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The H19 lincRNA is a developmental reservoir of miR-675 that suppresses growth and Igf1r

Abstract

The H19 large intergenic non-coding RNA (lincRNA) is one of the most highly abundant and conserved transcripts in mammalian development, being expressed in both embryonic and extra-embryonic cell lineages, yet its physiological function is unknown. Here we show that miR-675, a microRNA (miRNA) embedded in H19’s first exon, is expressed exclusively in the placenta from the gestational time point when placental growth normally ceases, and placentas that lack H19 continue to grow. Overexpression of miR-675 in a range of embryonic and extra-embryonic cell lines results in their reduced proliferation; targets of the miRNA are upregulated in the H19 null placenta, including the growth-promoting insulin-like growth factor 1 receptor (Igf1r) gene. Moreover, the excision of miR-675 from H19 is dynamically regulated by the stress-response RNA-binding protein HuR. These results suggest that H19’s main physiological role is in limiting growth of the placenta before birth, by regulated processing of miR-675. The controlled release of miR-675 from H19 may also allow rapid inhibition of cell proliferation in response to cellular stress or oncogenic signals.

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Figure 1: miR-675 is expressed in the late gestation placenta but suppressed in the embryo.
Figure 2: H u R binds to full-length H19 and inhibits processing of miR-675.
Figure 3: Evidence that HuR inhibits miR-675 at the Drosha processing step.
Figure 4: miR-675 overexpression decreases the proliferation rate of a number of cultured cell lines.
Figure 5: The phenotype and transcriptome of the H19Δ3 placenta imply that miR-675 is a negative growth regulator in this tissue.
Figure 6: Identification of miR-675 targets.

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References

  1. Brannan, C. I., Dees, E. C., Ingram, R. S. & Tilghman, S. M. The product of the H19 gene may function as an RNA. Mol. Cell. Biol. 10, 28–36 (1990).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Seidl, C. I., Stricker, S. H. & Barlow, D. P. The imprinted Air ncRNA is an atypical RNAPII transcript that evades splicing and escapes nuclear export. EMBO. J. 25, 3565–3575 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Bartolomei, M. S. Genomic imprinting: employing and avoiding epigenetic processes. Genes Dev. 23, 2124–2133 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Gabory, A., Jammes, H. & Dandolo, L. The H19 locus: role of an imprinted non-coding RNA in growth and development. Bioessays 32, 473–480 (2010).

    Article  CAS  PubMed  Google Scholar 

  5. Hao, Y., Crenshaw, T., Moulton, T., Newcomb, E. & Tycko, B. Tumour-suppressor activity of H19 RNA. Nature 365, 764–767 (1993).

    Article  CAS  PubMed  Google Scholar 

  6. Yoshimizu, T. et al. The H19 locus acts in vivo as a tumor suppressor. Proc. Natl Acad. Sci. USA 105, 12417–12422 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Smits, G. et al. Conservation of the H19 noncoding RNA and H19-IGF2 imprinting mechanism in therians. Nat. Genet. 40, 971–976 (2008).

    Article  CAS  PubMed  Google Scholar 

  8. Gabory, A. et al. H19 acts as a trans regulator of the imprinted gene network controlling growth in mice. Development 136, 3413–3421 (2009).

    Article  CAS  PubMed  Google Scholar 

  9. Wilusz, J. E., Sunwoo, H. & Spector, D. L. Long noncoding RNAs: functional surprises from the RNA world. Genes Dev. 23, 1494–1504 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Bartel, D. P. MicroRNAs: target recognition and regulatory functions. Cell 136, 215–233 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Huntzinger, E. & Izaurralde, E. Gene silencing by microRNAs: contributions of translational repression and mRNA decay. Nat. Rev. Genet. 12, 99–110 (2011).

    CAS  PubMed  Google Scholar 

  12. Cai, X. & Cullen, B. R. The imprinted H19 noncoding RNA is a primary microRNA precursor. RNA 13, 313–316 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Dudek, K. A., Lafont, J. E., Martinez-Sanchez, A. & Murphy, C. L. Type II collagen expression is regulated by tissue-specific miR-675 in human articular chondrocytes. J. Biol. Chem. 285, 24381–24387 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Chiang, H. R. et al. Mammalian microRNAs: experimental evaluation of novel and previously annotated genes. Genes Dev. 24, 992–1009 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Mineno, J. et al. The expression profile of microRNAs in mouse embryos. Nucleic Acids Res. 34, 1765–1771 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Yang, J. H., Shao, P., Zhou, H., Chen, Y. Q. & Qu, L. H. deepBase: a database for deeply annotating and mining deep sequencing data. Nucleic Acids Res. 38, D123-D130 (2010).

