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A pseudogene long-noncoding-RNA network regulates PTEN transcription and translation in human cells

Nature Structural & Molecular Biology volume 20, pages 440–446 (2013)Cite this article

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Abstract

PTEN is a tumor-suppressor gene that has been shown to be under the regulatory control of a PTEN pseudogene expressed noncoding RNA, PTENpg1. Here, we characterize a previously unidentified PTENpg1-encoded antisense RNA (asRNA), which regulates PTEN transcription and PTEN mRNA stability. We find two PTENpg1 asRNA isoforms, α and β. The α isoform functions in trans, localizes to the PTEN promoter and epigenetically modulates PTEN transcription by the recruitment of DNA methyltransferase 3a and Enhancer of Zeste. In contrast, the β isoform interacts with PTENpg1 through an RNA-RNA pairing interaction, which affects PTEN protein output through changes of PTENpg1 stability and microRNA sponge activity. Disruption of this asRNA-regulated network induces cell-cycle arrest and sensitizes cells to doxorubicin, which suggests a biological function for the respective PTENpg1 expressed asRNAs.

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Figure 1: High expression of PTENpg1 asRNA correlates with low PTEN mRNA expression.
Figure 2: Functional characterization of PTENpg1 asRNA α.
Figure 3: Mechanistic insights into PTENpg1 asRNA α regulation of PTEN.
Figure 4: Mechanistic insights into PTENpg1 asRNA β regulation of PTENpg1.
Figure 5: Functional impact of PTENpg1 asRNA α.
Figure 6: Model of PTENpg1 asRNA–based regulation of PTEN.

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References

  1. Xing, M. Genetic alterations in the phosphatidylinositol-3 kinase/Akt pathway in thyroid cancer. Thyroid 20, 697–706 (2010).

    Article  CAS  Google Scholar 

  2. Alimonti, A. et al. Subtle variations in Pten dose determine cancer susceptibility. Nat. Genet. 42, 454–458 (2010).

    Article  CAS  Google Scholar 

  3. Poliseno, L. et al. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature 465, 1033–1038 (2010).

    Article  CAS  Google Scholar 

  4. Khachane, A.N. & Harrison, P.M. Assessing the genomic evidence for conserved transcribed pseudogenes under selection. BMC Genomics 10, 435 (2009).

    Article  Google Scholar 

  5. Pei, B. et al. The GENCODE pseudogene resource. Genome Biol. 13, R51 (2012).

    Article  CAS  Google Scholar 

  6. Suo, G. et al. Oct4 pseudogenes are transcribed in cancers. Biochem. Biophys. Res. Commun. 337, 1047–1051 (2005).

    Article  CAS  Google Scholar 

  7. Hawkins, P.G. & Morris, K.V. Transcriptional regulation of Oct4 by a long non-coding RNA antisense to Oct4-pseudogene 5. Transcription 1, 165–175 (2010).

    Article  Google Scholar 

  8. Lin, H., Shabbir, A., Molnar, M. & Lee, T. Stem cell regulatory function mediated by expression of a novel mouse Oct4 pseudogene. Biochem. Biophys. Res. Commun. 355, 111–116 (2007).

    Article  CAS  Google Scholar 

  9. Piehler, A.P. et al. The human ABC transporter pseudogene family: evidence for transcription and gene-pseudogene interference. BMC Genomics 9, 165 (2008).

    Article  Google Scholar 

  10. Morris, K.V., Santoso, S., Turner, A.M., Pastori, C. & Hawkins, P.G. Bidirectional transcription directs both transcriptional gene activation and suppression in human cells. PLoS Genet. 4, e1000258 (2008).

    Article  Google Scholar 

  11. Yu, W. et al. Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA. Nature 451, 202–206 (2008).

    Article  CAS  Google Scholar 

  12. Yap, K.L. et al. Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a. Mol. Cell 38, 662–674 (2010).

    Article  CAS  Google Scholar 

  13. Weinberg, M.S. et al. The antisense strand of small interfering RNAs directs histone methylation and transcriptional gene silencing in human cells. RNA 12, 256–262 (2006).

    Article  CAS  Google Scholar 

  14. Turner, A.M., Ackley, A.M., Matrone, M.A. & Morris, K.V. Characterization of an HIV-targeted transcriptional gene-silencing RNA in primary cells. Hum. Gene Ther. 23, 473–483 (2012).

    Article  CAS  Google Scholar 

  15. Jeffery, L. & Nakielny, S. Components of the DNA methylation system of chromatin control are RNA-binding proteins. J. Biol. Chem. 279, 49479–49487 (2004).

    Article  CAS  Google Scholar 

  16. Viré, E. et al. The Polycomb group protein EZH2 directly controls DNA methylation. Nature 439, 871–874 (2006).

    Article  Google Scholar 

  17. Malecová, B. & Morris, K.V. Transcriptional gene silencing through epigenetic changes mediated by non-coding RNAs. Curr. Opin. Mol. Ther. 12, 214–222 (2010).

    PubMed  PubMed Central  Google Scholar 

  18. Kuzmichev, A., Nishioka, K., Erdjument-Bromage, H., Tempst, P. & Reinberg, D. Histone methyltransferase activity associated with a human multiprotein complex containing the Enhancer of Zeste protein. Genes Dev. 16, 2893–2905 (2002).

