Skip to main content
Log in

Sumoylation of SUVR2 contributes to its role in transcriptional gene silencing

Science China Life Sciences Aims and scope Submit manuscript

Abstract

The SU(VAR)-3-9-related protein family member SUVR2 has been previously identified to be involved in transcriptional gene silencing both in RNA-dependent and -independent pathways. It interacts with the chromatin-remodeling proteins CHR19, CHR27, and CHR28 (CHR19/27/28), which are also involved in transcriptional gene silencing. Here our study demonstrated that SUVR2 is almost fully mono-sumoylated in vivo. We successfully identified the exact SUVR2 sumoylation site by combining in vitro mass spectrometric analysis and in vivo immunoblotting confirmation. The luminescence imaging assay and quantitative RT-PCR results demonstrated that SUVR2 sumoylation is involved in transcriptional gene silencing. Furthermore, we found that SUVR2 sumoylation is required for the interaction of SUVR2 with CHR19/27/28, which is consistent with the fact that SUMO proteins are necessary for transcriptional gene silencing. These results suggest that SUVR2 sumoylation contributes to transcriptional gene silencing by facilitating the interaction of SUVR2 with the chromatin-remodeling proteins CHR19/27/28.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

References

  • Amedeo, P., Habu, Y., Afsar, K., Mittelsten Scheid, O., and Paszkowski, J. (2000). Disruption of the plant gene MOM releases transcriptional silencing of methylated genes. Nature 405, 203–206.

    Article  CAS  PubMed  Google Scholar 

  • Baumbusch, L.O., Thorstensen, T., Krauss, V., Fischer, A., Naumann, K., Assalkhou, R., Schulz, I., Reuter, G., and Aalen, R.B. (2001). The Arabidopsis thaliana genome contains at least 29 active genes encoding SET domain proteins that can be assigned to four evolutionarily conserved classes. Nucleic Acids Res 29, 4319–4333.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Budhiraja, R., Hermkes, R., Müller, S., Schmidt, J., Colby, T., Panigrahi, K., Coupland, G., and Bachmair, A. (2009). Substrates related to chromatin and to RNA-dependent processes are modified by Arabidopsis SUMO isoforms that differ in a conserved residue with influence on desumoylation. Plant Physiol 149, 1529–1540.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cubeñas-Potts, C., and Matunis, M.J. (2013). SUMO: a multifaceted modifier of chromatin structure and function. Dev Cell 24, 1–12.

    Article  PubMed  PubMed Central  Google Scholar 

  • Du, J., Johnson, L.M., Jacobsen, S.E., and Patel, D.J. (2015). DNA methylation pathways and their crosstalk with histone methylation. Nat Rev Mol Cell Biol 16, 519–532.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Elrouby, N., Villajuana Bonequi, M., Porri, A., and Coupland, G. (2013). Identification of Arabidopsis SUMO-interacting proteins that regulate chromatin activity and developmental transitions. Proc Natl Acad Sci USA 110, 19956–19961.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gareau, J.R., and Lima, C.D. (2010). The SUMO pathway: emerging mechanisms that shape specificity, conjugation and recognition. Nat Rev Mol Cell Biol 11, 861–871.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Geiss-Friedlander, R., and Melchior, F. (2007). Concepts in sumoylation: a decade on. Nat Rev Mol Cell Biol 8, 947–956.

    Article  CAS  PubMed  Google Scholar 

  • Gong, Z., Morales-Ruiz, T., Ariza, R.R., Roldán-Arjona, T., David, L., and Zhu, J.K. (2002). ROS1, a repressor of transcriptional gene silencing in Arabidopsis, encodes a DNA glycosylase/lyase. Cell 111, 803–814.