    Google Scholar 

  17. Lee, Y. S. & Dutta, A. The tumor suppressor microRNA let-7 represses the HMGA2 oncogene. Genes Dev. 21, 1025–1030 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Lim, L. P. et al. The microRNAs of Caenorhabditis elegans. Genes Dev. 17, 991–1008 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Knox, K. & Baker, J. C. Genomic evolution of the placenta using co-option and duplication and divergence. Genome Res. 18, 695–705 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Zhao, Z., Chang, F. C. & Furneaux, H. M. The identification of an endonuclease that cleaves within an HuR binding site in mRNA. Nucleic Acids Res. 28, 2695–2701 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Katsanou, V. et al. The RNA-binding protein Elavl1/HuR is essential for placental branching morphogenesis and embryonic development. Mol. Cell. Biol. 29, 2762–2776 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Kim, V. N., Han, J. & Siomi, M. C. Biogenesis of small RNAs in animals. Nat. Rev. Mol. Cell Biol. 10, 126–139 (2009).

    Article  CAS  PubMed  Google Scholar 

  23. Runge, S. et al. H19 RNA binds four molecules of insulin-like growth factor II mRNA-binding protein. J. Biol. Chem. 275, 29562–29569 (2000).

    Article  CAS  PubMed  Google Scholar 

  24. Mallanna, S. K. et al. Proteomic analysis of Sox2-associated proteins during early stages of mouse embryonic stem cell differentiation identifies Sox21 as a novel regulator of stem cell fate. Stem Cells 28, 1715–1727 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Coan, P. M., Ferguson-Smith, A. C. & Burton, G. J. Developmental dynamics of the definitive mouse placenta assessed by stereology. Biol. Reprod. 70, 1806–1813 (2004).

    Article  CAS  PubMed  Google Scholar 

  26. Angiolini, E. et al. Developmental adaptations to increased fetal nutrient demand in mouse genetic models of Igf2-mediated overgrowth. FASEB J. 25, 1737–1745 (2011).

    Article  CAS  PubMed  Google Scholar 

  27. Esquiliano, D. R., Guo, W., Liang, L., Dikkes, P. & Lopez, M. F. Placental glycogen stores are increased in mice with H19 null mutations but not in those with insulin or IGF type 1 receptor mutations. Placenta 30, 693–699 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Leighton, P. A., Ingram, R. S., Eggenschwiler, J., Efstratiadis, A. & Tilghman, S. M. Disruption of imprinting caused by deletion of the H19 gene region in mice. Nature 375, 34–39 (1995).

    Article  CAS  PubMed  Google Scholar 

  29. Thorvaldsen, J. L., Duran, K. L. & Bartolomei, M. S. Deletion of the H19 differentially methylated domain results in loss of imprinted expression of H19 and Igf2. Genes Dev. 12, 3693–3702 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Ripoche, M. A., Kress, C., Poirier, F. & Dandolo, L. Deletion of the H19 transcription unit reveals the existence of a putative imprinting control element. Genes Dev. 11, 1596–1604 (1997).

    Article  CAS  PubMed  Google Scholar 

  31. Liu, J. P., Baker, J., Perkins, A. S., Robertson, E. J. & Efstratiadis, A. Mice carrying null mutations of the genes encoding insulin-like growth factor I (Igf-1) and type 1 IGF receptor (Igf1r). Cell 75, 59–72 (1993).

    CAS  PubMed  Google Scholar 

  32. Baker, J., Liu, J. P., Robertson, E. J. & Efstratiadis, A. role of insulin-like growth factors in embryonic and postnatal growth. Cell 75, 73–82 (1993).

    Article  CAS  PubMed  Google Scholar 

  33. Jeyaraj, S. C., Dakhlallah, D., Hill, S. R. & Lee, B.S. Expression and distribution of HuR during ATP depletion and recovery in proximal tubule cells. Am. J. Physiol. Renal. Physiol. 291, F1255–F1263 (2006).

    Article  CAS  PubMed  Google Scholar 

  34. Kim, H. H., Abdelmohsen, K. & Gorospe, M. Regulation of HuR by DNA damage response kinases. J. Nucleic Acids 2010 (2010).

