Science China Life Sciences

, Volume 60, Issue 3, pp 264–270 | Cite as

Histone methyltransferase TXR1 is required for both H3 and H3.3 lysine 27 methylation in the well-known ciliated protist Tetrahymena thermophila

  • Xiaolu Zhao
  • Yuanyuan Wang
  • Yurui Wang
  • Yifan Liu
  • Shan Gao
Open Access
Research Paper

Abstract

DNA replication elongation is tightly controlled by histone-modifying enzymes. Our previous studies showed that the histone methytransferase TXR1 (Tetrahymena Trithorax related protein 1) specifically catalyzes H3K27 monomethylation and affects DNA replication elongation in Tetrahymena thermophila. In this study, we investigated whether TXR1 has a substrate preference to the canonical H3 over the replacement variant H3.3. We demonstrated by histone mutagenesis that K27Q mutation in H3.3 further aggravated the replication stress phenotype of K27Q mutation in canonical H3, supporting H3.3 as a physiologically relevant substrate of TXR1. This result is in apparent contrast to the strong preference for canonical H3 recently reported in Arabidopsis homologues ATXR5 and ATXR6, and further corroborates the role of TXR1 in DNA replication.

Keywords

replication histone TXR1 Tetrahymena substrate preference 

Notes

Acknowledgements

Our thanks are due to Prof. Weibo Song from Ocean University of China, for his kind help in preparing the draft and illustrations. We also thank Mr. Mingjian Liu, Lab. of Protozoology, Ocean University of China, for providing in vivo and protogal staining pictures of Tetrahymena. This work was supported by the Natural Science Foundation of China (31470064, 31522051 to Shan Gao), the National Institutes of Health (R01- GM087343 to Yifan Liu), AoShan Talents Program supported by Qingdao National Laboratory for Marine Science and Technology (2015ASTP), China and a research grant by Qingdao government (15-12-1-1-jch).