    Article  CAS  PubMed  Google Scholar 

  • Groth, M., Stroud, H., Feng, S., Greenberg, M.V.C., Vashisht, A.A., Wohlschlegel, J.A., Jacobsen, S.E., and Ausin, I. (2014). SNF2 chromatin remodeler-family proteins FRG1 and -2 are required for RNA-directed DNA methylation. Proc Natl Acad Sci USA 111, 17666–17671.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Han, Y.F., Zhao, Q.Y., Dang, L.L., Luo, Y.X., Chen, S.S., Shao, C.R., Huang, H.W., Li, Y.Q., Li, L., Cai, T., Chen, S., and He, X.J. (2016). The SUMO E3 ligase-like proteins PIAL1 and PIAL2 interact with MOM1 and form a novel complex required for transcriptional silencing. Plant Cell 28, 1215–1229.

    Article  PubMed  PubMed Central  Google Scholar 

  • Han, Y.F., Dou, K., Ma, Z.Y., Zhang, S.W., Huang, H.W., Li, L., Cai, T., Chen, S., Zhu, J.K., and He, X.J. (2014). SUVR2 is involved in transcriptional gene silencing by associating with SNF2-related chromatin-remodeling proteins in Arabidopsis. Cell Res 24, 1445–1465.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • He, X.J., Hsu, Y.F., Pontes, O., Zhu, J., Lu, J., Bressan, R.A., Pikaard, C., Wang, C.S., and Zhu, J.K. (2009). NRPD4, a protein related to the RPB4 subunit of RNA polymerase II, is a component of RNA polymerases IV and V and is required for RNA-directed DNA methylation. Genes Dev 23, 318–330.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ishida, T., Fujiwara, S., Miura, K., Stacey, N., Yoshimura, M., Schneider, K., Adachi, S., Minamisawa, K., Umeda, M., and Sugimoto, K. (2009). SUMO E3 ligase HIGH PLOIDY2 regulates endocycle onset and meristem maintenance in Arabidopsis. Plant Cell 21, 2284–2297.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jeddeloh, J.A., Stokes, T.L., and Richards, E.J. (1999). Maintenance of genomic methylation requires a SWI2/SNF2-like protein. Nat Genet 22, 94–97.

    Article  CAS  PubMed  Google Scholar 

  • Kanno, T., Mette, M.F., Kreil, D.P., Aufsatz, W., Matzke, M., and Matzke, A.J.M. (2004). Involvement of putative SNF2 chromatin remodeling protein DRD1 in RNA-directed DNA methylation. Curr Biol 14, 801–805.

    Article  CAS  PubMed  Google Scholar 

  • Kurepa, J., Walker, J.M., Smalle, J., Gosink, M.M., Davis, S.J., Durham, T.L., Sung, D.Y., and Vierstra, R.D. (2003). The small ubiquitin-like modifier (SUMO) protein modification system in Arabidopsis. J Biol Chem 278, 6862–6872.

    Article  CAS  PubMed  Google Scholar 

  • Law, J.A., Ausin, I., Johnson, L.M., Vashisht, A.A., Zhu, J.K., Wohlschlegel, J.A., and Jacobsen, S.E. (2010). A protein complex required for polymerase V transcripts and RNA-directed DNA methylation in Arabidopsis. Curr Biol 20, 951–956.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Law, J.A., and Jacobsen, S.E. (2010). Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 11, 204–220.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Law, J.A., Vashisht, A.A., Wohlschlegel, J.A., and Jacobsen, S.E. (2011). SHH1, a homeodomain protein required for DNA methylation, as well as RDR2, RDM4, and chromatin remodeling factors, associate with RNA polymerase IV. PLoS Genet 7, e1002195.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Matzke, M.A., and Mosher, R.A. (2014). RNA-directed DNA methylation: an epigenetic pathway of increasing complexity. Nat Rev Genet 15, 394–408.

