Plant Growth Regulation

, Volume 88, Issue 1, pp 49–59 | Cite as

PHD type zinc finger protein PFP represses flowering by modulating FLC expression in Arabidopsis thaliana

  • Yuri Yokoyama
  • Satoru Kobayashi
  • Shin-ichiro KidouEmail author
Original Paper


FLC is an integrative regulator of flowering in Arabidopsis thaliana. The expression of FLC gene is regulated by epigenetic control via histone modification. Plant homeodomain (PHD) finger is a sequence-specific histone binding motif evolutionary conserved in eukaryotes. It has been known that PHD finger proteins play a significant role as a regulator of epigenetic gene expression. In this study, we investigated the role of an Arabidopsis PHD finger protein homolog, named PFP (PHD finger domain containing protein). Phenotypic analysis using a loss-of-function line of PFP (SALK_034619) showed early flowering as compared with the control (Col-0) under long-day condition that promotes flowering, suggesting that PFP is essential in the flowering repression of Arabidopsis. The analyses of major flowering regulatory gene expressions (FLC, FT, CO, FCA, FLK, FLV, EBS, TFL2) indicated that the expression of floral repressor FLC was decreased, while the one of floral inducer FT was increased in the SALK_034619. On the contrary, in the transgenic Arabidopsis overexpressing PFP, the flowering time was delayed and the expression pattern of flowering regulatory genes was reversed in which FLC was upregulated and FT was downregulated, suggesting that PFP is sufficient to regulate flowering regulatory genes. Based on these results, we conclude that PFP controls flowering time by suppressing the upstream of major flowering regulatory genes via FLC expression in Arabidopsis.


Arabidopsis thaliana FLC Flowering Gene expression Histone H3 PHD finger 



















Green fluorescent protein


Glutathione S-transferase


Histone H3 lysine 4 trimethylation


Jumonji demethylase


Long day


Messenger RNA


Murashige and Skoog


Quantitative reverse transcription-PCR


Open reading frame




Plant homeodomain


PHD finger domain containing protein


Polycomb complex 2


Cauliflower mosaic virus 35S RNA


Short day












Wild type



We thank Dr. H. Tagami for help in preparing the manuscript. This work was supported by a grant-in aid for Research in Nagoya City University, Japan.

Supplementary material

10725_2019_487_MOESM1_ESM.pdf (1.2 mb)
Supplementary material 1 (PDF 1263 KB)
10725_2019_487_MOESM2_ESM.pdf (104 kb)
Supplementary material 2 (PDF 103 KB)


  1. Aasland R, Gibson TJ, Stewart AF (1995) The PHD finger: implications for chromatin-mediated transcriptional regulation. Trends Biochem Sci 20:56–59CrossRefGoogle Scholar
  2. Apweiler R (2004) UniProt: the universal protein knowledgebase. Nucleic Acids Res 32:115–119CrossRefGoogle Scholar
  3. Ausín I, Alonso-Blanco C, Jarillo JA, Ruiz-García L, Martínez-Zapater JM (2004) Regulation of flowering time by FVE, a retinoblastoma-associated protein. Nat Genet 36:162–166CrossRefGoogle Scholar
  4. Bouché F, Aloia MD, Tocquin P, Lobet G, Detry N, Périlleux C (2016) Integrating roots into a whole plant network of flowering time genes in Arabidopsis thaliana. Sci Rep 6:1–12CrossRefGoogle Scholar
  5. Chomczynski P, Sacchi N (1987) Single-step method of RNA isolation by acid guanidinium thiocyanate–phenol–chloroform extraction. Anal Biochem 162:156–159CrossRefGoogle Scholar
  6. De Lucia F, Crevillen P, Jones AM, Greb T, Dean C (2008) A PHD-polycomb repressive complex 2 triggers the epigenetic silencing of FLC during vernalization. Proc Natl Acad Sci USA 105:16831–16836CrossRefGoogle Scholar
  7. Finn RD, Attwood TK, Babbitt PC et al (2017) InterPro in 2017-beyond protein family and domain annotations. Nucleic Acids Res 45:190–199CrossRefGoogle Scholar
  8. Gan ES, Xu Y, Wong JY, Goh JG, Sun B, Wee WY, Huang J, Ito T (2014) Jumonji demethylases moderate precocious flowering at elevated temperature via regulation of FLC in Arabidopsis. Nat Commun 5:5098. CrossRefGoogle Scholar
  9. Henderson IR, Liu F, Drea S, Simpson GG, Dean C (2005) An allelic series reveals essential roles for FY in plant development in addition to flowering-time control. Development 132:3597–3607CrossRefGoogle Scholar
  10. Hepworth SR, Valverde F, Ravenscroft D, Mouradov A, Coupland G (2002) Antagonistic regulation of flowering-time gene SOC1 by CONSTANS and FLC via separate promoter motifs. EMBO J 21:4327–4337CrossRefGoogle Scholar
  11. Javerzat JP, Cranston G, Allshire RC (1996) Fission yeast genes which disrupt mitotic chromosome segregation when overexpressed. Nucleic Acids Res 24:4676–4683CrossRefGoogle Scholar
  12. Ji X, Dadon DB, Abraham BJ, Lee TI, Jaenisch R, Bradner JE, Young RA (2015) Chromatin proteomic profiling reveals novel proteins associated with histone-marked genomic regions. Proc Natl Acad Sci USA 112:3841–3846CrossRefGoogle Scholar
  13. Jiang D, Gu X, He Y (2009) Establishment of the winter-annual growth habit via FRIGIDA-mediated histone methylation at FLOWERING LOCUS C in Arabidopsis. Plant Cell 21:1733–1746CrossRefGoogle Scholar
  14. Johanson U, West J, Lister C, Michaels S, Amasino R, Dean C (2000) Molecular analysis of FRIGIDA, a major determinant of natural variation in Arabidopsis flowering time. Science 290:344–347CrossRefGoogle Scholar
  15. Jones DT, Taylor WR, Thornton JM (1992) The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 1992 8:275–282Google Scholar
  16. Kim DH, Sung S (2013) Coordination of the vernalization response through a VIN3 and FLC gene family regulatory network in Arabidopsis. Plant Cell 25:454–469CrossRefGoogle Scholar
  17. Kotake T, Takada S, Nakahigashi K, Ohto M, Goto K (2003) Arabidopsis Terminal Flower 2 gene encodes a heterochromatin protein 1 homolog and represses both FLOWERING LOCUS T to regulate flowering time and several floral homeotic genes. Plant Cell Physiol 44:555–564CrossRefGoogle Scholar
  18. Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874CrossRefGoogle Scholar
  19. Lee I, Amasino RM (1995) Effect of vernalization, photoperiod, and light quality on the flowering phenotype of Arabidopsis plants containing the FRIGIDA gene. Plant Physiol 108:157–162CrossRefGoogle Scholar
  20. Levy YY (1998) The transition to flowering. Plant Cell Online 10:1973–1990CrossRefGoogle Scholar
  21. Lim MH, Kim J, Kim YS et al (2004) A new Arabidopsis gene, FLK, encodes an RNA binding protein with K homology motifs and regulates flowering time via FLOWERING LOCUS C. Plant Cell 16:731–740CrossRefGoogle Scholar
  22. Liu F, Quesada V, Crevillén P, Bäurle I, Swiezewski S, Dean C (2007) The Arabidopsis RNA-binding protein FCA requires a lysine-specific demethylase 1 homolog to downregulate FLC. Mol Cell 28:398–407CrossRefGoogle Scholar
  23. Michaels SD, Amasino RM (1999) FLOWERING LOCUS C encodes a novel MADS domain protein that acts as a repressor of flowering. Plant Cell 11:949–956CrossRefGoogle Scholar
  24. Murashige T, Skoog F (1962) A revised medium for rapid growth and bio assays with tobacco tissue cultures. Physiol Plant 15:473–497CrossRefGoogle Scholar
  25. Notredame C, Higgins DG, Heringa J (2000) T-Coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Biol 302:205–217CrossRefGoogle Scholar
  26. Pikaard CS, Mittelsten Scheid O (2014) Epigenetic regulation in plants. Cold Spring Harb Perspect Biol 6(12):a019315CrossRefGoogle Scholar
  27. Piñeiro M, Gómez-Mena C, Schaffer R, Martínez-Zapater JM, Coupland G (2003) EARLY BOLTING IN SHORT DAYS is related to chromatin remodeling factors and regulates flowering in Arabidopsis by repressing FT. Plant Cell 15:1552–1562CrossRefGoogle Scholar
  28. Sanchez R, Zhou MM (2011) The PHD finger: a versatile epigenome reader. Trends Biochem Sci 36:364–372Google Scholar
  29. Searle I, He Y, Turck F, Vincent C, Fornara F, Kröber S, Amasino RA, Coupland G (2006) The transcription factor FLC confers a flowering response to vernalization by repressing meristem competence and systemic signaling in Arabidopsis. Genes Dev 20:898–912CrossRefGoogle Scholar
  30. Shen Y, Conde E, Silva N, Audonnet L, Servet C, Wei W, Zhou DX (2014) Over-expression of histone H3K4 demethylase gene JMJ15 enhances salt tolerance in Arabidopsis. Front Plant Sci 5:290 (eCollection 2014).
  31. Simpson GG, Dijkwel PP, Quesada V, Henderson I, Dean C (2003) FY is an RNA 3′ end-processing factor that interacts with FCA to control the Arabidopsis floral transition. Cell 113:777–787CrossRefGoogle Scholar
  32. Valvekens D, Van Montagu M, Van Lijsebettens M (1988) Agrobacterium tumefaciens-mediated transformation of Arabidopsis thaliana root explants by using kanamycin selection. Proc Natl Acad Sci USA 85:5536–5540CrossRefGoogle Scholar
  33. Wilson RN, Heckman JW, Somerville CR (1992) Gibberellin is required for flowering in Arabidopsis thaliana under short days. Plant Physiol 100:403–408CrossRefGoogle Scholar
  34. Wood CC, Robertson M, Tanner G, Peacock WJ, Dennis ES, Helliwell CA (2006) The Arabidopsis thaliana vernalization response requires a polycomb-like protein complex that also includes VERNALIZATION INSENSITIVE 3. Proc Natl Acad Sci USA 103:14631–14636CrossRefGoogle Scholar
  35. Xu K, Huang X, Wu M, Wang Y, Chang Y, Liu K, Zhang J, Zhang Y, Zhang F, Yi L, Li T, Wang R, Tan G, Li C (2014) A rapid, highly efficient and economical method of Agrobacterium-mediated in planta transient transformation in living onion epidermis. PLoS ONE 9:1–7Google Scholar
  36. Yang H, Han Z, Cao Y, Fan D, Li H, Mo H, Feng Y, Liu L, Wang Z, Yue Y, Cui S, Chen S, Chai J, Ma L (2012) A companion cell-dominant and developmentally regulated H3K4 demethylase controls flowering time in Arabidopsis via the repression of FLC expression. PLoS Genet 8:e1002664CrossRefGoogle Scholar

Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  • Yuri Yokoyama
    • 1
    • 3
  • Satoru Kobayashi
    • 2
  • Shin-ichiro Kidou
    • 1
    • 3
    Email author
  1. 1.Graduate School of Natural SciencesNagoya City UniversityNagoyaJapan
  2. 2.New York Institute of Technology College of Osteopathic MedicineOld WestburyUSA
  3. 3.Research Center for Biological DiversityNagoya City UniversityNagoyaJapan

Personalised recommendations