References

  1. Ahmad, K., and Henikoff, S. (2002). Epigenetic consequences of nucleosome dynamics. Cell 111, 281–284.CrossRefPubMedGoogle Scholar
  2. Allis, C.D., Glover, C.V.C., Bowen, J.K., and Gorovsky, M.A. (1980). Histone variants specific to the transcriptionally active, amitotically dividing macronucleus of the unicellular eucaryote, Tetrahymena thermophila. Cell 20, 609–617.CrossRefPubMedGoogle Scholar
  3. Bannon, G.A., Calzone, F.J., Bowen, J.K., Allis, C.D., and Gorovsky, M.A. (1983). Multiple, independently regulated, polyadenylated messages for histone H3 and H4 in Tetrahymena. Nucleic Acids Res 11, 3903–3917.CrossRefPubMedPubMedCentralGoogle Scholar
  4. Beh, L.Y., Müller, M.M., Muir, T.W., Kaplan, N., and Landweber, L.F. (2015). DNA-guided establishment of nucleosome patterns within coding regions of a eukaryotic genome. Genome Res 25, 1727–1738.CrossRefPubMedPubMedCentralGoogle Scholar
  5. Berger, S.L. (2002). Histone modifications in transcriptional regulation. Curr Opin Genet Dev 12, 142–148.CrossRefPubMedGoogle Scholar
  6. Burman, B., Zhang, Z.Z., Pegoraro, G., Lieb, J.D., and Misteli, T. (2015). Histone modifications predispose genome regions to breakage and translocation. Genes Dev 29, 1393–1402.CrossRefPubMedPubMedCentralGoogle Scholar
  7. Cassidy-Hanley, D., Bowen, J., Lee, J.H., Cole, E., VerPlank, L.A., Gaertig, J., Gorovsky, M.A., and Bruns, P.J. (1997). Germline and somatic transformation of mating Tetrahymena thermophila by particle bombardment. Genetics 146, 135–147..PubMedPubMedCentralGoogle Scholar
  8. Chen, X., Gao, S., Liu, Y., Wang, Y., Wang, Y., and Song, W. (2016). Enzymatic and chemical mapping of nucleosome distribution in purified micro- and macronuclei of the ciliated model organism, Tetrahymena thermophila. Sci China Life Sci doi: 101007/s11427-016-0137-3.Google Scholar
  9. Cole, E., and Sugai, T. (2012). Developmental progression of Tetrahymena through the cell cycle and conjugation. Methods Cell Biol 109, 177–236..CrossRefPubMedGoogle Scholar
  10. Cui, B., Liu, Y., and Gorovsky, M.A. (2006). Deposition and function of histone H3 variants in Tetrahymena thermophila. Mol Cell Biol 26, 7719–7730.CrossRefPubMedPubMedCentralGoogle Scholar
  11. Edgar, R.C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32, 1792–1797.CrossRefPubMedPubMedCentralGoogle Scholar
  12. Engelen, E., Brandsma, J.H., Moen, M.J., Signorile, L., Dekkers, D.H., Demmers, J., Kockx, C.E., Ozgür, Z., Van IJcken, W.F., and van den Berg, D.L. (2015). Proteins that bind regulatory regions identified by histone modification chromatin immunoprecipitations and mass spectrometry. Nat Commun 6, 7115.CrossRefGoogle Scholar
  13. Felsenfeld, G., and Groudine, M. (2003). Controlling the double helix. Nature 421, 448–453.CrossRefPubMedGoogle Scholar
  14. Gao, F., Warren, A., Zhang, Q., Gong, J., Miao, M., Sun, P., Xu, D., Huang, J., Yi, Z., and Song, W. (2016). The all-data-based evolutionary hypothesis of ciliated protists with a revised classification of the Phylum Ciliophora (Eukaryota, Alveolata). Sci Rep 6, 24874.CrossRefPubMedPubMedCentralGoogle Scholar
  15. Gao, S., Xiong, J., Zhang, C., Berquist, B.R., Yang, R., Zhao, M., Molascon, A.J., Kwiatkowski, S.Y., Yuan, D., Qin, Z., Wen, J., Kapler, G.M., Andrews, P.C., Miao, W., and Liu, Y. (2013). Impaired replication elongation in Tetrahymena mutants deficient in histone H3 Lys 27 monomethylation. Genes Dev 27, 1662–1679.CrossRefPubMedPubMedCentralGoogle Scholar
  16. Iizuka, M., and Smith, M.M. (2003). Functional consequences of histone modifications. Curr Opin Genets Dev 13, 154–160.CrossRefGoogle Scholar
  17. Jacob, Y., Bergamin, E., Donoghue, M.T.A., Mongeon, V., LeBlanc, C., Voigt, P., Underwood, C.J., Brunzelle, J.S., Michaels, S.D., Reinberg, D., Couture, J.F., and Martienssen, R.A. (2014). Selective methylation of histone H3 variant H3.1 regulates heterochromatin replication. Science 343, 1249–1253.CrossRefPubMedPubMedCentralGoogle Scholar
