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.

An in-frame deletion at the polymerase active site of POLD1 causes a multisystem disorder with lipodystrophy

Subjects

Abstract

DNA polymerase δ, whose catalytic subunit is encoded by POLD1, is responsible for lagging-strand DNA synthesis during DNA replication1. It carries out this synthesis with high fidelity owing to its intrinsic 3′- to 5′-exonuclease activity, which confers proofreading ability. Missense mutations affecting the exonuclease domain of POLD1 have recently been shown to predispose to colorectal and endometrial cancers2. Here we report a recurring heterozygous single-codon deletion in POLD1 affecting the polymerase active site that abolishes DNA polymerase activity but only mildly impairs 3′- to 5′-exonuclease activity. This mutation causes a distinct multisystem disorder that includes subcutaneous lipodystrophy, deafness, mandibular hypoplasia and hypogonadism in males. This discovery suggests that perturbing the function of the ubiquitously expressed POLD1 polymerase has unexpectedly tissue-specific effects in humans and argues for an important role for POLD1 function in adipose tissue homeostasis.

This is a preview of subscription content

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Figure 1: Clinical characteristics of individuals with MDP syndrome.
Figure 2: Protein schematic and modeling of POLD1 alterations.
Figure 3: Polymerase δ with Ser605del mutant POLD1 has no detectable polymerase activity but has robust exonuclease activity.

Accession codes

Primary accessions

NCBI Reference Sequence

Protein Data Bank

Referenced accessions

Swiss-Prot

References

  1. Prindle, M.J. & Loeb, L.A. DNA polymerase delta in DNA replication and genome maintenance. Environ. Mol. Mutagen. 53, 666–682 (2012).

    CAS  Article  Google Scholar 

  2. Palles, C. et al. Germline mutations affecting the proofreading domains of POLE and POLD1 predispose to colorectal adenomas and carcinomas. Nat. Genet. 45, 136–144 (2013).

    CAS  Article  Google Scholar 

  3. Shastry, S. et al. A novel syndrome of mandibular hypoplasia, deafness, and progeroid features associated with lipodystrophy, undescended testes, and male hypogonadism. J. Clin. Endocrinol. Metab. 95, E192–E197 (2010).

    CAS  Article  Google Scholar 

  4. Semple, R.K., Savage, D.B., Cochran, E.K., Gorden, P. & O'Rahilly, S. Genetic syndromes of severe insulin resistance. Endocr. Rev. 32, 498–514 (2011).

    CAS  Article  Google Scholar 

  5. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).

    CAS  Article  Google Scholar 

  6. McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010).

    CAS  Article  Google Scholar 

  7. Abecasis, G.R. et al. An integrated map of genetic variation from 1,092 human genomes. Nature 491, 56–65 (2012).

    Article  Google Scholar 

  8. Fu, W. et al. Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants. Nature 493, 216–220 (2013).

    CAS  Article  Google Scholar 

  9. Kaess, B.M. et al. The ratio of visceral to subcutaneous fat, a metric of body fat distribution, is a unique correlate of cardiometabolic risk. Diabetologia 55, 2622–2630 (2012).

    CAS  Article  Google Scholar 

  10. Kamath-Loeb, A.S., Shen, J.C., Schmitt, M.W. & Loeb, L.A. The Werner syndrome exonuclease facilitates DNA degradation and high fidelity DNA polymerization by human DNA polymerase δ. J. Biol. Chem. 287, 12480–12490 (2012).

    CAS  Article  Google Scholar 

  11. Oshima, J., Martin, G.M. & Hisama, F.M. Werner syndrome. GeneReviews <http://www.ncbi.nlm.nih.gov/books/NBK1514/> (2012).

  12. Novelli, G. et al. Mandibuloacral dysplasia is caused by a mutation in LMNA-encoding lamin A/C. Am. J. Hum. Genet. 71, 426–431 (2002).

    CAS  Article  Google Scholar 

  13. Agarwal, A.K., Fryns, J.P., Auchus, R.J. & Garg, A. Zinc metalloproteinase, ZMPSTE24, is mutated in mandibuloacral dysplasia. Hum. Mol. Genet. 12, 1995–2001 (2003).

    CAS  Article  Google Scholar 

  14. Uchimura, A., Hidaka, Y., Hirabayashi, T., Hirabayashi, M. & Yagi, T. DNA polymerase delta is required for early mammalian embryogenesis. PLoS ONE 4, e4184 (2009).

    Article  Google Scholar 

  15. Gandotra, S. et al. Perilipin deficiency and autosomal dominant partial lipodystrophy. N. Engl. J. Med. 364, 740–748 (2011).

    CAS  Article  Google Scholar 

  16. Henegar, C. et al. Adipose tissue transcriptomic signature highlights the pathological relevance of extracellular matrix in human obesity. Genome Biol. 9, R14 (2008).

    Article  Google Scholar 

  17. Swan, M.K., Johnson, R.E., Prakash, L., Prakash, S. & Aggarwal, A.K. Structural basis of high-fidelity DNA synthesis by yeast DNA polymerase δ. Nat. Struct. Mol. Biol. 16, 979–986 (2009).

    CAS  Article  Google Scholar 

  18. Reha-Krantz, L.J. & Nonay, R.L. Motif A of bacteriophage T4 DNA polymerase: role in primer extension and DNA replication fidelity. Isolation of new antimutator and mutator DNA polymerases. J. Biol. Chem. 269, 5635–5643 (1994).

