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.

An RNA thermoswitch regulates daytime growth in Arabidopsis

Abstract

Temperature is a major environmental cue affecting plant growth and development. Plants often experience higher temperatures in the context of a 24 h day–night cycle, with temperatures peaking in the middle of the day. Here, we find that the transcript encoding the bHLH transcription factor PIF7 undergoes a direct increase in translation in response to warmer temperature. Diurnal expression of PIF7 transcript gates this response, allowing PIF7 protein to quickly accumulate in response to warm daytime temperature. Enhanced PIF7 protein levels directly activate the thermomorphogenesis pathway by inducing the transcription of key genes such as the auxin biosynthetic gene YUCCA8, and are necessary for thermomorphogenesis to occur under warm cycling daytime temperatures. The temperature-dependent translational enhancement of PIF7 messenger RNA is mediated by the formation of an RNA hairpin within its 5′ untranslated region, which adopts an alternative conformation at higher temperature, leading to increased protein synthesis. We identified similar hairpin sequences that control translation in additional transcripts including WRKY22 and the key heat shock regulator HSFA2, suggesting that this is a conserved mechanism enabling plants to respond and adapt rapidly to high temperatures.

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

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

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

Fig. 1: Arabidopsis responds rapidly to daytime warm temperature cycles and this is mirrored by changes in translational efficiency of genes such as PIF7 within 15 min.
Fig. 2: PIF7 is necessary for thermomorphogenesis in response to warm daytime temperature cycles.
Fig. 3: PIF7 directly activates the warm temperature transcriptome in response to daytime thermal cycles.
Fig. 4: Thermosensitive hairpin structures in the HSFA2 and PIF7 5′-UTRs enhance translation in response to warm temperature.

Similar content being viewed by others

Data availability

Raw and processed data are available from ribo-seq/RNA-seq series E-MTAB-7717, RNA-seq series GSE124003 and ChIP–seq series GSE127745.

Code availability

Code is available from this Github repository: https://github.com/shouldsee/thermoPIF7.

References

  1. Quint, M. et al. Molecular and genetic control of plant thermomorphogenesis. Nat. Plants 2, 15190 (2016).

    Article  CAS  PubMed  Google Scholar 

  2. Scheffers, B. R. et al. The broad footprint of climate change from genes to biomes to people. Science 354, aaf7671 (2016).

    Article  PubMed  CAS  Google Scholar 

  3. Nusinow, D. A. et al. The ELF4–ELF3–LUX complex links the circadian clock to diurnal control of hypocotyl growth. Nature 475, 398–402 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Mizuno, T. et al. Ambient temperature signal feeds into the circadian clock transcriptional circuitry through the EC night-time repressor in Arabidopsis thaliana. Plant Cell Physiol. 55, 958–976 (2014).

    Article  CAS  PubMed  Google Scholar 

  5. Box, M. S. et al. ELF3 controls thermoresponsive growth in Arabidopsis. Curr. Biol. 25, 194–199 (2014).

    Article  PubMed  CAS  Google Scholar 

  6. Ezer, D. et al. The evening complex coordinates environmental and endogenous signals in Arabidopsis. Nat. Plants 3, 17087 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Jung, J.-H. et al. Phytochromes function as thermosensors in Arabidopsis. Science 354, 886–889 (2016).

    Article  CAS  PubMed  Google Scholar 

  8. Legris, M. et al. Phytochrome B integrates light and temperature signals in Arabidopsis. Science 354, 897–900 (2016).

    Article  CAS  PubMed  Google Scholar 

  9. Nozue, K. et al. Rhythmic growth explained by coincidence between internal and external cues. Nature 448, 358–361 (2007).

    Article  CAS  PubMed  Google Scholar 

  10. Nomoto, Y. et al. Circadian clock and PIF4-mediated external coincidence mechanism coordinately integrates both of the cues from seasonal changes in photoperiod and temperature to regulate plant growth in Arabidopsis thaliana. Plant Signal. Behav. 8, e22863 (2013).

