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.

  • Letter
  • Published:

The centrosomal protein nephrocystin-6 is mutated in Joubert syndrome and activates transcription factor ATF4

Abstract

The molecular basis of nephronophthisis1, the most frequent genetic cause of renal failure in children and young adults, and its association with retinal degeneration and cerebellar vermis aplasia in Joubert syndrome2 are poorly understood. Using positional cloning, we here identify mutations in the gene CEP290 as causing nephronophthisis. It encodes a protein with several domains also present in CENPF, a protein involved in chromosome segregation. CEP290 (also known as NPHP6) interacts with and modulates the activity of ATF4, a transcription factor implicated in cAMP-dependent renal cyst formation. NPHP6 is found at centrosomes and in the nucleus of renal epithelial cells in a cell cycle–dependent manner and in connecting cilia of photoreceptors. Abrogation of its function in zebrafish recapitulates the renal, retinal and cerebellar phenotypes of Joubert syndrome. Our findings help establish the link between centrosome function, tissue architecture and transcriptional control in the pathogenesis of cystic kidney disease, retinal degeneration, and central nervous system development.

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

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

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

Figure 1: Positional cloning of the CEP290 gene as mutated in NPHP6/SLSN6/JBTS6.
Figure 2: NPHP6 localizes to the centrosome during interphase, independent of microtubule polymerization.
Figure 3: nphp6 expression pattern and targeted knockdown of zebrafish nphp6 are consistent with the kidney, cerebellar and retinal phenotypes of Joubert syndrome.
Figure 4: The cep290 homolog of C. intestinalis shows a dynamic developmental expression pattern and results in developmental arrest upon targeted knockdown.
Figure 5: NPHP6 partially localizes to the nucleus, directly interacts with ATF4 and induces its transcriptional activation.

Similar content being viewed by others

Accession codes

Accessions

GenBank/EMBL/DDBJ

References

  1. Hildebrandt, F., Jungers, P., Robino, C. & Grundfeld, J.-P. Nephronophthisis, medullary cystic kidney disease and medullary sponge kidney disease. in Diseases of the Kidney and Urinary Tract (ed. Schrier, R.W.) (Lippincott Williams & Wilkins, Philadelphia, 2001).

    Google Scholar 

  2. Saraiva, J.M. & Baraitser, M. Joubert syndrome: a review. Am. J. Med. Genet. 43, 726–731 (1992).

    Article  CAS  Google Scholar 

  3. Hildebrandt, F. et al. A novel gene encoding an SH3 domain protein is mutated in nephronophthisis type 1. Nat. Genet. 17, 149–153 (1997).

    Article  CAS  Google Scholar 

  4. Olbrich, H. et al. Mutations in a novel gene, NPHP3, cause adolescent nephronophthisis, tapeto-retinal degeneration and hepatic fibrosis. Nat. Genet. 34, 455–459 (2003).

    Article  CAS  Google Scholar 

  5. Otto, E.A. et al. Mutations in INVS encoding inversin cause nephronophthisis type 2, linking renal cystic disease to the function of primary cilia and left-right axis determination. Nat. Genet. 34, 413–420 (2003).

    Article  CAS  Google Scholar 

  6. Otto, E. et al. A gene mutated in nephronophthisis and retinitis pigmentosa encodes a novel protein, nephroretinin, conserved in evolution. Am. J. Hum. Genet. 71, 1161–1167 (2002).

    Article  CAS  Google Scholar 

  7. Otto, E.A. et al. Nephrocystin-5, a ciliary IQ domain protein, is mutated in Senior-Loken syndrome and interacts with RPGR and calmodulin. Nat. Genet. 37, 282–288 (2005).

    Article  CAS  Google Scholar 

  8. Watnick, T. & Germino, G. From cilia to cyst. Nat. Genet. 34, 355–356 (2003).

    Article  CAS  Google Scholar 

  9. Simons, M. et al. Inversin, the gene product mutated in nephronophthisis type II, functions as a molecular switch between Wnt signaling pathways. Nat. Genet. 37, 537–543 (2005).

    Article  CAS  Google Scholar 

  10. Germino, G.G. Linking cilia to Wnts. Nat. Genet. 37, 455–457 (2005).

    Article  CAS  Google Scholar 

  11. Hildebrandt, F. & Otto, E. Cilia and centrosomes: a unifying pathogenic concept for cystic kidney disease? Nat. Rev. Genet. 6, 928–940 (2005).

