Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

miR-129-3p controls cilia assembly by regulating CP110 and actin dynamics

Nature Cell Biology volume 14, pages 697–706 (2012)Cite this article

Subjects

Abstract

Ciliogenesis requires the removal of CP110 from the mother centriole; actin dynamics also influence ciliation, at least partly by affecting the centrosomal accumulation of ciliogenic membrane vesicles. How these distinct processes are properly regulated remains unknown. Here we show that miR-129-3p, a microRNA conserved in vertebrates, controlled cilia biogenesis in cultured cells by concomitantly downregulating CP110 and repressing branched F-actin formation. Blocking miR-129-3p inhibited serum-starvation-induced ciliogenesis, whereas its overexpression potently induced ciliation in proliferating cells and also promoted cilia elongation. Gene expression analysis further identified ARP2, TOCA1, ABLIM1 and ABLIM3 as its targets in ciliation-related actin dynamics. Moreover, miR-129-3p inhibition in zebrafish embryos suppressed ciliation in Kupffer’s vesicle and the pronephros, and induced developmental abnormalities including a curved body, pericardial oedema and defective left–right asymmetry. Therefore, our results reveal a mechanism that orchestrates both the centriole-to-basal body transition and subsequent cilia assembly through microRNA-mediated post-transcriptional regulation.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: miR-129-3p is an important ciliogenic regulator that targets CP110.
Figure 2: miR-129-3p represses branched F-actin formation and stimulates the centrosomal accumulation of the PPC.
Figure 3: miR-129-3p targets multiple actin regulators that are critical for ciliation.
Figure 4: M129-induced ciliation is attributed to the downregulation of both CP110 and the actin regulators.
Figure 5: The expression levels of miR-129-3p and its target proteins alter following serum starvation.
Figure 6: miR-129-3p is specifically expressed in ciliated mouse tissues.
Figure 7: dre-miR-129* is critical for cilia formation and function in zebrafish.

Similar content being viewed by others

Accession codes

Primary accessions

Gene Expression Omnibus

References

  1. Fliegauf, M., Benzing, T. & Omran, H. When cilia go bad: cilia defects and ciliopathies. Nat. Rev. Mol. Cell Biol. 8, 880–893 (2007).

    Article  CAS  Google Scholar 

  2. Nigg, E. A. & Raff, J. W. Centrioles, centrosomes, and cilia in health and disease. Cell 139, 663–678 (2009).

    Article  CAS  Google Scholar 

  3. Berbari, N. F., O’Connor, A. K., Haycraft, C. J. & Yoder, B. K. The primary cilium as a complex signaling center. Curr. Biol. 19, R526–R535 (2009).

    Article  CAS  Google Scholar 

  4. Goetz, S. C. & Anderson, K. V. The primary cilium: a signalling centre during vertebrate development. Nat. Rev. Genet. 11, 331–344 (2010).

    Article  CAS  Google Scholar 

  5. Lawrence, C. J. et al. A standardized kinesin nomenclature. J. Cell Biol. 167, 19–22 (2004).

    Article  CAS  Google Scholar 

  6. Spektor, A., Tsang, W. Y., Khoo, D. & Dynlacht, B. D. Cep97 and CP110 suppress a cilia assembly program. Cell 130, 678–690 (2007).

    Article  CAS  Google Scholar 

  7. Kobayashi, T., Tsang, W. Y., Li, J., Lane, W. & Dynlacht, B. D. Centriolar kinesin Kif24 interacts with CP110 to remodel microtubules and regulate ciliogenesis. Cell 145, 914–925 (2011).

    Article  CAS  Google Scholar 

  8. Schmidt, T. I. et al. Control of centriole length by CPAP and CP110. Curr. Biol. 19, 1005–1011 (2009).

    Article  CAS  Google Scholar 

  9. Seeley, E. S. & Nachury, M. V. The perennial organelle: assembly and disassembly of the primary cilium. J. Cell Sci. 123, 511–518 (2010).

    Article  CAS  Google Scholar 

  10. Nachury, M. V. et al. A core complex of BBS proteins cooperates with the GTPase Rab8 to promote ciliary membrane biogenesis. Cell 129, 1201–1213 (2007).

    Article  CAS  Google Scholar 

  11. Tsang, W. Y. et al. CP110 suppresses primary cilia formation through its interaction with CEP290, a protein deficient in human ciliary disease. Dev. Cell 15, 187–197 (2008).

    Article  CAS  Google Scholar 

  12. Kobayashi, T. & Dynlacht, B. D. Regulating the transition from centriole to basal body. J. Cell Biol. 193, 435–444 (2011).