    Article  PubMed  CAS  Google Scholar 

  11. Nomoto, Y., Kubozono, S., Yamashino, T., Nakamichi, N. & Mizuno, T. Circadian clock- and PIF4-controlled plant growth: a coincidence mechanism directly integrates a hormone signaling network into the photoperiodic control of plant architectures in Arabidopsis thaliana. Plant Cell Physiol. 53, 1950–1964 (2012).

    Article  CAS  PubMed  Google Scholar 

  12. Kunihiro, A. et al. PHYTOCHROME-INTERACTING FACTOR 4 and 5 (PIF4 and PIF5) activate the homeobox ATHB2 and auxin-inducible IAA29 genes in the coincidence mechanism underlying photoperiodic control of plant growth of Arabidopsis thaliana. Plant Cell Physiol. 52, 1315–1329 (2011).

    Article  CAS  PubMed  Google Scholar 

  13. Michael, T. P. et al. A morning-specific phytohormone gene expression program underlying rhythmic plant growth. PLoS Biol. 6, e225 (2008).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  14. Niwa, Y., Yamashino, T. & Mizuno, T. The circadian clock regulates the photoperiodic response of hypocotyl elongation through a coincidence mechanism in Arabidopsis thaliana. Plant Cell Physiol. 50, 838–854 (2009).

    Article  CAS  PubMed  Google Scholar 

  15. Qiu, Y., Li, M., Kim, R. J.-A., Moore, C. M. & Chen, M. Daytime temperature is sensed by phytochrome B in Arabidopsis through a transcriptional activator HEMERA. Nat. Commun. 10, 140 (2019).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  16. Park, Y.-J., Lee, H.-J., Ha, J.-H., Kim, J. Y. & Park, C.-M. COP1 conveys warm temperature information to hypocotyl thermomorphogenesis. New Phytol. 215, 269–280 (2017).

    Article  CAS  PubMed  Google Scholar 

  17. Song, Y. H. et al. Molecular basis of flowering under natural long-day conditions in Arabidopsis. Nat. Plants 4, 824–835 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Sun, J., Qi, L., Li, Y., Chu, J. & Li, C. Pif4-mediated activation of yucca8 expression integrates temperature into the auxin pathway in regulating Arabidopsis hypocotyl growth. PLoS Genet. 8, e1002594 (2012).

  19. Charng, Y. Y. et al. A heat-inducible transcription factor, HsfA2, is required for extension of acquired thermotolerance in Arabidopsis. Plant Physiol. 143, 251–262 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Kortmann, J. & Narberhaus, F. Bacterial RNA thermometers: molecular zippers and switches. Nat. Rev. Microbiol. 10, 255–265 (2012).

    Article  CAS  PubMed  Google Scholar 

  21. Morita, M. T. et al. Translational induction of heat shock transcription factor sigma32: evidence for a built-in RNA thermosensor. Genes Dev. 13, 655–665 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Altuvia, S., Kornitzer, D., Teff, D. & Oppenheim, A. B. Alternative mRNA structures of the cIII gene of bacteriophage lambda determine the rate of its translation initiation. J. Mol. Biol. 210, 265–280 (1989).

    Article  CAS  PubMed  Google Scholar 

  23. Hartwig, R., Schweiger, R. & Schweiger, H. Circadian rhythm of the synthesis of a high molecular weight protein in anucleate cells of the green alga Acetabularia. Eur. J. Cell Biol. 41, 139–141 (1986).

    CAS  Google Scholar 

  24. Juntawong, P. & Bailey-Serres, J. Dynamic light regulation of translation status in Arabidopsis thaliana. Front. Plant Sci. 3, 66 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Floris, M., Bassi, R., Robaglia, C., Alboresi, A. & Lanet, E. Post-transcriptional control of light-harvesting genes expression under light stress. Plant Mol. Biol. 82, 147–154 (2013).