    CAS  PubMed  Google Scholar 

  19. Venkatesan, R.N. et al. Mutation at the polymerase active site of mouse DNA polymerase δ increases genomic instability and accelerates tumorigenesis. Mol. Cell. Biol. 27, 7669–7682 (2007).

    CAS  Article  Google Scholar 

  20. Branzei, D. & Foiani, M. Maintaining genome stability at the replication fork. Nat. Rev. Mol. Cell Biol. 11, 208–219 (2010).

    CAS  Article  Google Scholar 

  21. Kokoska, R.J., Stefanovic, L., DeMai, J. & Petes, T.D. Increased rates of genomic deletions generated by mutations in the yeast gene encoding DNA polymerase δ or by decreases in the cellular levels of DNA polymerase δ. Mol. Cell. Biol. 20, 7490–7504 (2000).

    CAS  Article  Google Scholar 

  22. Lemoine, F.J., Degtyareva, N.P., Kokoska, R.J. & Petes, T.D. Reduced levels of DNA polymerase δ induce chromosome fragile site instability in yeast. Mol. Cell. Biol. 28, 5359–5368 (2008).

    CAS  Article  Google Scholar 

  23. Goldsby, R.E. et al. High incidence of epithelial cancers in mice deficient for DNA polymerase δ proofreading. Proc. Natl. Acad. Sci. USA 99, 15560–15565 (2002).

    CAS  Article  Google Scholar 

  24. Schmitt, M.W. et al. Active site mutations in mammalian DNA polymerase δ alter accuracy and replication fork progression. J. Biol. Chem. 285, 32264–32272 (2010).

    CAS  Article  Google Scholar 

  25. Savage, D.B. Mouse models of inherited lipodystrophy. Dis. Model. Mech. 2, 554–562 (2009).

    CAS  Article  Google Scholar 

  26. Chomczynski, P. & Sacchi, N. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal. Biochem. 162, 156–159 (1987).

    CAS  Article  Google Scholar 

  27. Pfaffl, M.W. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 29, e45 (2001).

    CAS  Article  Google Scholar 

  28. Neville, M.J., Collins, J.M., Gloyn, A.L., McCarthy, M.I. & Karpe, F. Comprehensive human adipose tissue mRNA and microRNA endogenous control selection for quantitative real-time-PCR normalization. Obesity (Silver Spring) 19, 888–892 (2011).

    CAS  Article  Google Scholar 

  29. Fazlieva, R. et al. Proofreading exonuclease activity of human DNA polymerase δ and its effects on lesion-bypass DNA synthesis. Nucleic Acids Res. 37, 2854–2866 (2009).

    CAS  Article  Google Scholar 

  30. Schmitt, M.W., Matsumoto, Y. & Loeb, L.A. High fidelity and lesion bypass capability of human DNA polymerase δ. Biochimie 91, 1163–1172 (2009).

    CAS  Article  Google Scholar 

Download references

Acknowledgements

We thank M. Day, A. Damhuis and R. Gilbert for technical assistance. We thank K. Knapp for providing the data for the DEXA calculations. We thank L. Tung (University of Cambridge) for providing the human tissue whole-RNA panel. This work was supported by the NIHR Exeter Clinical Research Facility through funding for S.E. and A.T.H., and general infrastructure. S.E., A.T.H. and S.O. are supported by Wellcome Trust Senior Investigator awards 098395/Z/12/A and 098395/Z/12/Z. D.B.S. and R.K.S. are supported by Wellcome Trust Senior Research Fellowships in Clinical Science (098498/Z/12/Z). M.N.W. is supported by the Wellcome Trust as part of Wellcome Trust Biomedical Informatics Hub funding. R.O. is supported by Diabetes UK. D.B.S., R.K.S. and S.O. are supported by the UK NIHR Cambridge Biomedical Research Centre. K.J.G. is supported by the Agency for Science, Technology and Research, Singapore (A*STAR). Research reported in this publication by M.J.P. and L.A.L. was supported by the National Cancer Institute of the US National Institutes of Health under awards R01CA102029 and P01CA077852. The opinions in this paper are soley those of the authors and do not necessarily represent the views of the US National Institutes of Health, the Department of Health (England) or other funders.

Author information

Authors and Affiliations

Authors

Contributions

S.E. and A.T.H. designed the study. M.N.W. and H.L.A. performed bioinformatics analyses. R.C. performed the exome sequencing and structural modeling. M.J.P., K.J.G., Y.W., J.F., L.J.M., L.A.L., K.K. and R.K.S. performed the functional studies. R.C. and S.E. performed the Sanger sequencing analysis and interpreted the results. R.O., K.G., C.S.Y., P.S., G.N., P.T., E.M., D.B.S., S.O., R.K.S. and A.T.H. analyzed the clinical data. M.N.W., S.E., M.J.P., R.K.S. and A.T.H. prepared the draft manuscript. All authors contributed to discussion of the results and manuscript preparation.

Corresponding author

Correspondence to Andrew T Hattersley.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–4 and Supplementary Tables 1–4 (PDF 257 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Weedon, M., Ellard, S., Prindle, M. et al. An in-frame deletion at the polymerase active site of POLD1 causes a multisystem disorder with lipodystrophy. Nat Genet 45, 947–950 (2013). https://doi.org/10.1038/ng.2670

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/ng.2670

Further reading

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