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.

  • Article
  • Published:

Embryonic resetting of the parental vernalized state by two B3 domain transcription factors in Arabidopsis

Nature Plants volume 5, pages 424–435 (2019)Cite this article

Subjects

Abstract

Some overwintering plants acquire competence to flower, after experiencing prolonged cold in winter, through a process termed vernalization. In the crucifer plant Arabidopsis thaliana, prolonged cold induces chromatin-mediated silencing of the potent floral repressor FLOWERING LOCUS C (FLC) by Polycomb proteins. This vernalized state is epigenetically maintained or ‘memorized’ in warm rendering plants competent to flower in spring, but is reset in the next generation. Here, we show that in early embryogenesis, two homologous B3 domain transcription factors LEAFY COTYLEDON 2 (LEC2) and FUSCA3 (FUS3) compete against two repressive B3-containing epigenome readers and Polycomb partners known as VAL1 and VAL2 for the cis-regulatory cold memory element (CME) of FLC to disrupt Polycomb silencing. Consistently, crystal structures of B3–CME complexes show that B3FUS3, B3LEC2 and B3VAL1 employ a nearly identical binding interface for CME. We further found that LEC2 and FUS3 recruit the scaffold protein FRIGIDA in association with active chromatin modifiers to establish an active chromatin state at FLC, which results in resetting of the silenced FLC to active and erasing the epigenetic parental memory of winter cold in early embryos. Following embryo development, LEC2 and FUS3 are developmentally silenced throughout post-embryonic stages, enabling VALs to bind to the CME again at seedling stages at which plants experience winter cold. Our findings illustrate how overwintering crucifer annuals or biennials in temperate climates employ a subfamily of B3 domain proteins to switch on, off and on again the expression of a key flowering gene in the embryo-to-plant-to-embryo cycle, and thus to synchronize growth and development with seasonal temperature changes in their life cycles.

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

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: LEC2 and FUS3 function in partial redundancy to reactivate FLC expression in early embryogenesis.
Fig. 2: LEC2 and FUS3 act to reset the silenced FLC to active in embryogenesis following parental vernalization.
Fig. 3: FUS3 and LEC2 bind to the CME region and antagonize VAL1 binding to the CME to erase Polycomb silencing at FLC.
Fig. 4: The structure of B3FUS3 in complex with DNA (CME).
Fig. 5: LEC2 and FUS3 interact with and recruit FRI to the CME region to establish an active chromatin state at FLC.
Fig. 6: A schematic view of the dynamic epigenetic control of FLC expression by a subfamily of B3 domain proteins throughout the Arabidopsis life cycle.

Similar content being viewed by others

Data availability

The data that support the findings of this study are available within the paper and its Supplementary Information or from the corresponding authors on request. The coordinates and structure factors of the B3–CME complexes have been deposited in the RCSB Protein Data Bank with the accession codes: B3LEC2–DNACME: 6J9C; B3FUS3–DNACME: 6J9B; and B3VAL1–DNACME: 6J9A.

References

  1. Tang, W. W., Kobayashi, T., Irie, N., Dietmann, S. & Surani, M. A. Specification and epigenetic programming of the human germ line. Nat. Rev. Genet. 17, 585–600 (2016).

    Article  CAS  Google Scholar 

  2. Baroux, C., Raissig, M. T. & Grossniklaus, U. Epigenetic regulation and reprogramming during gamete formation in plants. Curr. Opin. Genet. Dev. 21, 124–133 (2011).

    Article  CAS  Google Scholar 

  3. Tao, Z. et al. Embryonic epigenetic reprogramming by a pioneer transcription factor in plants. Nature 551, 124–128 (2017).

    Article  Google Scholar 

  4. Lamke, J. & Baurle, I. Epigenetic and chromatin-based mechanisms in environmental stress adaptation and stress memory in plants. Genome Biol. 18, 124 (2017).

    Article  Google Scholar 

  5. Kinoshita, T. & Seki, M. Epigenetic memory for stress response and adaptation in plants. Plant Cell Physiol. 55, 1859–1863 (2014).

    Article  CAS  Google Scholar 

  6. Andres, F. & Coupland, G. The genetic basis of flowering responses to seasonal cues. Nat. Rev. Genet. 13, 627–639 (2012).