    Article  CAS  PubMed  Google Scholar 

  26. Missra, A. et al. The circadian clock modulates global daily cycles of mRNA ribosome loading. Plant Cell 27, 2582–2599 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Koini, M. A. et al. High temperature-mediated adaptations in plant architecture require the bHLH transcription factor PIF4. Curr. Biol. 19, 408–413 (2009).

    Article  CAS  PubMed  Google Scholar 

  28. Stavang, J. A. et al. Hormonal regulation of temperature-induced growth in Arabidopsis. Plant J. 60, 589–601 (2009).

    Article  CAS  PubMed  Google Scholar 

  29. Leivar, P. et al. The Arabidopsis phytochrome-interacting factor PIF7, together with PIF3 and PIF4, regulates responses to prolonged red light by modulating phyB levels. Plant Cell 20, 337–352 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Li, L. et al. Linking photoreceptor excitation to changes in plant architecture. Genes Dev. 26, 785–790 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. de Wit, M., Ljung, K. & Fankhauser, C. Contrasting growth responses in lamina and petiole during neighbor detection depend on differential auxin responsiveness rather than different auxin levels. New Phytol. 208, 198–209 (2015).

    Article  PubMed  CAS  Google Scholar 

  32. Leivar, P. & Quail, P. H. PIFs: pivotal components in a cellular signaling hub. Trends Plant Sci. 16, 19–28 (2011).

    Article  CAS  PubMed  Google Scholar 

  33. Xu, X., Paik, I., Zhu, L. & Huq, E. Illuminating progress in phytochrome-mediated light signaling pathways. Trends Plant Sci. 20, 641–650 (2015).

    Article  CAS  PubMed  Google Scholar 

  34. Lorrain, S., Allen, T., Duek, P. D., Whitelam, G. C. & Fankhauser, C. Phytochrome-mediated inhibition of shade avoidance involves degradation of growth-promoting bHLH transcription factors. Plant J. 53, 312–323 (2008).

    Article  CAS  PubMed  Google Scholar 

  35. Fernández, V., Takahashi, Y., Le Gourrierec, J. & Coupland, G. Photoperiodic and thermosensory pathways interact through CONSTANS to promote flowering at high temperature under short days. Plant J. 86, 426–440 (2016).

    Article  PubMed  CAS  Google Scholar 

  36. Oh, E., Zhu, J.-Y. & Wang, Z.-Y. Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses. Nat. Cell Biol. 14, 802–809 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Ezer, D. et al. The G-box transcriptional regulatory code in Arabidopsis. Plant Physiol. 175, 628–640 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Kidokoro, S. et al. The phytochrome-interacting factor PIF7 negatively regulates DREB1 expression under circadian control in Arabidopsis. Plant Physiol. 151, 2046–2057 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Yao, Y. & Kovalchuk, I. Multiple roles of WRKY22 in Arabidopsis thaliana. In 19th International Conference on Arabidopsis Research (Eds. Kieber, J. & Chen, X.) (NAASC, 2008).

  40. David, M. et al. Preferential translation of Hsp83 in Leishmania requires a thermosensitive polypyrimidine-rich element in the 3′ UTR and involves scanning of the 5′ UTR. RNA 16, 364–374 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Su, Z. et al. Genome-wide RNA structurome reprogramming by acute heat shock globally regulates mRNA abundance. Proc. Natl Acad. Sci. USA 115, 12170–12175 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Nieto, C., López-Salmerón, V., Davière, J.-M. & Prat, S. ELF3–PIF4 interaction regulates plant growth independently of the evening complex. Curr. Biol. 25, 187–193 (2015).