  18. Jacob, Y., Feng, S., LeBlanc, C.A., Bernatavichute, Y.V., Stroud, H., Cokus, S., Johnson, L.M., Pellegrini, M., Jacobsen, S.E., and Michaels, S.D. (2009). ATXR5 and ATXR6 are H3K27 monomethyltransferases required for chromatin structure and gene silencing. Nat Struct Mol Biol 16, 763–768.CrossRefPubMedPubMedCentralGoogle Scholar
  19. Jacob, Y., Stroud, H., LeBlanc, C., Feng, S., Zhuo, L., Caro, E., Hassel, C., Gutierrez, C., Michaels, S.D., and Jacobsen, S.E. (2010). Regulation of heterochromatic DNA replication by histone H3 lysine 27 methyltransferases. Nature 466, 987–991.CrossRefPubMedPubMedCentralGoogle Scholar
  20. Karrer, K.M., and VanNuland, T.A. (2002). Methylation of adenine in the nuclear DNA of Tetrahymena is internucleosomal and independent of histone H1. Nucleic Acids Res 30, 1364–1370.CrossRefPubMedPubMedCentralGoogle Scholar
  21. Kornberg, R.D., and Thonmas, J.O. (1974). Chromatin structure: oligomers of the histones. Science 184, 865–868.CrossRefPubMedGoogle Scholar
  22. Liu, M., Fan, X., Gao, F., Gao, S., Yu, Y., Warren, A., and Huang, J. (2016). Tetrahymena australis (Protozoa, Ciliophora): a well-known but “non-existing” taxon—consideration of its identification, definition and systematic position. J Eukaryot Microbiol doi: 10.1111/jeu.12323.Google Scholar
  23. Liu, Y., Mochizuki, K., and Gorovsky, M.A. (2004). Histone H3 lysine 9 methylation is required for DNA elimination in developing macronuclei in Tetrahymena. Proc Natl Acad Sci USA 101, 1679–1684.CrossRefPubMedPubMedCentralGoogle Scholar
  24. Meyer, E., and Chalker, D.L. (2007). In: Epigenetics, C.D. Allis, M.L. Caparros, T. Jenuwein and D. Reinberg, eds. (Cold Spring Harbor, New York) pp. 127–150.Google Scholar
  25. Ray-Gallet, D., Quivy, J.P., Scamps, C., Martini, E.M.D., Lipinski, M., and Almouzni, G. (2002). HIRA is critical for a nucleosome assembly pathway independent of DNA synthesis. Mol Cell 9, 1091–1100.CrossRefPubMedGoogle Scholar
  26. Strahl, B.D., and Allis, C.D. (2000). The language of covalent histone modifications. Nature 403, 41–45.CrossRefPubMedGoogle Scholar
  27. Tagami, H., Ray-Gallet, D., Almouzni, G., and Nakatani, Y. (2004). Histone H3.1 and H3.3 complexes mediate nucleosome assembly pathways dependent or independent of DNA synthesis. Cell 116, 51–61.CrossRefPubMedGoogle Scholar
  28. Thatcher, T.H., and Gorovsky, M.A. (1994). Phylogenetic analysis of the core histones H2A, H2B, H3, and H4. Nucleic Acids Res 22, 174–179.CrossRefPubMedPubMedCentralGoogle Scholar
  29. Thatcher, T.H., MacGaffey, J., Bowen, J., Horowitz, S., Shapiro, D.L., and Gorovsky, M.A. (1994). Independent evolutionary origin of histone H3.3-like variants of animals and Tetrahymena. Nucleic Acids Res 22, 180–186.CrossRefPubMedPubMedCentralGoogle Scholar
  30. Woodard, J., Kaneshiro, E., and Gorovsky, M.A. (1972). Cytochemical studies on the problem of macronuclear subnuclei in Tetrahymena. Genetics 70, 251.PubMedPubMedCentralGoogle Scholar
  31. Zhang, C., Gao, S., Molascon, A.J., Liu, Y., and Andrews, P.C. (2014). Quantitative proteomics reveals histone modifications in crosstalk with H3 lysine 27 methylation. Mol Cell Proteomics 13, 749–759.CrossRefPubMedPubMedCentralGoogle Scholar
  32. Zhang, C., Molascon, A.J., Gao, S., Liu, Y., and Andrews, P.C. (2013). Quantitative proteomics reveals that the specific methyltransferases Txr1p and Ezl2p differentially affect the mono-, di- and trimethylation states of histone H3 lysine 27 (H3K27). Mol Cell Proteomics 12, 1678–1688.CrossRefPubMedGoogle Scholar

Copyright information

© The Author(s) 2016

Authors and Affiliations

  • Xiaolu Zhao
    • 1
  • Yuanyuan Wang
    • 1
  • Yurui Wang
    • 1
  • Yifan Liu
    • 2
  • Shan Gao
    • 1
    • 3
  1. 1.Institute of Evolution & Marine BiodiversityOcean University of ChinaQingdaoChina
  2. 2.Department of PathologyUniversity of MichiganAnn ArborUSA
  3. 3.Laboratory for Marine Biology and BiotechnologyQingdao National Laboratory for Marine Science and TechnologyQingdaoChina

Personalised recommendations