  35. Pan, Y. X., Chen, H. & Kilberg, M. S. Interaction of RNA-binding proteins HuR and AUF1 with the human ATF3 mRNA 3’-untranslated region regulates its amino acid limitation-induced stabilization. J. Biol. Chem. 280, 34609–34616 (2005).

    Article  CAS  PubMed  Google Scholar 

  36. Wang, W. et al. HuR regulates p21 mRNA stabilization by UV light. Mol. Cell. Biol. 20, 760–769 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Blaxall, B. C. et al. Differential expression and localization of the mRNA binding proteins, AU-rich element mRNA binding protein (AUF1) and Hu antigen R (HuR), in neoplastic lung tissue. Mol. Carcinog. 28, 76–83 (2000).

    Article  CAS  PubMed  Google Scholar 

  38. Lebedeva, S. et al. Transcriptome-wide analysis of regulatory interactions of the RNA-binding protein HuR. Mol. Cell 43, 340–352 (2011).

    Article  CAS  PubMed  Google Scholar 

  39. Reddy, S. D., Ohshiro, K., Rayala, S. K. & Kumar, R. MicroRNA-7, a homeobox D10 target, inhibits p21-activated kinase 1 and regulates its functions. Cancer Res. 68, 8195–8200 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Saydam, O. et al. miRNA-7 attenuation in Schwannoma tumors stimulates growth by upregulating three oncogenic signaling pathways. Cancer Res. 71, 852–861 (2011).

    Article  CAS  PubMed  Google Scholar 

  41. Jiang, L. et al. MicroRNA-7 targets IGF1R (insulin-like growth factor 1 receptor) in tongue squamous cell carcinoma cells. Biochem. J. 432, 199–205 (2010).

    Article  CAS  PubMed  Google Scholar 

  42. Lim, D. H. & Maher, E. R. Genomic imprinting syndromes and cancer. Adv. Genet. 70, 145–175 (2010).

    Article  CAS  PubMed  Google Scholar 

  43. Tanaka, S., Kunath, T., Hadjantonakis, A. K., Nagy, A. & Rossant, J. Promotion of trophoblast stem cell proliferation by FGF4. Science 282, 2072–2075 (1998).

    Article  CAS  PubMed  Google Scholar 

  44. Ficz, G. et al. Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation. Nature 473, 398–402 (2011).

    Article  CAS  PubMed  Google Scholar 

  45. Caputi, M., Mayeda, A., Krainer, A. R. & Zahler, A. M. hnRNP A/B proteins are required for inhibition of HIV-1 pre-mRNA splicing. EMBO J. 18, 4060–4067 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Baroni, T. E., Chittur, S. V., George, A. D. & Tenenbaum, S. A. Advances in RIP-chip analysis: RNA-binding protein immunoprecipitation-microarray profiling. Methods Mol. Biol. 419, 93–108 (2008).

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

We thank D. L. Kontoyiannis (Alexander Fleming Biomedical Sciences Research Center, Greece) for supplying H u R−/− MEF cells. We also thank H. Jammes and A. Gabory for assisting with collection of the H19Δ3 phenotypic data, J. Webster for preparing samples for mass spectrometry and W. Dean for tissue collections. The authors would also like to thank K. Tabbada, A. Segonds-Pichon and S. Andrews for RNA sequencing, statistical and bioinformatic assistance, respectively. We thank M. Iacovino for creating the A2lox-cre ES cell line. We would also like to thank T. Hore, C. Krueger and J. Houseley for critical reading of the manuscript and all members of the laboratories of W. Reik, M. Hemberger, E. Vigorito and J. Houseley for helpful discussions. This work was supported by BBSRC, the Wellcome Trust, MRC, EU NoE EpiGeneSys, EU BLUEPRINT, NIH/NHLBI (U01HL100407) and the Cambridge Commonwealth Trust.

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A.K. designed and carried out experiments and interpreted results. D.O. performed mass spectrometry. P.M. collected and dissected placentas for RNA sequencing. M.K. made the A2lox.cre ES cell line. L.D., G.S. and W.R. designed and supervised this work and interpreted results. A.K. and W.R. wrote the manuscript.

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Correspondence to Wolf Reik.

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Keniry, A., Oxley, D., Monnier, P. et al. The H19 lincRNA is a developmental reservoir of miR-675 that suppresses growth and Igf1r. Nat Cell Biol 14, 659–665 (2012). https://doi.org/10.1038/ncb2521

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