    Article  CAS  PubMed  Google Scholar 

  43. Han, X. et al. Arabidopsis transcription factor TCP5 controls plant thermomorphogenesis by positively regulating PIF4 activity. iScience 15, 611–622 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Zhou, Y. et al. TCP transcription factors associate with PHYTOCHROME INTERACTING FACTOR 4 and CRYPTOCHROME 1 to regulate thermomorphogenesis in Arabidopsis thaliana. iScience 15, 600–610 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Feng, S. et al. Coordinated regulation of Arabidopsis thaliana development by light and gibberellins. Nature 451, 475–479 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. de Lucas, M. et al. A molecular framework for light and gibberellin control of cell elongation. Nature 451, 480–484 (2008).

    Article  PubMed  CAS  Google Scholar 

  47. Fiorucci, A.-S. et al. PHYTOCHROME INTERACTING FACTOR 7 is important for early responses to elevated temperature in Arabidopsis seedlings. New Phytol. 226, 50–58 (2020).

    Article  CAS  PubMed  Google Scholar 

  48. Yamashino, T. et al. Verification at the protein level of the PIF4-mediated external coincidence model for the temperature-adaptive photoperiodic control of plant growth in Arabidopsis thaliana. Plant Signal. Behav. 8, e23390 (2013).

  49. Lee, C.-M. & Thomashow, M. F. Photoperiodic regulation of the C-repeat binding factor (CBF) cold acclimation pathway and freezing tolerance in Arabidopsis thaliana. Proc. Natl Acad. Sci. USA 109, 15054–15059 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Huang, X. et al. Shade-induced nuclear localization of PIF7 is regulated by phosphorylation and 14-3-3 proteins in Arabidopsis. eLife 7, e31636 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  51. Qiu, Y. et al. HEMERA couples the proteolysis and transcriptional activity of PHYTOCHROME INTERACTING FACTORs in Arabidopsis photomorphogenesis. Plant Cell 27, 1409–1427 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Dong, J. et al. Arabidopsis DE-ETIOLATED1 represses photomorphogenesis by positively regulating phytochrome-interacting factors in the dark. Plant Cell 26, 3630–3645 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Delker, C. et al. The DET1–COP1–HY5 pathway constitutes a multipurpose signaling module regulating plant photomorphogenesis and thermomorphogenesis. Cell Reports 9, 1983–1989 (2014).

    Article  CAS  PubMed  Google Scholar 

  54. Fujimori, T., Yamashino, T., Kato, T. & Mizuno, T. Circadian-controlled basic/helix-loop-helix factor, PIL6, implicated in light-signal transduction in Arabidopsis thaliana. Plant Cell Physiol. 45, 1078–1086 (2004).

    Article  CAS  PubMed  Google Scholar 

  55. Chung, B. Y. et al. The use of duplex-specific nuclease in ribosome profiling and a user-friendly software package for Ribo-seq data analysis. RNA 21, 1731–1745 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Chung, B. Y.-W., Deery, M. J., Groen, A. J., Howard, J. & Baulcombe, D. C. Endogenous miRNA in the green alga Chlamydomonas regulates gene expression through CDS-targeting. Nat. Plants 3, 787 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Hardcastle, T. J. & Kelly, K. A. baySeq: empirical Bayesian methods for identifying differential expression in sequence count data. BMC Bioinformatics 11, 422 (2010).

    Article  PubMed  PubMed Central  Google Scholar 

  58. Xiao, Z., Zou, Q., Liu, Y. & Yang, X. Genome-wide assessment of differential translations with ribosome profiling data. Nat. Commun. 7, 11194 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Szklarczyk, D. et al. The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible. Nucleic Acids Res. 45, D362–D368 (2017).

    Article  CAS  PubMed  Google Scholar 

  60. Yeast Protocols Handbook (Clontech Laboratories, Inc., 2009); http://www.takara.co.kr/file/manual/pdf/PT3024-1.pdf

  61. Goodstein, D. M. et al. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res. 40, D1178–D1186 (2011).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  62. Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Kim, D., Langmead, B. & Salzberg, S. L. HISAT: a fast spliced aligner with low memory requirements. Nat. Methods 12, 357–360 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Pertea, M. et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat. Biotechnol. 33, 290 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Banerjee, A. Clustering on the unit hypersphere using von Mises–Fisher distributions. J. Mach. Learn. Res. 6, 1345–1382 (2005).