    Article  CAS  PubMed  Google Scholar 

  • Miller, M.J., Barrett-Wilt, G.A., Hua, Z., and Vierstra, R.D. (2010). Proteomic analyses identify a diverse array of nuclear processes affected by small ubiquitin-like modifier conjugation in Arabidopsis. Proc Natl Acad Sci USA 107, 16512–16517.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nathan, D., Ingvarsdottir, K., Sterner, D.E., Bylebyl, G.R., Dokmanovic, M., Dorsey, J.A., Whelan, K.A., Krsmanovic, M., Lane, W.S., and Meluh, P.B. (2006). Histone sumoylation is a negative regulator in Saccharomyces cerevisiae and shows dynamic interplay with positive-acting histone modifications. Genes Dev 20, 966–976.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pontvianne, F., Blevins, T., and Pikaard, C.S. (2010). Arabidopsis histone lysine methyltransferases. Adv Bot Res 53, 1–22.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shiio, Y., and Eisenman, R.N. (2003). Histone sumoylation is associated with transcriptional repression. Proc Natl Acad Sci USA 100, 13225–13230.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shin, J.A., Choi, E.S., Kim, H.S., Ho, J.C.Y., Watts, F.Z., Park, S.D., and Jang, Y.K. (2005). SUMO modification is involved in the maintenance of heterochromatin stability in fission yeast. Mol Cell 19, 817–828.

    Article  CAS  PubMed  Google Scholar 

  • Smith, L.M., and Baulcombe, D.C. (2007). Dissection of silencing signal movement in Arabidopsis. Plant Signal Behav 2, 501–502.

    Article  PubMed  PubMed Central  Google Scholar 

  • Smith, L.M., Pontes, O., Searle, I., Yelina, N., Yousafzai, F.K., Herr, A.J., Pikaard, C.S., and Baulcombe, D.C. (2007). An SNF2 protein associated with nuclear RNA silencing and the spread of a silencing signal between cells in Arabidopsis. Plant Cell 19, 1507–1521.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Stielow, B., Sapetschnig, A., Krüger, I., Kunert, N., Brehm, A., Boutros, M., and Suske, G. (2008). Identification of SUMO-dependent chromatin-associated transcriptional repression components by a genome-wide RNAi screen. Mol Cell 29, 742–754.

    Article  CAS  PubMed  Google Scholar 

  • Stroud, H., Greenberg, M.V.C., Feng, S., Bernatavichute, Y.V., and Jacobsen, S.E. (2013). Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome. Cell 152, 352–364.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tomanov, K., Zeschmann, A., Hermkes, R., Eifler, K., Ziba, I., Grieco, M., Novatchkova, M., Hofmann, K., Hesse, H., and Bachmair, A. (2014). Arabidopsis PIAL1 and 2 promote SUMO chain formation as E4-type SUMO ligases and are involved in stress responses and sulfur metabolism. Plant Cell 26, 4547–4560.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zemach, A., Kim, M.Y., Hsieh, P.H., Coleman-Derr, D., Eshed-Williams, L., Thao, K., Harmer, S.L., and Zilberman, D. (2013). The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell 153, 193–205.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang, H., Ma, Z.Y., Zeng, L., Tanaka, K., Zhang, C.J., Ma, J., Bai, G., Wang, P., Zhang, S.W., Liu, Z.W., Cai, T., Tang, K., Liu, R., Shi, X., He, X.J., and Zhu, J.K. (2013). DTF1 is a core component of RNA-directed DNA methylation and may assist in the recruitment of Pol IV. Proc Natl Acad Sci USA 110, 8290–8295.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhu, J., Kapoor, A., Sridhar, V.V., Agius, F., and Zhu, J.K. (2007). The DNA glycosylase/lyase ROS1 functions in pruning DNA methylation patterns in Arabidopsis. Curr Biol 17, 54–59.

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This work was supported by the National Key Research and Development Program of China (2016YFA0500801 to Xinjian He).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Xin-Jian He.

Electronic supplementary material

Supplementary material, approximately 2.33 MB.

Supplemental Dataset 1

. Full lists of co-purified proteins identified by mass spectrometric analyses.

Supplementary Dataset 2

. Lists of primers in this study.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Luo, YX., Han, YF., Zhao, QY. et al. Sumoylation of SUVR2 contributes to its role in transcriptional gene silencing. Sci. China Life Sci. 61, 235–243 (2018). https://doi.org/10.1007/s11427-017-9146-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11427-017-9146-2

Keywords

Navigation