    Article  CAS  Google Scholar 

  13. Westlake, C. J. et al. Primary cilia membrane assembly is initiated by Rab11 and transport protein particle II (TRAPPII) complex-dependent trafficking of Rabin8 to the centrosome. Proc. Natl Acad. Sci. USA 108, 2759–2764 (2011).

    Article  CAS  Google Scholar 

  14. Knodler, A. et al. Coordination of Rab8 and Rab11 in primary ciliogenesis. Proc. Natl Acad. Sci. USA 107, 6346–6351 (2010).

    Article  CAS  Google Scholar 

  15. Stenmark, H. Rab GTPases as coordinators of vesicle traffic. Nat. Rev. Mol. Cell Biol. 10, 513–525 (2009).

    Article  CAS  Google Scholar 

  16. Kim, J. et al. Functional genomic screen for modulators of ciliogenesis and cilium length. Nature 464, 1048–1051 (2010).

    Article  CAS  Google Scholar 

  17. Filipowicz, W., Bhattacharyya, S.N. & Sonenberg, N. Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nat. Rev. Genet. 9, 102–114 (2008).

    Article  CAS  Google Scholar 

  18. Flynt, A. S. & Lai, E. C. Biological principles of microRNA-mediated regulation: shared themes amid diversity. Nat. Rev. Genet. 9, 831–842 (2008).

    Article  CAS  Google Scholar 

  19. Tsang, J. S., Ebert, M. S. & van Oudenaarden, A. Genome-wide dissection of microRNA functions and cotargeting networks using gene set signatures. Mol. Cell 38, 140–153 (2010).

    Article  CAS  Google Scholar 

  20. Marcet, B. et al. Control of vertebrate multiciliogenesis by miR-449 through direct repression of the Delta/Notch pathway. Nat. Cell Biol. 13, 694–701 (2011).

    Google Scholar 

  21. Dyrskjot, L. et al. Genomic profiling of microRNAs in bladder cancer: miR-129 is associated with poor outcome and promotes cell death in vitro. Cancer Res. 69, 4851–4860 (2009).

    Article  CAS  Google Scholar 

  22. Wu, J. et al. miR-129 regulates cell proliferation by downregulating Cdk6 expression. Cell Cycle 9, 1809–1818 (2010).

    Article  CAS  Google Scholar 

  23. 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 

  24. Huang, Y. W. et al. Epigenetic repression of microRNA-129-2 leads to overexpression of SOX4 oncogene in endometrial cancer. Cancer Res. 69, 9038–9046 (2009).

    Article  CAS  Google Scholar 

  25. Shan, Y. et al. Nudel and FAK as antagonizing strength modulators of nascent adhesions through paxillin. PLoS Biol. 7, e1000116 (2009).

    Article  Google Scholar 

  26. Chhabra, E. S. & Higgs, H. N. The many faces of actin: matching assembly factors with cellular structures. Nat. Cell Biol. 9, 1110–1121 (2007).

    Article  CAS  Google Scholar 

  27. Shen, Y. et al. Nudel binds Cdc42GAP to modulate Cdc42 activity at the leading edge of migrating cells. Dev. Cell 14, 342–353 (2008).

    Article  CAS  Google Scholar 

  28. Goley, E. D. & Welch, M. D. The ARP2/3 complex: an actin nucleator comes of age. Nat. Rev. Mol. Cell Biol. 7, 713–726 (2006).

    Article  CAS  Google Scholar 

  29. Lim, L. P. et al. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433, 769–773 (2005).

    Article  CAS  Google Scholar 

  30. Ho, H. Y. et al. Toca-1 mediates Cdc42-dependent actin nucleation by activating the N-WASP-WIP complex. Cell 118, 203–216 (2004).

    Article  CAS  Google Scholar 

  31. Barrientos, T. et al. Two novel members of the ABLIM protein family, ABLIM-2 and -3, associate with STARS and directly bind F-actin. J. Biol. Chem. 282, 8393–8403 (2007).

    Article  CAS  Google Scholar 

  32. Roof, D. J., Hayes, A., Adamian, M., Chishti, A. H. & Li, T. Molecular characterization of abLIM, a novel actin-binding and double zinc finger protein. J. Cell Biol. 138, 575–588 (1997).

    Article  CAS  Google Scholar 

  33. Zaoui, K., Honore, S., Isnardon, D., Braguer, D. & Badache, A. Memo-RhoA-mDia1 signaling controls microtubules, the actin network, and adhesion site formation in migrating cells. J. Cell Biol. 183, 401–408 (2008).

    Article  CAS  Google Scholar 

  34. Demarco, R. S. & Lundquist, E. A. RACK-1 acts with Rac GTPase signaling and UNC-115/abLIM in Caenorhabditis elegans axon pathfinding and cell migration. PLoS Genet. 6, e1001215 (2010).