    Google Scholar 

  66. Jaeger, K. E., Pullen, N., Lamzin, S., Morris, R. J. & Wigge, P. A. Interlocking feedback loops govern the dynamic behavior of the floral transition in Arabidopsis. Plant Cell 25, 820–833 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Zhang, Y. et al. Model-based analysis of ChIP–Seq (MACS). Genome Biol. 9, R137 (2008).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  69. Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Bailey, T. L. et al. MEME Suite: tools for motif discovery and searching. Nucleic Acids Res. 37, W202–W208 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Lorenz, R. et al. ViennaRNA Package 2.0. Algorithms Mol. Biol. 6, 26 (2011).

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We thank C. Fankhauser for discussions of unpublished results. This work was supported by: Wellcome Trust grant no. 096082 and Medical Research Council grant no. MR/R021821/1 to B.Y.W.C.; EMBO long-term postdoctoral fellowship grant no. ALTF 1418-2015 to M.B.; Wellcome Trust grant no. 106207 to A.E.F.; Gates Foundation Studentship to K.F.; and BBSRC David Phillips Fellowship grant no. BB/R011605/1 to M.D.A. P.A.W.’s laboratory was supported by a Fellowship from the Gatsby Foundation grant no. GAT3273/GLB. P.A.W’s Department is supported by the Leibniz Association.

Author information

Authors and Affiliations

Authors

Contributions

B.Y.W.C. and P.A.W. conceived the research. B.Y.W.C., M.B. and P.A.W. designed experiments and wrote the manuscript. B.Y.W.C. and M.B. performed most of the experiments. B.Y.W.C. performed ribosome profiling and RNA-seq. B.Y.W.C., M.B. and P.A.W. performed RNA structure analysis, and identified and characterized RNA thermometers. M.B. performed RNA-seq, phenotypic and molecular analyses. M.D.A. performed CD and FRET analysis. K.E.J. performed ChIP–seq. M.B. and P.M. generated tagged PIF7 transgenic plants. B.Y.W.C., K.F. and F.G. performed bioinformatics analysis. A.E.F., M.D.A. and I.B. commented on and revised the manuscript.

Corresponding authors

Correspondence to Betty Y. W. Chung or Philip A. Wigge.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Peer review information Nature Plants thanks Jorge Casal, Meng Chen, Ive De Smet and the 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.

Extended data

Extended Data Fig. 1 PIF7, HSFA2 and WRKY22 show enhanced translation at warm temperature.

a, Scatter plot of log fold changes in TE and mRNA abundance observed in Ribo-seq with parallel RNA-seq. bd, Histograms of 5′ end positions of normalized 28-nucleotide RPF reads (blue, green and red for frames 0, 1 and 2, left axis) and RNA-Seq reads (grey, right axis) mapped to the HSP70 (b), HSFA2 (c) and WRKY22 (d) transcript.

Extended Data Fig. 2 PIF7–MYC protein accumulation in response to warm temperature.