    Article  CAS  Google Scholar 

  7. Sharma, N. et al. A FLOWERING LOCUS C homolog is a vernalization-regulated repressor in Brachypodium and is cold regulated in wheat. Plant Physiol. 173, 1301–1315 (2017).

    Article  CAS  Google Scholar 

  8. Bouche, F., Woods, D. P. & Amasino, R. M. Winter memory throughout the plant kingdom: different paths to flowering. Plant Physiol. 173, 27–35 (2017).

    Article  CAS  Google Scholar 

  9. Crevillen, P. et al. Epigenetic reprogramming that prevents transgenerational inheritance of the vernalized state. Nature 515, 587–590 (2014).

    Article  CAS  Google Scholar 

  10. Choi, J. et al. Resetting and regulation of FLOWERING LOCUS C expression during Arabidopsis reproductive development. Plant J. 57, 918–931 (2009).

    Article  CAS  Google Scholar 

  11. Michaels, S. D. & Amasino, R. M. Loss of FLOWERING LOCUS C activity eliminates the late-flowering phenotype of FRIGIDA and autonomous pathway mutations but not responsiveness to vernalization. Plant Cell 13, 935–941 (2001).

    Article  CAS  Google Scholar 

  12. Choi, K. et al. The FRIGIDA complex activates transcription of FLC, a strong flowering repressor in Arabidopsis, by recruiting chromatin modification factors. Plant Cell 23, 289–303 (2011).

    Article  CAS  Google Scholar 

  13. Yang, H. et al. Distinct phases of Polycomb silencing to hold epigenetic memory of cold in Arabidopsis. Science 357, 1142–1145 (2017).

    Article  CAS  Google Scholar 

  14. Sung, S. & Amasino, R. M. Vernalization in Arabidopsis thaliana is mediated by the PHD finger protein VIN3. Nature 427, 159–164 (2004).

    Article  CAS  Google Scholar 

  15. Heo, J. B. & Sung, S. Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA. Science 331, 76–79 (2011).

    Article  CAS  Google Scholar 

  16. Jiang, D. & Berger, F. DNA replication-coupled histone modification maintains Polycomb gene silencing in plants. Science 357, 1146–1149 (2017).

    Article  CAS  Google Scholar 

  17. Questa, J. I., Song, J., Geraldo, N., An, H. & Dean, C. Arabidopsis transcriptional repressor VAL1 triggers Polycomb silencing at FLC during vernalization. Science 353, 485–488 (2016).

    Article  Google Scholar 

  18. Yuan, W. et al. A cis cold memory element and a trans epigenome reader mediate Polycomb silencing of FLC by vernalization in Arabidopsis. Nat. Genet. 48, 1527–1534 (2016).

    Article  CAS  Google Scholar 

  19. Chen, N., Veerappan, V., Abdelmageed, H., Kang, M. & Allen, R. D. HSI2/VAL1 silences AGL15 to regulate the developmental transition from seed maturation to vegetative growth in Arabidopsis. Plant Cell 30, 600–619 (2018).

    Article  CAS  Google Scholar 

  20. Sheldon, C. C. et al. Resetting of FLOWERING LOCUS C expression after epigenetic repression by vernalization. Proc. Natl Acad. Sci. USA 105, 2214–2219 (2008).

    Article  CAS  Google Scholar 

  21. Swaminathan, K., Peterson, K. & Jack, T. The plant B3 superfamily. Trends Plant Sci. 13, 647–655 (2008).

    Article  CAS  Google Scholar 

  22. Wang, F. & Perry, S. E. Identification of direct targets of FUSCA3, a key regulator of Arabidopsis seed development. Plant Physiol. 161, 1251–1264 (2013).

    Article  CAS  Google Scholar 

  23. Braybrook, S. A. et al. Genes directly regulated by LEAFY COTYLEDON2 provide insight into the control of embryo maturation and somatic embryogenesis. Proc. Natl Acad. Sci. USA 103, 3468–3473 (2006).

    Article  CAS  Google Scholar 

  24. Le, B. H. et al. Global analysis of gene activity during Arabidopsis seed development and identification of seed-specific transcription factors. Proc. Natl Acad. Sci. USA 107, 8063–8070 (2010).

    Article  CAS  Google Scholar 

  25. Yang, C. et al. VAL- and AtBMI1-mediated H2Aub initiate the switch from embryonic to postgerminative growth in Arabidopsis. Curr. Biol. 23, 1324–1329 (2013).

    Article  CAS  Google Scholar 

  26. Suzuki, M., Wang, H. H. & McCarty, D. R. Repression of the LEAFY COTYLEDON 1/B3 regulatory network in plant embryo development by VP1/ABSCISIC ACID INSENSITIVE 3-LIKE B3 genes. Plant Physiol. 143, 902–911 (2007).

    Article  CAS  Google Scholar 

  27. Lee, I., Michaels, S. D., Masshardt, A. S. & Amasino, R. M. The late-flowering phenotype of FRIGIDA and LUMINIDEPENDENS is suppressed in the Landsberg erecta strain of Arabidopsis. Plant J. 6, 903–909 (1994).

    Article  CAS  Google Scholar 

  28. Pelletier, J. M. et al. LEC1 sequentially regulates the transcription of genes involved in diverse developmental processes during seed development. Proc. Natl Acad. Sci. USA 114, E6710–E6719 (2017).

    Article  CAS  Google Scholar 

  29. Santos-Mendoza, M. et al. Deciphering gene regulatory networks that control seed development and maturation in Arabidopsis. Plant J. 54, 608–620 (2008).

    Article  CAS  Google Scholar 

  30. Craft, J. et al. New pOp/LhG4 vectors for stringent glucocorticoid-dependent transgene expression in Arabidopsis. Plant J. 41, 899–918 (2005).

    Article  CAS  Google Scholar 

  31. Boer, D. R. et al. Structural basis for DNA binding specificity by the auxin-dependent ARF transcription factors. Cell 156, 577–589 (2014).

    Article  CAS  Google Scholar 

  32. Yamasaki, K. et al. Solution structure of the B3 DNA binding domain of the Arabidopsis cold-responsive transcription factor RAV1. Plant Cell 16, 3448–3459 (2004).

    Article  CAS  Google Scholar 

  33. Sasnauskas, G., Kauneckaite, K. & Siksnys, V. Structural basis of DNA target recognition by the B3 domain of Arabidopsis epigenome reader VAL1. Nucleic Acids Res. 46, 4316–4324 (2018).

    Article  CAS  Google Scholar 

  34. Wu, B. et al. Structural insight into the role of VAL1 B3 domain for targeting to FLC locus in Arabidopsis thaliana. Biochem. Biophys. Res. Commun. 501, 415–422 (2018).

    Article  CAS  Google Scholar 

  35. Ko, J. H. et al. Growth habit determination by the balance of histone methylation activities in Arabidopsis. EMBO J. 29, 3208–3215 (2010).

    Article  CAS  Google Scholar 

  36. Li, Z., Jiang, D. & He, Y. FRIGIDA establishes a local chromosomal environment for FLOWERING LOCUS C mRNA production. Nat. Plants 4, 836–846 (2018).

    Article  CAS  Google Scholar 

  37. Schneider, A. et al. Potential targets of VIVIPAROUS1/ABI3-LIKE1 (VAL1) repression in developing Arabidopsis thaliana embryos. Plant J. 85, 305–319 (2016).

    Article  CAS  Google Scholar 

  38. Rosa, S., Duncan, S. & Dean, C. Mutually exclusive sense-antisense transcription at FLC facilitates environmentally induced gene repression. Nat. Commun. 7, 13031 (2016).

    Article  CAS  Google Scholar 

  39. Schonrock, N. et al. Polycomb-group proteins repress the floral activator AGL19 in the FLC-independent vernalization pathway. Genes Dev. 20, 1667–1678 (2006).

    Article  CAS  Google Scholar 

  40. Michaels, S. D. & Amasino, R. M. FLOWERING LOCUS C encodes a novel MADS domain protein that acts as a repressor of flowering. Plant Cell 11, 949–956 (1999).

    Article  CAS  Google Scholar 

  41. Jefferson, R. A. Assaying chimeric genes in plants: the GUS gene fusion system. Plant Mol. Biol. Rep. 5, 387–405 (1987).

    Article  CAS  Google Scholar 

  42. Wang, Y., Gu, X., Yuan, W., Schmitz, R. J. & He, Y. Photoperiodic control of the floral transition through a distinct Polycomb repressive complex. Dev. Cell 28, 727–736 (2014).