    Article  CAS  Google Scholar 

  12. Utsch, B. et al. Identification of the first AHI1 gene mutations in families with Joubert syndrome and nephronophthisis. Pediatr. Nephrol. 21, 32–35 (2005).

    Article  Google Scholar 

  13. Andersen, J.S. et al. Proteomic characterization of the human centrosome by protein correlation profiling. Nature 426, 570–574 (2003).

    Article  CAS  Google Scholar 

  14. Nasmyth, K. & Haering, C.H. The structure and function of smc and kleisin complexes. Annu. Rev. Biochem. 74, 595–648 (2005).

    Article  CAS  Google Scholar 

  15. Zhou, X. et al. Mitosin/CENP-F as a negative regulator of activating transcription factor-4. J. Biol. Chem. 280, 13973–13977 (2005).

    Article  CAS  Google Scholar 

  16. Khanna, H. et al. RPGR-ORF15, which is mutated in retinitis pigmentosa, associates with SMC1, SMC3, and microtubule transport proteins. J. Biol. Chem. 280, 33580–33587 (2005).

    Article  CAS  Google Scholar 

  17. Morgan, D. et al. Expression analyses and interaction with the anaphase promoting complex protein Apc2 suggest a role for inversin in primary cilia and involvement in the cell cycle. Hum. Mol. Genet. 11, 3345–3350 (2002).

    Article  CAS  Google Scholar 

  18. Mollet, G. et al. The gene mutated in juvenile nephronophthisis type 4 encodes a novel protein that interacts with nephrocystin. Nat. Genet. 32, 300–305 (2002).

    Article  CAS  Google Scholar 

  19. Chen, D. & Shou, C. Molecular cloning of a tumor-associated antigen recognized by monoclonal antibody 3H11. Biochem. Biophys. Res. Commun. 280, 99–103 (2001).

    Article  CAS  Google Scholar 

  20. Vaughan, K.T. & Vallee, R.B. Cytoplasmic dynein binds dynactin through a direct interaction between the intermediate chains and p150Glued. J. Cell Biol. 131, 1507–1516 (1995).

    Article  CAS  Google Scholar 

  21. Kim, J.C. et al. MKKS/BBS6, a divergent chaperonin-like protein linked to the obesity disorder Bardet-Biedl syndrome, is a novel centrosomal component required for cytokinesis. J. Cell Sci. 118, 1007–1020 (2005).

    Article  CAS  Google Scholar 

  22. Mollet, G. et al. Characterization of the nephrocystin/nephrocystin-4 complex and subcellular localization of nephrocystin-4 to primary cilia and centrosomes. Hum. Mol. Genet. 14, 645–656 (2005).

    Article  CAS  Google Scholar 

  23. Pazour, G.J. & Witman, G.B. The vertebrate primary cilium is a sensory organelle. Curr. Opin. Cell Biol. 15, 105–110 (2003).

    Article  CAS  Google Scholar 

  24. 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 

  25. Mazet, F. et al. Molecular evidence from Ciona intestinalis for the evolutionary origin of vertebrate sensory placodes. Dev. Biol. 282, 494–508 (2005).

    Article  CAS  Google Scholar 

  26. Nakashima, Y. et al. Origin of the vertebrate visual cycle: genes encoding retinal photoisomerase and two putative visual cycle proteins are expressed in whole brain of a primitive chordate. J. Comp. Neurol. 460, 180–190 (2003).

    Article  CAS  Google Scholar 

  27. Barthel, L.K. & Raymond, P.A. In situ hybridization studies of retinal neurons. Methods Enzymol. 316, 579–590 (2000).

    Article  CAS  Google Scholar 

  28. Westerfield, M. The Zebrafish Book (University of Oregon Press, Portland, Oregon, 1995).

    Google Scholar 

  29. Piperno, G. & Fuller, M.T. Monoclonal antibodies specific for an acetylated form of alpha-tubulin recognize the antigen in cilia and flagella from a variety of organisms. J. Cell Biol. 101, 2085–2094 (1985).