ad, Western blots of PIF7–MYC protein used for the quantification shown in Fig. 1m. The PIF7::PIF7–MYC line is in the Col-0 background. Actin levels are shown as loading control. e,f, Western blot (e) and quantification (f) of PIF7–MYC protein of an independent transgenic PIF7:: PIF7–MYC line in Col-0 background at ZT0 (dawn) and ZT12; seedlings were grown in LD at constant 17 °C or with a 27 °C midday for 7 d. Protein levels were normalized to actin. Bars represent the mean, error bars indicate the SEM (n = 3). The experiment was repeated once with similar results. gi, Western blots (g) and quantification (h) of PIF7–MYC protein as well as PIF7–MYC transcript levels (i) of PIF7::PIF7–MYC (Col-0) seedlings grown at constant 17 °C for 7 d and then either shifted to 27 °C at ZT4 (= 0 h) or kept at 17 °C for the indicated amount of time. Actin levels are shown as loading control. Protein levels were normalized to actin and expressed relative to levels at 0 h, transcript levels were normalized to PP2A and expressed relative to levels at 0 h. Data points represent the mean, error bars indicate the SEM (n = 3). The experiment was repeated once with similar results. j,k, Western blot of PIF7–MYC protein at ZT8 and ZT12 of PIF7::PIF7–MYC (Col-0) seedlings grown in LD at constant 17°C (j) or with a 27°C midday (k). Seedlings were treated with 100 µM cyclo- heximide (CHX), 50 µM MG132, a combination of the two or mock-treated at ZT4 on the day of sampling. Actin levels are shown as loading control. Two biological replicates are shown. The experiment was repeated once with similar results. The open arrow indicates an unspecific signal. Asterisks indicate significant differences to 17 °C control treatment (Two-sided Student’s t-test, * p < 0.05, ** p < 0.01, *** p < 0.001).

Extended Data Fig. 3 Additional thermomorphogenesis phenotypes in pif mutants.

ad, Hypocotyl length of 7-d-old Col-0 and pif mutant seedlings grown in LD at constant 17 °C, 22 °C and 27 °C (a) (n = 15), in SD at constant 17 °C, 22 °C and 27 °C (b) (n = 23, except for pif4 17 °C and 22 °C with n = 21 and pif7 27 °C with n = 22), in SD at constant 17 °C or with a daytime temperature at 27 °C (c) (n = 24 except for Col-0 27 °C with n= 19 and pif7 27 °C with n = 22) and in LD at constant 17 °C or with a warm midday of 27 °C (d) (n = 20 except for Col-0 17 °C and pif7 27 °C with n = 22), respectively. Seedlings were grown at 40 μmol m−2 s−1 in LD and 80 μmol m−2 s−1 in SD. e,f, Flowering time of Col-0 and pif mutant plants grown in LD at constant 17 °C or with a warm 37 °C midday (n = 12 except for pif4 pif7 with n = 11). Flowering time was scored as leaves at bolting (e) and days to bolting (f). gi, Hypocotyl length (g, h; n = 20–25) and stomatal index (SI) (i; n = 12) of 7-d-old and 14-d-old seedlings of two independent PIF7::PIF7–MYC complementation lines in the pif7-1 background, respectively. Seedlings were grown in LD at 17 °C with a warm midday of 27 °C. Box plots display the 25th and 75th percentile with the median as centre value and whiskers representing 1.5 times the IQR. Letters indicate significance groups; samples with the same letters are not significantly different (2-way ANOVA followed by two-sided Tukey test, p < 0.05). Asterisks indicate samples that are significantly different to Col-0 wild type (One-way ANOVA followed by two-sided Dunnett’s test, * p < 0.05, ** p < 0.01, *** p < 0.001). All experiments were repeated once with similar results.

Extended Data Fig. 4 The pif7 mutant lacks induction of a subset of temperature-responsive genes at 27 °C.

a,b, Average log fold change between expression at 27 °C and 17 °C for genes differentially expressed in pif7-1 (n = 1007) (a) and genes of cluster 7 identified in Fig. 3b (n = 293) (b). Box plots display the 25th and 75th percentile with the median as centre value and whiskers representing 1.5 times the IQR. Asterisks indicate significant differences (Two-sided Student’s t-test, * p < 0.05, ** p < 0.01, *** p < 0.001).

Extended Data Fig. 5 PIF7 affects auxin biosynthesis.

a,b, IGV browser view of PIF7–MYC binding at the YUC8 (a) and YUC9 (b) promoters. c,d, Relative expression of YUC8 (c) and YUC9 (d) observed in the RNA-seq experiment displayed in Fig. 3. Data are expressed relative to Col-0 27 °C at ZT8. e,f, Hypocotyl length of 7-d-old Col-0 or pif7-1 seedlings treated with 100 or 500 nM picloram (PIC) or mock-treated (n = 24). Box plots display the 25th and 75th percentile with the median as centre value and whiskers representing 1.5 times the IQR. Letters indicate significance groups; samples with the same letters are not significantly different (2-way ANOVA followed by two-sided Tukey test, p < 0.05). The experiment was repeated once with similar results.

Extended Data Fig. 6 PIF7 and PIF4 are likely to interact.

a, Venn diagram showing the overlap between PIF7–MYC and PIF4-HA ChIP–seq peaks. p-value was obtained by Fisher’s exact test for the independence of the two gene sets in comparison with the genomic background (n = 33554). b, IGV browser view of PIF7–MYC and PIF4-HA binding in the ATHB2 promoter. c, Yeast-2-hybrid assay testing interaction of PIF4 and PIF7 proteins expressed as fusions to a GAL4 binding domain (BD) or activation domain (AD). Empty vectors expressing BD and AD served as negative controls. The experiment was repeated once with similar results.

Extended Data Fig. 7 Hairpin structures in the 5′ UTR confer responsiveness to warm temperature.

a, mfe plot of the WRKY22 5′ UTR using a 40 nt sliding window. b, Predicted hairpin structure in the WRKY22 5′ UTR; mutated sequences used in in vitro studies are indicated in boxes. ce, In vitro translation of 5′ UTR hairpin::FLUC RNA fusions at different temperatures, using FLUC activity as read-out. Translation assays with WRKY22 (c) and 5′ -capped PIF7 (d) wild-type (WT), 3′ and 5′ disrupted (d3, d5), reconstituted (r) and stabilized (st) hairpin constructs as well as with PIF7 WT and mutated hairpin loop (mLoop) constructs (e) were performed. Data points represent the mean of two technical replicates. The experiments were repeated twice with similar results.

Extended Data Fig. 8 Mutations in the 5′ UTR hairpin affect PIF7–MYC protein accumulation.

Western blots of PIF7–MYC protein of independent PIF7::PIF7–MYC transgenic lines harbouring wild-type (WT), 3′ and 5′ disrupted (d3, d5), reconstituted (r) and stabilized (st) hairpin sequences. Seedlings were grown in LD at constant 17°C or with a 27°C midday. Actin levels are shown as loading control. Blots were used for quantifications shown in Fig. 4j–l and Extended Data Fig. 9b. The experiment was repeated once with similar results.

Extended Data Fig. 9 PIF7–MYC protein accumulation and hypocotyl elongation of transgenic PIF7::PIF7–MYC lines harbouring mutant hairpin sequences.

a, Quantification of PIF7–MYC protein at ZT12 in independent PIF7::PIF7–MYC transgenic lines har- bouring wild-type (WT), 3′ and 5′ disrupted (d3, d5), reconstituted (r) and stabilized (st) hairpin sequences. Seedlings were grown in LD at constant 17°C (left) or with a 27°C midday (right). Protein levels were normalized to actin and levels were expressed relative to the levels of the PIF7::PIF7–MYC (Col-0) line used in previous experiments to allow for comparisons across blots. Data points represent the mean, error bars indicate the SEM (n = 3). b, Hypocotyl length of the transgenic lines analysed in (a) (n = 25). Seedlings were grown in LD at constant 17°C (left) or with a 27°C midday (right) for 7 d. Box plots display the 25th and 75th percentile with the median as centre value and whiskers representing 1.5 times the IQR. The experiment was repeated once with similar results.

Supplementary information

Reporting Summary

Supplementary Tables

Supplementary Tables 1–7.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Chung, B.Y.W., Balcerowicz, M., Di Antonio, M. et al. An RNA thermoswitch regulates daytime growth in Arabidopsis. Nat. Plants 6, 522–532 (2020). https://doi.org/10.1038/s41477-020-0633-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41477-020-0633-3

This article is cited by

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