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.

A histone H3 lysine 36 trimethyltransferase links Nkx2-5 to Wolf–Hirschhorn syndrome

Abstract

Diverse histone modifications are catalysed and recognized by various specific proteins, establishing unique modification patterns that act as transcription signals1,2. In particular, histone H3 trimethylation at lysine 36 (H3K36me3) is associated with actively transcribed regions and has been proposed to provide landmarks for continuing transcription3,4; however, the control mechanisms and functions of H3K36me3 in higher eukaryotes are unknown. Here we show that the H3K36me3-specific histone methyltransferase (HMTase) Wolf–Hirschhorn syndrome candidate 1 (WHSC1, also known as NSD2 or MMSET) functions in transcriptional regulation together with developmental transcription factors whose defects overlap with the human disease Wolf–Hirschhorn syndrome (WHS)5,6. We found that mouse Whsc1, one of five putative Set2 homologues2,7,8, governed H3K36me3 along euchromatin by associating with the cell-type-specific transcription factors Sall1, Sall4 and Nanog in embryonic stem cells, and Nkx2-5 in embryonic hearts, regulating the expression of their target genes. Whsc1-deficient mice showed growth retardation and various WHS-like midline defects, including congenital cardiovascular anomalies. The effects of Whsc1 haploinsufficiency were increased in Nkx2-5 heterozygous mutant hearts, indicating their functional link. We propose that WHSC1 functions together with developmental transcription factors to prevent the inappropriate transcription that can lead to various pathophysiologies.

Your institute does not have access to this article

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: Whsc1 methylates histone H3 on lysine 36.
Figure 2: Whsc1 associates with transcription factors to repress abnormal transcription.
Figure 3: The Whsc1 gene is required for normal mouse development.
Figure 4: Whsc1 is required for the appropriate transcription of Nkx2-5 -dependent genes.

References

  1. Sims, R. J. & Reinberg, D. Histone H3 Lys 4 methylation: caught in a bind? Genes Dev. 20, 2779–2786 (2006)

    CAS  Article  Google Scholar 

  2. Li, B., Carey, M. & Workman, J. L. The role of chromatin during transcription. Cell 128, 707–719 (2007)

    CAS  Article  Google Scholar 

  3. Barski, A. et al. High-resolution profiling of histone methylations in the human genome. Cell 129, 823–837 (2007)

    CAS  Article  Google Scholar 

  4. Mikkelsen, T. S. et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448, 553–560 (2007)

    ADS  CAS  Article  Google Scholar 

  5. Hirschhorn, K. & Cooper, H. L. Chromosomal aberrations in human disease. A review of the status of cytogenetics in medicine. Am. J. Med. 31, 442–470 (1961)

    CAS  Article  Google Scholar 

  6. Bergemann, A. D., Cole, F. & Hirschhorn, K. The etiology of Wolf–Hirschhorn syndrome. Trends Genet. 21, 188–195 (2005)

    CAS  Article  Google Scholar 

  7. Strahl, B. D. et al. Set2 is a nucleosomal histone H3-selective methyltransferase that mediates transcriptional repression. Mol. Cell. Biol. 22, 1298–1306 (2002)

    CAS  Article  Google Scholar 

  8. Sun, X. J. et al. Identification and characterization of a novel human histone H3 lysine 36-specific methyltransferase. J. Biol. Chem. 280, 35261–35271 (2005)

    CAS  Article  Google Scholar 

  9. Stec, I. et al. WHSC1, a 90 kb SET domain-containing gene, expressed in early development and homologous to a Drosophila dysmorphy gene maps in the Wolf-Hirschhorn syndrome critical region and is fused to IgH in t(4;14) multiple myeloma. Hum. Mol. Genet. 7, 1071–1082 (1998)

    CAS  Article  Google Scholar 

  10. Marango, J. et al. The MMSET protein is a histone methyltransferase with characteristics of a transcriptional corepressor. Blood 111, 3145–3154 (2008)

