription initiation is poorly understood. Here, we show that the homeoprotein Nkx2-5 and the 5'-3' exonuclease Xrn2 are involved in the regulation of alternative polyadenylation (APA) during mouse heart development. Nkx2-5 occupied not only the transcription start sites (TSSs) but also the downstream regions of genes, serving to connect these regions in primary embryonic cardiomyocytes (eCMs). Nkx2-5 deficiency affected Xrn2 binding to target loci and resulted in increases in RNA polymerase II (RNAPII) occupancy and in the expression of mRNAs with long 3'untranslated regions (3' UTRs) from genes related to heart development. siRNA-mediated suppression of Nkx2-5 and Xrn2 led to heart looping anomaly. Moreover, Nkx2-5 genetically interacts with Xrn2 because Nkx2-5+/-Xrn2+/-, but neither Nkx2-5+/- nor Xrn2+/-, newborns exhibited a defect in ventricular septum formation, suggesting that the association between Nkx2-5 and Xrn2 is essential for heart development. Our results indicate that Nkx2-5 regulates not only the initiation but also the usage of poly(A) sites during heart development. Our findings suggest that tissue-specific transcription factors is involved in the regulation of APA.

Article and author information

Author details

  1. Keisuke Nimura

    Division of Gene Therapy Science, Osaka University Graduate School of Medicine, Suita, Japan
    For correspondence
    nimura@gts.med.osaka-u.ac.jp
    Competing interests
    The authors declare that no competing interests exist.
  2. Masamichi Yamamoto

    Department of Nephrology, Kyoto University Graduate School of Medicine, Kyoto, Japan
    Competing interests
    The authors declare that no competing interests exist.
  3. Makiko Takeichi

    Division of Gene Therapy Science, Osaka University Graduate School of Medicine, Suita, Japan
    Competing interests
    The authors declare that no competing interests exist.
  4. Kotaro Saga

    Division of Gene Therapy Science, Osaka University Graduate School of Medicine, Suita, Japan
    Competing interests
    The authors declare that no competing interests exist.
  5. Katsuyoshi Takaoka

    Developmental Genetics Group, Osaka University, Suita, Japan
    Competing interests
    The authors declare that no competing interests exist.
  6. Norihiko Kawamura

    Division of Gene Therapy Science, Osaka University Graduate School of Medicine, Suita, Japan
    Competing interests
    The authors declare that no competing interests exist.
  7. Hirohisa Nitta

    Division of Gene Therapy Science, Osaka University Graduate School of Medicine, Suita, Japan
    Competing interests
    The authors declare that no competing interests exist.
  8. Hiromichi Nagano

    Division of Gene Therapy Science, Osaka University Graduate School of Medicine, Suita, Japan
    Competing interests
    The authors declare that no competing interests exist.
  9. Saki Ishino

    Center for Medical Research and Education, Osaka University Graduate School of Medicine, Suita, Japan
    Competing interests
    The authors declare that no competing interests exist.
  10. Tatsuya Tanaka

    Center for Medical Research and Education, Osaka University Graduate School of Medicine, Suita, Japan
    Competing interests
    The authors declare that no competing interests exist.
  11. Robert J Schwartz

    Department of Biology and Biochemistry, University of Houston, Houston, United States
    Competing interests
    The authors declare that no competing interests exist.
  12. Hiroyuki Aburatani

    Genome Science Division, The University of Tokyo, Tokyo, Japan
    Competing interests
    The authors declare that no competing interests exist.
  13. Yasufumi Kaneda

    Division of Gene Therapy Science, Osaka University Graduate School of Medicine, Suita, Japan
    Competing interests
    The authors declare that no competing interests exist.

Ethics

Animal experimentation: The protocols (3422-1 and 24-084-012) are approved by the Ethics Committee for Animal Experiments of the Osaka University Graduate School of Medicine.with protocols

Reviewing Editor

  1. Nick J Proudfoot, University of Oxford, United Kingdom

Publication history

  1. Received: March 14, 2016
  2. Accepted: June 21, 2016
  3. Accepted Manuscript published: June 22, 2016 (version 1)
  4. Version of Record published: August 12, 2016 (version 2)

Copyright

© 2016, Nimura et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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