    Article  Google Scholar 

  35. Norris, A. D., Dyer, J. O. & Lundquist, E. A. The Arp2/3 complex, UNC-115/abLIM, and UNC-34/Enabled regulate axon guidance and growth cone filopodia formation in Caenorhabditis elegans. Neural Dev. 4, 38–57 (2009).

    Article  Google Scholar 

  36. Struckhoff, E. C. & Lundquist, E. A. The actin-binding protein UNC-115 is an effector of Rac signaling during axon pathfinding in C. elegans. Development 130, 693–704 (2003).

    Article  CAS  Google Scholar 

  37. Zhang, Q., Taulman, P. D. & Yoder, B. K. Cystic kidney diseases: all roads lead to the cilium. Physiology (Bethesda) 19, 225–230 (2004).

    CAS  Google Scholar 

  38. Deane, J. A. & Ricardo, S. D. Polycystic kidney disease and the renal cilium. Nephrology (Carlton) 12, 559–564 (2007).

    Article  CAS  Google Scholar 

  39. Fuchs, J. L. & Schwark, H. D. Neuronal primary cilia: a review. Cell Biol. Int. 28, 111–118 (2004).

    Article  CAS  Google Scholar 

  40. Bishop, G. A., Berbari, N. F., Lewis, J. & Mykytyn, K. Type III adenylyl cyclase localizes to primary cilia throughout the adult mouse brain. J. Comp. Neurol. 505, 562–571 (2007).

    Article  Google Scholar 

  41. Bachmann-Gagescu, R. et al. The ciliopathy gene cc2d2a controls zebrafish photoreceptor outer segment development through a role in Rab8-dependent vesicle trafficking. Hum. Mol. Genet. 20, 4041–4055 (2011).

    Article  CAS  Google Scholar 

  42. Sedmak, T. & Wolfrum, U. Intraflagellar transport proteins in ciliogenesis of photoreceptor cells. Biol. Cell 103, 449–466 (2011).

    Article  CAS  Google Scholar 

  43. Tramontin, A. D., Garcia-Verdugo, J. M., Lim, D. A. & Alvarez-Buylla, A. Postnatal development of radial glia and the ventricular zone (VZ): a continuum of the neural stem cell compartment. Cereb. Cortex 13, 580–587 (2003).

    Article  Google Scholar 

  44. Vladar, E. K. & Stearns, T. Molecular characterization of centriole assembly in ciliated epithelial cells. J. Cell Biol. 178, 31–42 (2007).

    Article  CAS  Google Scholar 

  45. Kramer-Zucker, A. G. et al. Cilia-driven fluid flow in the zebrafish pronephros, brain and Kupffer’s vesicle is required for normal organogenesis. Development 132, 1907–1921 (2005).

    Article  CAS  Google Scholar 

  46. Wessely, O. & Obara, T. Fish and frogs: models for vertebrate cilia signaling. Front Biosci. 13, 1866–1880 (2008).

    Article  CAS  Google Scholar 

  47. Yelon, D., Horne, S. A. & Stainier, D. Y. Restricted expression of cardiac myosin genes reveals regulated aspects of heart tube assembly in zebrafish. Dev. Biol. 214, 23–37 (1999).

    Article  CAS  Google Scholar 

  48. Essner, J. J., Amack, J. D., Nyholm, M. K., Harris, E. B. & Yost, H. J. Kupffer’s vesicle is a ciliated organ of asymmetry in the zebrafish embryo that initiates left–right development of the brain, heart and gut. Development 132, 1247–1260 (2005).

    Article  CAS  Google Scholar 

  49. Ma, M. & Jiang, Y. J. Jagged2a-notch signaling mediates cell fate choice in the zebrafish pronephric duct. PLoS Genet. 3, e18 (2007).

    Article  Google Scholar 

  50. Pitaval, A., Tseng, Q., Bornens, M. & Thery, M. Cell shape and contractility regulate ciliogenesis in cell cycle-arrested cells. J. Cell Biol. 191, 303–312 (2010).

    Article  CAS  Google Scholar 

  51. Pugacheva, E. N., Jablonski, S. A., Hartman, T. R., Henske, E. P. & Golemis, E. A. HEF1-dependent Aurora A activation induces disassembly of the primary cilium. Cell 129, 1351–1363 (2007).