    CAS  Article  Google Scholar 

  11. Kohlhase, J., Wischermann, A., Reichenbach, H., Froster, U. & Engel, W. Mutations in the SALL1 putative transcription factor gene cause Townes-Brocks syndrome. Nature Genet. 18, 81–83 (1998)

    CAS  Article  Google Scholar 

  12. Shafi, R. et al. The O-GlcNAc transferase gene resides on the X chromosome and is essential for embryonic stem cell viability and mouse ontogeny. Proc. Natl Acad. Sci. USA 97, 5735–5739 (2000)

    ADS  CAS  Article  Google Scholar 

  13. Sakaki-Yumoto, M. et al. The murine homolog of SALL4, a causative gene in Okihiro syndrome, is essential for embryonic stem cell proliferation, and cooperates with Sall1 in anorectal, heart, brain and kidney development. Development 133, 3005–3013 (2006)

    CAS  Article  Google Scholar 

  14. Wu, Q. et al. Sall4 interacts with Nanog and co-occupies Nanog genomic sites in embryonic stem cells. J. Biol. Chem. 281, 24090–24094 (2006)

    CAS  Article  Google Scholar 

  15. Liang, J. et al. Nanog and Oct4 associate with unique transcriptional repression complexes in embryonic stem cells. Nature Cell Biol. 10, 731–739 (2008)

    ADS  CAS  Article  Google Scholar 

  16. Carrozza, M. J. et al. Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell 123, 581–592 (2005)

    CAS  Article  Google Scholar 

  17. Li, B. et al. Combined action of PHD and chromo domains directs the Rpd3S HDAC to transcribed chromatin. Science 316, 1050–1054 (2007)

    ADS  CAS  Article  Google Scholar 

  18. Li, M. et al. Solution structure of the Set2-Rpb1 interacting domain of human Set2 and its interaction with the hyperphosphorylated C-terminal domain of Rpb1. Proc. Natl Acad. Sci. USA 102, 17636–17641 (2005)

    ADS  CAS  Article  Google Scholar 

  19. Liu, K. J., Arron, J. R., Stankunas, K., Crabtree, G. R. & Longaker, M. T. Chemical rescue of cleft palate and midline defects in conditional GSK-3β mice. Nature 446, 79–82 (2007)

    ADS  CAS  Article  Google Scholar 

  20. Bruneau, B. G. The developmental genetics of congenital heart disease. Nature 451, 943–948 (2008)

    ADS  CAS  Article  Google Scholar 

  21. Prall, O. W. et al. An Nkx2-5/Bmp2/Smad1 negative feedback loop controls heart progenitor specification and proliferation. Cell 128, 947–959 (2007)

    CAS  Article  Google Scholar 

  22. Hiroi, Y. et al. Tbx5 associates with Nkx2-5 and synergistically promotes cardiomyocyte differentiation. Nature Genet. 28, 276–280 (2001)

    CAS  Article  Google Scholar 

  23. Moses, K. A., DeMayo, F., Braun, R. M., Reecy, J. L. & Schwartz, R. J. Embryonic expression of an Nkx2-5/Cre gene using ROSA26 reporter mice. Genesis 31, 176–180 (2001)

    CAS  Article  Google Scholar 

  24. Biben, C. et al. Cardiac septal and valvular dysmorphogenesis in mice heterozygous for mutations in the homeobox gene Nkx2-5. Circ. Res. 87, 888–895 (2000)

    CAS  Article  Google Scholar 

  25. Koshiba-Takeuchi, K. et al. Cooperative and antagonistic interactions between Sall4 and Tbx5 pattern the mouse limb and heart. Nature Genet. 38, 175–183 (2006)

    CAS  Article  Google Scholar 

  26. Gromak, N. et al. The PTB interacting protein raver1 regulates α-tropomyosin alternative splicing. EMBO J. 22, 6356–6364 (2003)

