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.

Multidomain integration in the structure of the HNF-4α nuclear receptor complex

Subjects

Abstract

The hepatocyte nuclear factor 4α (HNF-4α; also known as NR2A1) is a member of the nuclear receptor (NR) family of transcription factors, which have conserved DNA-binding domains and ligand-binding domains1,2. HNF-4α is the most abundant DNA-binding protein in the liver, where some 40% of the actively transcribed genes have a HNF-4α response element1,3,4. These regulated genes are largely involved in the hepatic gluconeogenic program and lipid metabolism3,5,6. In the pancreas HNF-4α is also a master regulator, controlling an estimated 11% of islet genes7. HNF-4α protein mutations are linked to maturity-onset diabetes of the young, type 1 (MODY1) and hyperinsulinaemic hypoglycaemia8,9,10,11. Previous structural analyses of NRs, although productive in elucidating the structure of individual domains, have lagged behind in revealing the connectivity patterns of NR domains. Here we describe the 2.9 Å crystal structure of the multidomain human HNF-4α homodimer bound to its DNA response element and coactivator-derived peptides. A convergence zone connects multiple receptor domains in an asymmetric fashion, joining distinct elements from each monomer. An arginine target of PRMT1 methylation protrudes directly into this convergence zone and sustains its integrity. A serine target of protein kinase C is also responsible for maintaining domain–domain interactions. These post-translational modifications lead to changes in DNA binding by communicating through the tightly connected surfaces of the quaternary fold. We find that some MODY1 mutations, positioned on the ligand-binding domain and hinge regions of the receptor, compromise DNA binding at a distance by communicating through the interjunctional surfaces of the complex. The overall domain representation of the HNF-4α homodimer is different from that of the PPAR-γ–RXR-α heterodimer, even when both NR complexes are assembled on the same DNA element. Our findings suggest that unique quaternary folds and interdomain connections in NRs could be exploited by small-molecule allosteric modulators that affect distal functions in these polypeptides.

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

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Figure 1: Overall organization of the HNF-4α homodimer on DNA.
Figure 2: Domain–domain contacts of HNF-4α.
Figure 3: Disease-linked mutations in HNF-4α.
Figure 4: Comparison the HNF-4α homodimer and the PPAR-γ–RXR-α heterodimer complexes on DR1 DNA.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Data have been deposited in the Protein Data Bank under accession 4IQR.

References

  1. Sladek, F. M., Zhong, W. M., Lai, E. & Darnell, J. E., Jr Liver-enriched transcription factor HNF-4 is a novel member of the steroid hormone receptor superfamily. Genes Dev. 4, 2353–2365 (1990)

    CAS  Article  Google Scholar 

  2. Mangelsdorf, D. J. & Evans, R. M. The RXR heterodimers and orphan receptors. Cell 83, 841–850 (1995)

    CAS  Article  Google Scholar 

  3. Bolotin, E. et al. Integrated approach for the identification of human hepatocyte nuclear factor 4α target genes using protein binding microarrays. Hepatology 51, 642–653 (2010)

    CAS  Article  Google Scholar 

  4. Wallerman, O. et al. Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing. Nucleic Acids Res. 37, 7498–7508 (2009)

    CAS  Article  Google Scholar 

  5. Yoon, J. C. et al. Control of hepatic gluconeogenesis through the transcriptional coactivator PGC-1. Nature 413, 131–138 (2001)

    ADS  CAS  Article  Google Scholar 

  6. Fang, B., Mane-Padros, D., Bolotin, E., Jiang, T. & Sladek, F. M. Identification of a binding motif specific to HNF4 by comparative analysis of multiple nuclear receptors. Nucleic Acids Res. 40, 5343–5356 (2012)

    CAS  Article  Google Scholar 

  7. Odom, D. T. et al. Control of pancreas and liver gene expression by HNF transcription factors. Science 303, 1378–1381 (2004)

    ADS  CAS  Article  Google Scholar 

  8. Ryffel, G. U. Mutations in the human genes encoding the transcription factors of the hepatocyte nuclear factor (HNF)1 and HNF4 families: functional and pathological consequences. J. Mol. Endocrinol. 27, 11–29 (2001)

    CAS  Article  Google Scholar 

  9. Ellard, S. & Colclough, K. Mutations in the genes encoding the transcription factors hepatocyte nuclear factor 1 alpha (HNF1A) and 4 alpha (HNF4A) in maturity-onset diabetes of the young. Hum. Mutat. 27, 854–869 (2006)

    CAS  Article  Google Scholar 

  10. Kapoor, R. R. et al. Hyperinsulinaemic hypoglycaemia. Arch. Dis. Child. 94, 450–457 (2009)

    CAS  Article  Google Scholar 

  11. Flanagan, S. E. et al. Diazoxide-responsive hyperinsulinemic hypoglycemia caused by HNF4A gene mutations. Eur. J. Endocrinol. 162, 987–992 (2010)