    Article  CAS  Google Scholar 

  52. Huang, C., Jacobson, K. & Schaller, M. D. MAP kinases and cell migration. J. Cell Sci. 117, 4619–4628 (2004).

    Article  CAS  Google Scholar 

  53. Burridge, K. & Wennerberg, K. Rho and Rac take center stage. Cell 116, 167–179 (2004).

    Article  CAS  Google Scholar 

  54. Selbach, M. et al. Widespread changes in protein synthesis induced by microRNAs. Nature 455, 58–63 (2008).

    Article  CAS  Google Scholar 

  55. Rottner, K., Hanisch, J. & Campellone, K. G. WASH, WHAMM and JMY: regulation of Arp2/3 complex and beyond. Trends Cell Biol. 20, 650–661 (2010).

    Article  CAS  Google Scholar 

  56. You, Y., Richer, E. J., Huang, T. & Brody, S. L. Growth and differentiation of mouse tracheal epithelial cells: selection of a proliferative population. Am. J. Physiol. Lung Cell Mol. Physiol. 283, L1315–L1321 (2002).

    Article  CAS  Google Scholar 

  57. Gentner, B. et al. Stable knockdown of microRNA in vivo by lentiviral vectors. Nat. Methods 6, 63–66 (2009).

    Article  CAS  Google Scholar 

  58. Matsuda, T. & Cepko, C. L. Electroporation and RNA interference in the rodent retina in vivo and in vitro. Proc. Natl Acad. Sci. USA 101, 16–22 (2004).

    Article  CAS  Google Scholar 

  59. Tang, C. J., Fu, R. H., Wu, K. S., Hsu, W. B. & Tang, T. K. CPAP is a cell-cycle regulated protein that controls centriole length. Nat. Cell Biol. 11, 825–831 (2009).

    Article  CAS  Google Scholar 

  60. Wloga, D. et al. TTLL3 Is a tubulin glycine ligase that regulates the assembly of cilia. Dev. Cell 16, 867–876 (2009).

    Article  CAS  Google Scholar 

  61. Chen, C. et al. Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res. 33, e179 (2005).

    Article  Google Scholar 

  62. Pena, J. T. et al. miRNA in situ hybridization in formaldehyde and EDC-fixed tissues. Nat. Methods 6, 139–141 (2009).

    Article  CAS  Google Scholar 

  63. Kloosterman, W. P., Wienholds, E., de Bruijn, E., Kauppinen, S. & Plasterk, R. H. In situ detection of miRNAs in animal embryos using LNA-modified oligonucleotide probes. Nat. Methods 3, 27–29 (2006).

    Article  CAS  Google Scholar 

  64. Oxtoby, E. & Jowett, T. Cloning of the zebrafish krox-20 gene (krx-20) and its expression during hindbrain development. Nucleic Acids Res. 21, 1087–1095 (1993).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

The authors thank X. Yuan and D. Li for helpful suggestions, and Y. You, S. L. Brody (Washington University School of Medicine) and D. J. Davidson (University of Edinburgh) for tips on MTEC culture. We also thank H. Zhao, M. Yao, J. Sun and Y. Wang for technical assistance. This work was supported by the National Basic Research Program of China (2012CB945003 and 2010CB912102), the National Science Foundation of China (30971430, 30830060 and 31010103910) and the Chinese Academy of Sciences (XDA01010107).

Author information

Author notes

  1. Jingli Cao and Yidong Shen: These authors contributed equally to this work

Authors and Affiliations

  1. State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China

    Jingli Cao, Yidong Shen, Lei Zhu, Yanan Xu, Yizhuo Zhou, Zhili Wu, Yiping Li, Xiumin Yan & Xueliang Zhu

Authors
  1. Jingli Cao
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yidong Shen
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Lei Zhu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yanan Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Yizhuo Zhou
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Zhili Wu
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Yiping Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Xiumin Yan
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Xueliang Zhu
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

X.Y. and X.Z. conceived and directed the project. Y.S. initiated the project and discovered the relationship between miR-129-3p and CP110 in cilia formation. J.C. discovered the regulation of miR-129-3p on actin regulators and performed most experiments. L.Z. carried out part of the luciferase and qRT-PCR assays. Y.X. fulfilled experiments with 129-MO2. Y.Z. performed wound-healing assays. Z.W. and Y.L. provided zebrafish eggs and microinjected 129-MO. X.Z., X.Y., J.C and Y.S designed experiments, interpreted data and wrote the paper.

Corresponding authors

Correspondence to Xiumin Yan or Xueliang Zhu.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

Supplementary Information (PDF 1971 kb)

Supplementary Table 1

Supplementary Information (XLS 33 kb)

Supplementary Table 2

(XLS 61 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Cao, J., Shen, Y., Zhu, L. et al. miR-129-3p controls cilia assembly by regulating CP110 and actin dynamics. Nat Cell Biol 14, 697–706 (2012). https://doi.org/10.1038/ncb2512

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/ncb2512

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing