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DICER- and AGO3-dependent generation of retinoic acid–induced DR2 Alu RNAs regulates human stem cell proliferation

Nature Structural & Molecular Biology volume 19, pages 1168–1175 (2012)Cite this article

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Abstract

Although liganded nuclear receptors have been established to regulate RNA polymerase II (Pol II)-dependent transcription units, their role in regulating Pol III–transcribed DNA repeats remains largely unknown. Here we report that ~2–3% of the ~100,000–200,000 total human DR2 Alu repeats located in proximity to activated Pol II transcription units are activated by the retinoic acid receptor (RAR) in human embryonic stem cells to generate Pol III–dependent RNAs. These transcripts are processed, initially in a DICER-dependent fashion, into small RNAs (~28–65 nt) referred to as repeat-induced RNAs that cause the degradation of a subset of crucial stem-cell mRNAs, including Nanog mRNA, which modulate exit from the proliferative stem-cell state. This regulation requires AGO3-dependent accumulation of processed DR2 Alu transcripts and the subsequent recruitment of AGO3-associated decapping complexes to the target mRNA. In this way, the RAR-dependent and Pol III–dependent DR2 Alu transcriptional events in stem cells functionally complement the Pol II–dependent neuronal transcriptional program.

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Figure 1: atRA induction of DR2 Alu transcription.
Figure 2: DR2 Alu transcripts associate with AGO3 and produce riRNAs in a DICER-dependent manner.
Figure 3: riRNAs recognize complementary sequences in the 3′ UTRs of target mRNAs.
Figure 4: Role of the riRNA complementary sequence in post-transcriptional regulation.
Figure 5: Role of the AGO3-associated decapping complex in post-transcriptional regulation.
Figure 6: DR2 Alu transcripts and riRNAs regulate stem-cell proliferation.
Figure 7: Working model for atRA-induced Pol II and Pol III transcription programs in stem cells resulting in the generation of DR2 Alu–derived riRNAs that act on a subset of mRNAs containing complementary sequences and exert developmental effects.

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Change history

  • 31 January 2013

    In the version of this article initially published, an accession number for the ChIP-seq, RNA-seq and small RNA–seq data was missing. H3K36me3 ChIP-seq, RNA-seq and small RNA–seq data are now available with GEO accession number GSE42602. This information has now been included in the HTML and PDF versions of the article.

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Acknowledgements

We thank M. Mercola (Sanford Burnham Medical Research Institute, La Jolla, California) and S. Ding (The Scripps Research Institute, La Jolla, California) for providing H9 human embryonic stem cells; N. Kim (Seoul National University, Gwanak-gu, Seoul, South Korea) for DICER expression constructs; J. Nand for assistance with the RNA-Seq data analysis; C. Nelson for cell culture assistance; J. Hightower for assistance with figure and manuscript preparation; and M. Ghassemian from the University of California San Diego (UCSD) Biomolecular/Proteomics Mass Spectrometry Facility for assistance in mass spectrometry. We thank A. Pasquinelli at UCSD for invaluable discussions and comments. We also acknowledge the UCSD Cancer Center Specialized Support Grant P30 CA23100 for confocal microscopy. Q.H. is a Cancer Research Institute postdoctoral fellow. M.G.R. is an investigator with the Howard Hughes Medical Institute. This work was supported by grants from the US National Institutes of Health (DK018477, DK39949, HL065445, NS034934) and the National Cancer Institute (CA097134) to M.G.R. and awards from the US Department of Defense and the Prostate Cancer Foundation to M.G.R.

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Author notes

  1. Michele Trabucchi

    Present address: Present address: Centre Méditerranéen de Médecine Moléculaire, Nice, France.,

  2. Bogdan Tanasa and Michele Trabucchi: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Medicine, Howard Hughes Medical Institute, School of Medicine, University of California, San Diego, La Jolla, California, USA.,

    QiDong Hu, Bogdan Tanasa, Michele Trabucchi, Wenbo Li, Jie Zhang, Kenneth A Ohgi & Michael G Rosenfeld

  2. Kellogg School of Science and Technology, The Scripps Research Institute, La Jolla, California, USA

    Bogdan Tanasa

  3. Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, California, USA.,

    David W Rose & Christopher K Glass

  4. Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, California, USA.,

    Christopher K Glass

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Contributions

Q.H. performed the majority of the experiments. B.T. contributed the bioinformatics analysis and made the initial finding that the 3′ UTRs of specific stem-cell mRNAs harbored sequences complementary to DR2 Alu-derived riRNAs. M.T. contributed part of the northern blot data. W.L. contributed GRO-Seq. J.Z. provided sequencing and microinjection assistance. K.A.O. provided sequencing and vector construction assistance. D.W.R. contributed microinjection. C.K.G. helped design experiments and critically read the manuscript. M.G.R. designed the experiments and evaluated the data. Q.H. and M.G.R. wrote the manuscript.

Corresponding author

Correspondence to Michael G Rosenfeld.

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Hu, Q., Tanasa, B., Trabucchi, M. et al. DICER- and AGO3-dependent generation of retinoic acid–induced DR2 Alu RNAs regulates human stem cell proliferation. Nat Struct Mol Biol 19, 1168–1175 (2012). https://doi.org/10.1038/nsmb.2400

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