    Article  CAS  Google Scholar 

  43. Luo, X. et al. The NUCLEAR FACTOR-CONSTANS complex antagonizes Polycomb repression to de-repress FLOWERING LOCUS T expression in response to inductive long days in Arabidopsis. Plant J. 95, 17–29 (2018).

    Article  CAS  Google Scholar 

  44. Olsen, L. J. et al. Targeting of glyoxysomal proteins to peroxisomes in leaves and roots of a higher plant. Plant Cell 5, 941–952 (1993).

    Article  CAS  Google Scholar 

  45. Curtis, M. D. & Grossniklaus, U. A gateway cloning vector set for high-throughput functional analysis of genes in planta. Plant Physiol. 133, 462–469 (2003).

    Article  CAS  Google Scholar 

  46. Karimi, M., De Meyer, B. & Hilson, P. Modular cloning in plant cells. Trends Plant Sci. 10, 103–105 (2005).

    Article  CAS  Google Scholar 

  47. Hajdukiewicz, P., Svab, Z. & Maliga, P. The small, versatile pPZP family of Agrobacterium binary vectors for plant transformation. Plant Mol. Biol. 25, 989–994 (1994).

    Article  CAS  Google Scholar 

  48. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997).

    Article  CAS  Google Scholar 

  49. Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213–221 (2010).

    Article  CAS  Google Scholar 

  50. Strong, M. et al. Toward the structural genomics of complexes: crystal structure of a PE/PPE protein complex from Mycobacterium tuberculosis. Proc. Natl Acad. Sci. USA 103, 8060–8065 (2006).

    Article  CAS  Google Scholar 

  51. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486–501 (2010).

    Article  CAS  Google Scholar 

  52. Davis, I. W. et al. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res. 35, W375–W383 (2007).

    Article  Google Scholar 

  53. Di Tommaso, P. et al. T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension. Nucleic Acids Res. 39, W13–W17 (2011).

    Article  Google Scholar 

  54. Robert, X. & Gouet, P. Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Res. 42, W320–W224 (2014).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We are very grateful to R. M. Amasino for providing the FRI-Col and FRI flc seeds. We thank T. Chen and Z. Gao for anti-CLF antibody validation and the staff members at the beamline BL19U1 of the National Center for Protein Sciences Shanghai (NCPSS) at the Shanghai Synchrotron Radiation Facility (SSRF) for data collection, the staff members at the Core Facility for Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, CAS, for the help of the Octet-based in vitro binding assay. This work was supported in part by the National Key Research and Development Program of China (2016YFA0503200 to J.D. and 2017YFA0503803 to Y.H.), the National Natural Science Foundation of China (31830049 to Y.H. and 31622032 to J.D.) and the Chinese Academy of Sciences (XDB27030202 to Y.H.).

Author information

Author notes

  1. Zeng Tao

    Present address: College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China

  2. These authors contributed equally: Zeng Tao, Hongmiao Hu, Xiao Luo.

Authors and Affiliations

  1. Shanghai Center for Plant Stress Biology & National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai, China

    Zeng Tao, Hongmiao Hu, Xiao Luo, Bei Jia, Jiamu Du & Yuehui He

  2. University of Chinese Academy of Sciences, Beijing, China

    Hongmiao Hu

  3. Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China

    Yuehui He

Authors
  1. Zeng Tao
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Hongmiao Hu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Xiao Luo
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Bei Jia
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Jiamu Du
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Yuehui He
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Y.H. and J.D. designed and supervised the research. H.H. and B.J. performed the structure-related analyses and the in vitro protein–DNA binding assays. Z.T. and X.L. conducted the other experiments. All authors took part in data analysis. Y.H. and J.D. wrote the manuscript.

Corresponding authors

Correspondence to Jiamu Du or Yuehui He.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Journal peer review information Nature Plants thanks Richard Amasino and other anonymous reviewer(s) for their contribution to the peer review of this work.

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Supplementary Information

Supplementary Figures 1–8 and Supplementary Tables 1 and 2.

Reporting Summary

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Tao, Z., Hu, H., Luo, X. et al. Embryonic resetting of the parental vernalized state by two B3 domain transcription factors in Arabidopsis. Nat. Plants 5, 424–435 (2019). https://doi.org/10.1038/s41477-019-0402-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41477-019-0402-3

This article is cited by

Search

Advanced 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