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Noncanonical translation via deadenylated 3′ UTRs maintains primordial germ cells

Nature Chemical Biology volume 14, pages 844–852 (2018)Cite this article

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Abstract

Primordial germ cells (PGCs) form during early embryogenesis with a supply of maternal mRNAs that contain shorter poly(A) tails. How translation of maternal mRNAs is regulated during PGC development remains elusive. Here we describe a small-molecule screen with zebrafish embryos that identified primordazine, a compound that selectively ablates PGCs. Primordazine’s effect on PGCs arises from translation repression through primordazine-response elements in the 3′ UTRs. Systematic dissection of primordazine’s mechanism of action revealed that translation of mRNAs during early embryogenesis occurs by two distinct pathways, depending on the length of their poly(A) tails. In addition to poly(A)-tail-dependent translation (PAT), early embryos perform poly(A)-tail-independent noncanonical translation (PAINT) via deadenylated 3′ UTRs. Primordazine inhibits PAINT without inhibiting PAT, an effect that was also observed in quiescent, but not proliferating, mammalian cells. These studies reveal that PAINT is an alternative form of translation in the early embryo and is indispensable for PGC maintenance.

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Fig. 1: Discovery of small molecules, primordazine A and B, that ablate PGCs.
Fig. 2: Primordazine inhibits translation via the 3′ UTR of nanos3 or dnd1.
Fig. 3: Primordazine inhibits Poly(A)-tail-independent noncanonical translation (PAINT) without inhibiting canonical, poly(A)-tail-mediated translation (PAT).
Fig. 4: Primordazine inhibits translation of a subgroup of endogenous genes.
Fig. 5: Primordazine induces the formation of abnormal RNA granules.
Fig. 6: Primordazine inhibits PAINT in quiescent-like but not in proliferating cells.

Data availability

The data that support the findings of this study including RNA-seq and proteomics analysis are available from the corresponding authors upon reasonable request.

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  • 26 July 2019

    In the version of this article originally published, numbered compounds were not linked correctly to their respective compound pages. The error has been corrected in the HTML version of this paper.

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Acknowledgements

We thank S. Vasudevan, T. Shioda, S. Lee, N. Dyson, W. Miles, and Y. Yu for discussions related to this manuscript. Thanks to K. Inoue (Kobe University, Japan), E. Raz (University of Münster, Germany), M. Bushell (MedicalResearch Council, UK), and J. Wilusz (University of Pennsylvania, USA) for providing plasmids. Thanks to U. Kim (next generation sequencing core at Massachusetts General Hospital) for help with the RNA-seq process, to A. Gonzales and D. Harrison for technical assistance, and to C. Reilly for chemical validation. Funding was provided by NIH grants 5T32HL007208-37 (Y.N.J.), R01GM088040 (R.T.P.), USDA grant 2014-07998 (R.T.P.), the Charles and Ann Sanders MGH Scholar Award (R.T.P.), and the L. S. Skaggs Presidential Endowed Chair (R.T.P.).

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Author notes

  1. Youngnam N. Jin, Pui-Ying Lam & Randall T. Peterson

    Present address: College of Pharmacy, University of Utah, Salt Lake City, UT, USA

  2. Shao-En Ong

    Present address: Department of Pharmacology, University of Washington, Seattle, WA, USA

  3. These authors contributed equally: Youngnam N. Jin, Peter J. Schlueter.

Authors and Affiliations

  1. Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA, USA

    Youngnam N. Jin, Peter J. Schlueter, Nathalie Jurisch-Yaksi, Pui-Ying Lam, Shan Jin, Woong Y. Hwang, Jing-Ruey Joanna Yeh & Randall T. Peterson

  2. Department of Medicine, Massachusetts General Hospital, Charlestown, MA, USA

    Youngnam N. Jin, Peter J. Schlueter, Nathalie Jurisch-Yaksi, Pui-Ying Lam, Shan Jin, Woong Y. Hwang, Jing-Ruey Joanna Yeh & Randall T. Peterson

  3. Department of Medicine, Harvard Medical School, Boston, MA, USA

    Youngnam N. Jin, Peter J. Schlueter, Nathalie Jurisch-Yaksi, Pui-Ying Lam, Shan Jin, Jing-Ruey Joanna Yeh & Randall T. Peterson

  4. Department of Systems Biology, Harvard Medical School, Boston, MA, USA

    Youngnam N. Jin, Pui-Ying Lam & Randall T. Peterson

  5. Broad Institute, Cambridge, MA, USA

    Youngnam N. Jin, Pui-Ying Lam, Shao-En Ong, Monica Schenone, Christina R. Hartigan, Steven A. Carr & Randall T. Peterson

  6. Department of Pediatrics, University of Utah, Salt Lake City, UT, USA

    Masaaki Yoshigi

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Contributions

Y.N.J., P.J.S., N.J.-Y., and R.T.P. designed the study and experiments. Y.N.J., P.J.S., N.J.-Y., and P.-Y.L. performed the experiments. Y.N.J. and P.J.S. performed data analysis. P.-Y.L. and Y.N.J. performed RNA-seq. Y.N.J. performed bioinformatics. S.J. synthesized chemicals. W.Y.H. and J.-R.J.Y. generated knockout fish. M.Y., S.-E.O., M.S., C.R.H., and S.A.C. contributed to 2D gel electrophoresis and proteomic analysis. Y.N.J. and R.T.P. wrote the paper. All authors commented on the manuscript.

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Correspondence to Youngnam N. Jin or Randall T. Peterson.

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P.J.S. and R.T.P. have applied for a patent for primordazine.

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Jin, Y.N., Schlueter, P.J., Jurisch-Yaksi, N. et al. Noncanonical translation via deadenylated 3′ UTRs maintains primordial germ cells. Nat Chem Biol 14, 844–852 (2018). https://doi.org/10.1038/s41589-018-0098-0

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