Tissue-selective effects of nucleolar stress and rDNA damage in developmental disorders

  • Nature volume 554, pages 112117 (01 February 2018)
  • doi:10.1038/nature25449
  • Download Citation


Many craniofacial disorders are caused by heterozygous mutations in general regulators of housekeeping cellular functions such as transcription or ribosome biogenesis1,2. Although it is understood that many of these malformations are a consequence of defects in cranial neural crest cells, a cell type that gives rise to most of the facial structures during embryogenesis3,4, the mechanism underlying cell-type selectivity of these defects remains largely unknown. By exploring molecular functions of DDX21, a DEAD-box RNA helicase involved in control of both RNA polymerase (Pol) I- and II-dependent transcriptional arms of ribosome biogenesis5, we uncovered a previously unappreciated mechanism linking nucleolar dysfunction, ribosomal DNA (rDNA) damage, and craniofacial malformations. Here we demonstrate that genetic perturbations associated with Treacher Collins syndrome, a craniofacial disorder caused by heterozygous mutations in components of the Pol I transcriptional machinery or its cofactor TCOF1 (ref. 1), lead to relocalization of DDX21 from the nucleolus to the nucleoplasm, its loss from the chromatin targets, as well as inhibition of rRNA processing and downregulation of ribosomal protein gene transcription. These effects are cell-type-selective, cell-autonomous, and involve activation of p53 tumour-suppressor protein. We further show that cranial neural crest cells are sensitized to p53-mediated apoptosis, but blocking DDX21 loss from the nucleolus and chromatin rescues both the susceptibility to apoptosis and the craniofacial phenotypes associated with Treacher Collins syndrome. This mechanism is not restricted to cranial neural crest cells, as blood formation is also hypersensitive to loss of DDX21 functions. Accordingly, ribosomal gene perturbations associated with Diamond–Blackfan anaemia disrupt DDX21 localization. At the molecular level, we demonstrate that impaired rRNA synthesis elicits a DNA damage response, and that rDNA damage results in tissue-selective and dosage-dependent effects on craniofacial development. Taken together, our findings illustrate how disruption in general regulators that compromise nucleolar homeostasis can result in tissue-selective malformations.

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We thank J. Stack and J. Wu for providing the endothelial and cardiomyocyte cells, J. Chen for Xenopus splicing morpholino validations, C. Santoriello and L. Zon for ddx21 zebrafish morpholino, the Swanson Biotechnology Center at the Koch Institute for Integrative Cancer Research, especially E. Vasile for microscopy and A. Amsterdam for zebrafish work, and K. Cimprich and members of the Wysocka, Calo, and Chang laboratories for discussions. This work was supported by the Howard Hughes Medical Institute (J.W.), R01 GM112720 (J.W.), the March of Dimes Birth Defects Foundation (J.W.), March of Dimes Foundation grants 6-FY15-189 and RC35CA197591 (L.D.A.), Ludwig Foundation (J.W.), Stanford Medical Scientist Training Program and T32CA09302 (R.A.F.), the Helen Hay Whitney Foundation (E.C.), EMBO (ALTF 275-2015), the European Commission (LTFCOFUND2013, GA-2013-609409), and the Marie Curie Actions (A.Z.), Jane Coffin Childs Memorial Fund postdoctoral fellowship (M.E.B.), Stanford Graduate Student Fellowship (B.G.) and National Institutes of Health P50-HG007735 and R01-ES023168 (H.Y.C.).

Author information


  1. Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA

    • Eliezer Calo
    • , Fardin Aryan
    •  & Jialiang Liang
  2. David H. Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts 02139, USA

    • Eliezer Calo
  3. Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA

    • Bo Gu
    • , Antoine Zalc
    • , Tomek Swigut
    •  & Joanna Wysocka
  4. Department of Radiation Oncology, Division of Radiation and Cancer Biology, Stanford University School of Medicine, Stanford, California 94305, USA

    • Margot E. Bowen
    •  & Laura D. Attardi
  5. Department of Chemistry, Stanford University, Stanford, California 94305, USA

    • Ryan A. Flynn
  6. Center for Personal Dynamic Regulomes, Stanford University, 269 Campus Drive, Stanford, California 94305, USA

    • Howard Y. Chang
  7. Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA

    • Laura D. Attardi
  8. Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA

    • Joanna Wysocka
  9. Howard Hughes Medical Institute, Stanford School of Medicine, Stanford University, Stanford, California 94305, USA

    • Joanna Wysocka


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J.W. supervised the project; E.C. conceived and designed the study; E.C. performed experiments with help from F.A. and J.L.; B.G. performed image analyses. E.C. and R.A.F. analysed ChIP–seq data; R.A.F. analysed the iCLIP data; F.A. and E.C. performed zebrafish experiments; M.E.B. performed mouse embryo dissections and immunostainings; A.Z. performed p53 in situ hybridization; J.L. and E.C. performed DNA damage experiments; T.S., L.D.A., and H.Y.C. provided advice on experimental designs, data analyses, and interpretation of the data; E.C. and J.W. wrote the manuscript with input from all co-authors.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Joanna Wysocka.

Reviewer Information Nature thanks D. Tollervey and the other anonymous reviewer(s) for their contribution to the peer review of this work.

Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

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    Life Sciences Reporting Summary

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    Supplementary Figure 1

    This file contains uncropped western blots presented in the main and extended data figures.

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    Supplementary Figure 2

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    Supplementary Table

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