    CAS  Article  Google Scholar 

  27. Nimura, K. et al. Dnmt3a2 targets endogenous Dnmt3L to ES cell chromatin and induces regional DNA methylation. Genes Cells 11, 1225–1237 (2006)

    CAS  Article  Google Scholar 

  28. Hayashi, M. et al. Comparative roles of Twist-1 and Id1 in transcriptional regulation by BMP signaling. J. Cell Sci. 120, 1350–1357 (2007)

    CAS  Article  Google Scholar 

  29. Ura, K. & Kaneda, Y. Reconstitution of chromatin in vitro. Methods Mol. Biol. 181, 309–325 (2001)

    CAS  PubMed  Google Scholar 

  30. Tachiwana, H., Osakabe, A., Kimura, H. & Kurumizaka, H. Nucleosome formation with the testis-specific histone H3 variant, H3t, by human nucleosome assembly proteins in vitro. Nucleic Acids Res. 36, 2208–2218 (2008)

    CAS  Article  Google Scholar 

  31. Lowary, P. T. & Widom, J. New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. J. Mol. Biol. 276, 19–42 (1998)

    CAS  Article  Google Scholar 

  32. Dorigo, B., Schalch, T., Bystricky, K. & Richmond, T. J. Chromatin fiber folding: requirement for the histone H4 N-terminal tail. J. Mol. Biol. 327, 85–96 (2003)

    CAS  Article  Google Scholar 

  33. Saeki, H. et al. Linker histone variants control chromatin dynamics during early embryogenesis. Proc. Natl Acad. Sci. USA 102, 5697–5702 (2005)

    ADS  CAS  Article  Google Scholar 

  34. Nishioka, K. & Reinberg, D. Methods and tips for the purification of human histone methyltransferases. Methods 31, 49–58 (2003)

    CAS  Article  Google Scholar 

  35. Seo, H. et al. Rapid generation of specific antibodies by enhanced homologous recombination. Nature Biotechnol. 23, 731–735 (2005)

    CAS  Article  Google Scholar 

  36. Wade, P. A. et al. Mi-2 complex couples DNA methylation to chromatin remodelling and histone deacetylation. Nature Genet. 23, 62–66 (1999)

    CAS  Article  Google Scholar 

  37. Rigaut, G. et al. A generic protein purification method for protein complex characterization and proteome exploration. Nature Biotechnol. 17, 1030–1032 (1999)

    CAS  Article  Google Scholar 

  38. Bruneau, B. G. et al. A murine model of Holt–Oram syndrome defines roles of the T-box transcription factor Tbx5 in cardiogenesis and disease. Cell 106, 709–721 (2001)

    CAS  Article  Google Scholar 

Download references

Acknowledgements

We thank T. Richmond, R. Nishinakamura, H. Kurumizaka and M. Shirai for providing reagents and mice; S. Khochbin, S. Hirose, J. Godde and J. Takeuchi for their critical reading of the manuscript; and H. Niwa, H. Hamada, M. Yamamoto, S. Ohishi, H. Nakagami and members of the GTS laboratory for discussion and support. This work was supported by grants from the Ministry of Education, Culture, Sports, Science, and Technology of Japan (MEXT) and the Naito Foundation, and by funds from Osaka University for female researchers.

Author Contributions Y.K. provided support and general guidance for this work. K.U. planned and organized the project. K.N. designed and performed experiments. H.S. performed histological analysis of hearts. R.J.S., M.I. and M.O. contributed mouse resources. K.U. wrote the paper with K.N. and Y.K.

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Kiyoe Ura or Yasufumi Kaneda.

Supplementary information

Supplementary Information

This file contains Supplementary Figures S1-S16 with Legends, Supplementary Table 1 and Supplementary References. (PDF 1951 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Nimura, K., Ura, K., Shiratori, H. et al. A histone H3 lysine 36 trimethyltransferase links Nkx2-5 to Wolf–Hirschhorn syndrome. Nature 460, 287–291 (2009). https://doi.org/10.1038/nature08086

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature08086

Further reading

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