    Article  CAS  Google Scholar 

  30. Khanna, H. et al. Early-onset retinal degeneration in the rd16 mouse is associated with an in-frame deletion in the novel centrosomal protein CEP290 (NPHP6) that interacts with retinitis pigmentosa GTPase regulator (RPGR). Hum. Mol. Genet. (in the press).

Download references

Acknowledgements

We sincerely thank the affected individuals and their families for participation. We acknowledge R.H. Lyons for excellent large-scale sequencing. We are grateful to the following physicians for contribution of materials and clinical data from patients: J. Kuehr (Karlsruhe, Germany), B. Polak (University of Rotterdam, The Netherlands), D. Doherty (University of Washington, Seattle) and N. Illum (Odense, Denmark). This research was supported by grants from the US National Institutes of Health to F.H. (DK1069274, DK1068306, DK064614), to A.S. (EY07961 and EY07003), to D.S.W. (EY13408) and to I.D. (DK53093), and by grants to A.S. from the Foundation Fighting Blindness and Research to Prevent Blindness (RPB). F.H. is the Frederick G. L. Huetwell Professor. A.S. is the Harold F. Falls Collegiate Professor and recipient of RPB Senior Scientific Investigator Award. M.R.L. holds Michael Smith Foundation for Health Research (MSFHR) and Canadian Institutes of Health Research (CIHR) scholar awards. The work was further supported by the German Federal Ministry of Science and Education through the National Genome Research Network (G.N., C.B., H.C.H. and P.N.); by grants from the German Research Foundation (A.K.); by the National Science Foundation of China (X.Z., grant numbers 30330330 and 30421005); by the March of Dimes and CIHR (grant CBM134736) (M.R.L.); by a grant from the Michigan Economic Development Corporation, Life Sciences Corridor, to D.G. (MEDC38) and a Vision Research Pre-doctoral Training Grant (B.F.); by a grant from the N.K.F. (N004727) (J.F.O.); by grants from the Japanese Ministry of Education, Culture, Sports, Science and Technology (MEXT) to T.K. (17018018) and to M.T. (16370075) and by a grant from Japan Space Forum to M.T. (h160179). We thank D. Slusarski for providing maternal pipetail mutant embryos.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Friedhelm Hildebrandt.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Fig. 1

Total genome search for linkage by homozygosity mapping for an NPHP/SLSN/JBTS locus in three consanguineous Turkish kindred with two affected children each. (PDF 124 kb)

Supplementary Fig. 2

Alignment of predicted human NPHP6/CEP290 exon structure and EST clones. (PDF 70 kb)

Supplementary Fig. 3

Predicted protein domains and motifs of human NPHP6. (PDF 46 kb)

Supplementary Fig. 4

Characterization of monoclonal antibody to NPHP6 3G4 in HEK293 cells. (PDF 79 kb)

Supplementary Fig. 5

NPHP6 localizes to the centrosome during interphase in COS7 and IMCD3 cells. (PDF 107 kb)

Supplementary Fig. 6

NPHP6 localizes to the centrosome during interphase independent of dynein function. (PDF 421 kb)

Supplementary Fig. 7

Immunogold labeling of NPHP6 with 3G4 antibody in mouse photoreceptor cells. (PDF 273 kb)

Supplementary Table 1

Exon-flanking oligonucleotide primers for PCR in the human CEP290 gene. (PDF 68 kb)

Supplementary Video 1

Pronephric cilia motility in larvae injected with cep290 morpholino (0.05 mM). Cilia beat rate is equivalent or slightly faster than wild-type controls. High-speed video was acquired at 250 fps and replayed at 15 fps (250 frames total; 1 s in real time). (MOV 8388 kb)

Supplementary Video 2

Pronephric cilia motility in zebrafish control wild-type larva. Cilia beat in a helical pattern at 28 Hz in the lumen of the pronephric duct. High-speed video was acquired at 250 fps and replayed at 15 fps (250 frames total; 1 s in real time). (MOV 6814 kb)

Supplementary Methods (PDF 34 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Sayer, J., Otto, E., O'Toole, J. et al. The centrosomal protein nephrocystin-6 is mutated in Joubert syndrome and activates transcription factor ATF4. Nat Genet 38, 674–681 (2006). https://doi.org/10.1038/ng1786

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/ng1786

This article is cited by

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