    Article  CAS  Google Scholar 

  19. Cao, R. et al. Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 298, 1039–1043 (2002).

    Article  CAS  Google Scholar 

  20. Han, J., Kim, D. & Morris, K.V. Promoter-associated RNA is required for RNA-directed transcriptional gene silencing in human cells. Proc. Natl. Acad. Sci. USA 104, 12422–12427 (2007).

    Article  CAS  Google Scholar 

  21. Bernstein, P., Peltz, S.W. & Ross, J. The poly(A)-poly(A)-binding protein complex is a major determinant of mRNA stability in vitro. Mol. Cell Biol. 9, 659–670 (1989).

    Article  CAS  Google Scholar 

  22. Fuke, H. & Ohno, M. Role of poly (A) tail as an identity element for mRNA nuclear export. Nucleic Acids Res. 36, 1037–1049 (2008).

    Article  CAS  Google Scholar 

  23. Brodsky, A.S. & Silver, P.A. Pre-mRNA processing factors are required for nuclear export. RNA 6, 1737–1749 (2000).

    Article  CAS  Google Scholar 

  24. Mahmoudi, S. et al. Wrap53, a natural p53 antisense transcript required for p53 induction upon DNA damage. Mol. Cell 33, 462–471 (2009).

    Article  CAS  Google Scholar 

  25. Chang, F. et al. Involvement of PI3K/Akt pathway in cell cycle progression, apoptosis, and neoplastic transformation: a target for cancer chemotherapy. Leukemia 17, 590–603 (2003).

    Article  CAS  Google Scholar 

  26. Weng, L., Brown, J. & Eng, C. PTEN induces apoptosis and cell cycle arrest through phosphoinositol-3-kinase/Akt-dependent and -independent pathways. Hum. Mol. Genet. 10, 237–242 (2001).

    Article  CAS  Google Scholar 

  27. Ebert, M.S., Neilson, J.R. & Sharp, P.A. MicroRNA sponges: competitive inhibitors of small RNAs in mammalian cells. Nat. Methods 4, 721–726 (2007).

    Article  CAS  Google Scholar 

  28. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).

    Article  Google Scholar 

  29. Robinson, J.T. et al. Integrative genomics viewer. Nat. Biotechnol. 29, 24–26 (2011).

    Article  CAS  Google Scholar 

  30. Amarzguioui, M., Rossi, J.J. & Kim, D. Approaches for chemically synthesized siRNA and vector-mediated RNAi. FEBS Lett. 579, 5974–5981 (2005).

    Article  CAS  Google Scholar 

  31. Polson, A., Durrett, E. & Reisman, D. A bidirectional promoter reporter vector for the analysis of the p53/WDR79 dual regulatory element. Plasmid 66, 169–179 (2011).

    Article  CAS  Google Scholar 

  32. Han, J., Kim, D. & Morris, K.V. Promoter-associated RNA is required for RNA-directed transcriptional gene silencing in human cells. Proc. Natl. Acad. Sci. USA 104, 12422–12427 (2007).

    Article  CAS  Google Scholar 

  33. Weinberg, M.S. et al. The antisense strand of small interfering RNAs directs histone methylation and transcriptional gene silencing in human cells. RNA 12, 256–262 (2006).

    Article  CAS  Google Scholar 

  34. Turner, A.M., De La Cruz, J. & Morris, K.V. Mobilization-competent lentiviral vector-mediated sustained transcriptional modulation of HIV-1 expression. Mol. Ther. 17, 360–368 (2009).

    Article  CAS  Google Scholar 

  35. Turner, A.M., Ackley, A.M., Matrone, M.A. & Morris, K.V. Characterization of an HIV-targeted transcriptional gene-silencing RNA in primary cells. Hum. Gene Ther. 23, 473–483 (2012).

    Article  CAS  Google Scholar 

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Acknowledgements

The project was supported by: the US National Institute of Allergy and Infectious Disease grants R56 AI096861-01 and P01 AI099783-01 to K.V.M. and National Cancer Institute grant R01 CA151574 and US National Institutes of Health grant R01 CA153124 to P.K. Vogt (supporting K.V.M.); the Swedish Childhood Cancer Foundation, The Swedish Cancer Society, Radiumhemmets Forskningsfonder, the Karolinska Institutet PhD support programme and Vetenskapsrådet to D.G.; and the Erik and Edith Fernstrom Foundation for medical research to P.J. and the Swedish Childhood Cancer Foundation.

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Author notes

  1. Amanda Ackley and Linda Vidarsdottir: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden

    Per Johnsson, Linda Vidarsdottir, Weng-Onn Lui, Martin Corcoran & Dan Grandér

  2. Department of Molecular and Experimental Medicine, Scripps Research Institute, La Jolla, California, USA

    Amanda Ackley & Kevin V Morris

  3. School of Biotechnology and Biomedical Sciences, University of New South Wales, Sydney, Australia

    Kevin V Morris

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  1. Per Johnsson
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Contributions

P.J. and K.V.M. designed, performed and supervised the experiments. A.A. and L.V. performed experiments. M.C. provided helpful discussions. W.-O.L. supervised ChIP-sequencing analysis. D.G. supervised the experiments. P.J., D.G. and K.V.M. wrote the paper.

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Correspondence to Dan Grandér or Kevin V Morris.

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The authors declare no competing financial interests.

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Johnsson, P., Ackley, A., Vidarsdottir, L. et al. A pseudogene long-noncoding-RNA network regulates PTEN transcription and translation in human cells. Nat Struct Mol Biol 20, 440–446 (2013). https://doi.org/10.1038/nsmb.2516

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