    CAS  Article  Google Scholar 

  12. Chandra, V. et al. Structure of the intact PPAR-γ–RXR-α nuclear receptor complex on DNA. Nature 456, 350–356 (2008)

    Article  Google Scholar 

  13. Nielsen, R. et al. Genome-wide profiling of PPARγ:RXR and RNA polymerase II occupancy reveals temporal activation of distinct metabolic pathways and changes in RXR dimer composition during adipogenesis. Genes Dev. 22, 2953–2967 (2008)

    CAS  Article  Google Scholar 

  14. Jiang, G., Lee, U. & Sladek, F. M. Proposed mechanism for the stabilization of nuclear receptor DNA binding via protein dimerization. Mol. Cell. Biol. 17, 6546–6554 (1997)

    CAS  Article  Google Scholar 

  15. Wisely, G. B. et al. Hepatocyte nuclear factor 4 is a transcription factor that constitutively binds fatty acids. Structure 10, 1225–1234 (2002)

    CAS  Article  Google Scholar 

  16. Dhe-Paganon, S., Duda, K., Iwamoto, M., Chi, Y. I. & Shoelson, S. E. Crystal structure of the HNF4α ligand binding domain in complex with endogenous fatty acid ligand. J. Biol. Chem. 277, 37973–37976 (2002)

    CAS  Article  Google Scholar 

  17. Yuan, X. et al. Identification of an endogenous ligand bound to a native orphan nuclear receptor. PLoS ONE 4, e5609 (2009)

    ADS  Article  Google Scholar 

  18. Weigel, N. L. & Moore, N. L. Steroid receptor phosphorylation: a key modulator of multiple receptor functions. Mol. Endocrinol. 21, 2311–2319 (2007)

    CAS  Article  Google Scholar 

  19. Barrero, M. J. & Malik, S. Two functional modes of a nuclear receptor-recruited arginine methyltransferase in transcriptional activation. Mol. Cell 24, 233–243 (2006)

    CAS  Article  Google Scholar 

  20. Sun, K. et al. Phosphorylation of a conserved serine in the deoxyribonucleic acid binding domain of nuclear receptors alters intracellular localization. Mol. Endocrinol. 21, 1297–1311 (2007)

    CAS  Article  Google Scholar 

  21. Gineste, R. et al. Phosphorylation of farnesoid X receptor by protein kinase C promotes its transcriptional activity. Mol. Endocrinol. 22, 2433–2447 (2008)

    CAS  Article  Google Scholar 

  22. Lu, P. et al. Structural basis of natural promoter recognition by a unique nuclear receptor, HNF4α. J. Biol. Chem. 283, 33685–33697 (2008)

    CAS  Article  Google Scholar 

  23. Rochel, N. et al. Common architecture of nuclear receptor heterodimers on DNA direct repeat elements with different spacings. Nature Struct. Mol. Biol. 18, 564–570 (2011)

    CAS  Article  Google Scholar 

  24. Hall, J. M., McDonnell, D. P. & Korach, K. S. Allosteric regulation of estrogen receptor structure, function, and coactivator recruitment by different estrogen response elements. Mol. Endocrinol. 16, 469–486 (2002)

    CAS  Article  Google Scholar 

  25. Meijsing, S. H. et al. DNA binding site sequence directs glucocorticoid receptor structure and activity. Science 324, 407–410 (2009)

    ADS  CAS  Article  Google Scholar 

  26. Helsen, C. et al. Evidence for DNA-binding domain–ligand-binding domain communications in the androgen receptor. Mol. Cell. Biol. 32, 3033–3043 (2012)

    CAS  Article  Google Scholar 

  27. Choi, J. H. et al. Anti-diabetic drugs inhibit obesity-linked phosphorylation of PPARγ by Cdk5. Nature 466, 451–456 (2010)

    ADS  CAS  Article  Google Scholar 

  28. Choi, J. H. et al. Antidiabetic actions of a non-agonist PPARγ ligand blocking Cdk5-mediated phosphorylation. Nature 477, 477–481 (2011)

    ADS  CAS  Article  Google Scholar 

Download references

Acknowledgements

This work was supported by National Institutes of Health grants R01 DK094147 and R01 DK097475.

Author information

Authors and Affiliations

Authors

Contributions

V.C. expressed, purified and crystallized the complex. P.H., along with V.C., solved and refined the structure and carried out the mutational binding studies. Y.K. collected, processed and reduced the X-ray diffraction data, and assisted with the molecular replacement search in structure determination. N.P., along with V.C., made the expression constructs for crystallization and for DNA-binding studies. D.W. carried out the transcription assays. F.R. supervised the work and wrote the manuscript.

Corresponding author

Correspondence to Fraydoon Rastinejad.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Figures 1-13, Supplementary Tables 1-2 and Supplementary References. (PDF 4227 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Chandra, V., Huang, P., Potluri, N. et al. Multidomain integration in the structure of the HNF-4α nuclear receptor complex. Nature 495, 394–398 (2013). https://doi.org/10.1038/nature11966

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature11966

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

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