Research

Research Area #1: Photobodies in light signaling. 

We investigate how the plant photoreceptor and thermosensor phytochrome B (phyB) controls gene expression through the dynamic assembly and disassembly of phyB-containing subnuclear biomolecular condensates, termed photobodies. Our goal is to define the mechanisms governing photobody formation, function, and regulation in phyB signaling and environmental control of transcription. We have identified both intrinsic phyB determinants and extrinsic factors required for photobody formation. In particular, we showed that photobody localization is mediated by phyB’s C-terminal signal-output module and depends on dimerization/oligomerization of the histidine-kinase-like domain. Using forward genetic screens, we discovered three key phyB signaling components—HEMERA, RCB, and NCP—that are required for photobody formation. More recently, we established a two-compartment logic of phyB signaling, in which photobodies and the surrounding nucleoplasm partition distinct—and in some cases opposing—signaling outputs to regulate transcription factor activity. We also showed that photobody number is not random but is controlled through regulated nucleation at defined subnuclear sites, providing a mechanism by which cells tune condensate abundance and signaling capacity in vivo. Our studies link these spatial behaviors to the regulation of the stability and activity of Phytochrome-Interacting Factors (PIFs), a small set of nodal transcriptional regulators that control growth and photosynthetic development. Together, these advances establish photobodies as a powerful genetic model for understanding how stimulus-regulated nuclear condensates organize signaling outputs and tune transcriptional programs in response to light and temperature.

– Du J., He J., Chen E.M., Deng T., Talati S., Chang D., Mikhail T., Chen, M. (2026) Phytochrome B sets condensate number through graded nucleator states and seeding-site efficacy. Nat Commun https://doi.org/10.1038/s41467-026-73929-w.
– Du J., Fan D., He J., Chen M. (2026) Twenty-five years of photobodies: formation, composition, and the two-compartment logic of phytochrome B signaling. Plant Physiol https://doi.org/10.1093/plphys/kiag058.
– Du J., Kim K., Chen M. (2024) Distinguishing individual photobodies using Oligopaints reveals thermo-sensitive and -insensitive phytochrome B condensation at distinct subnuclear locations. Nat Commun 15:3620.
– Kim R.J.*, Fan D.*, He J.*, Kim K., Du J., Chen M. (2024) Photobody formation spatially segregates two opposing phytochrome B actions of PIF5 degradation and stabilization. Nat Commun 15:3519.
– Liu, W, Lowrey, H, Leung, CC, Adamchek, C, Du, J, He, J, Chen, M, Gendron JM (2023) The circadian clock regulates PIF3 protein stability in parallel to red light. bioRxiv doi: https://doi.org/10.1101/2023.09.18.558326.
– Yoo, C.Y., He, J., Sang, Q., Qiu, Y., Long, L., Kim, R.J., Chong, E., Hahm, J., Morffy, N., Zhou, P., Strader, L.C., Nagatani, A., Mo, B., Chen, X., Chen, M. (2021) Direct photoresponsive inhibition of a p53-like transcriptional activation domain in PIF3 by Arabidopsis phytochrome B. Nat Commun 12:5614.
– Hahm, J., Kim, K., Qiu, Y., Chen, M. (2020) Increasing ambient temperature progressively disassembles Arabidopsis phytochrome B from individual photobodies with distinct thermostabilities. Nat Commun 11:1660.
– Yoo, C.Y., Pasoreck, E.K., Wang, H., Cao, J., Blaha, G.M., Weigel, D., Chen, M. (2019) Phytochrome activates the plastid-encoded RNA polymerase for chloroplast biogenesis via nucleus-to-plastid signaling. Nat Commun 10:2629. doi: 10.1038/s41467-019-10518-0.
– Qiu, Y., Li, M., Kim, R.J., Moore, C.M., Chen, M. (2019) Daytime temperature is sensed by phytochrome B in Arabidopsis through a transcriptional activator HEMERA. Nat Commun 10:140. doi: 10.1038/s41467-018-08059-z.
– Qiu, Y., Pasoreck, E.K., Reddy, A.K., Nagatani, A., Ma, W., Chory, J., Chen, M. (2017) Mechanism of early light signaling by the carboxy-terminal output module of Arabidopsis phytochrome B. Nat Commun 8(1):1905. doi: 10.1038/s41467-017-02062-6.
– Huang, H., Yoo, C., Bindbeutel, R.K., Goldsworthy, J., Tielking, A., Alvarez, S., Naldrett, M.J., Evans, B., Chen, M., Nusinow, D.A. (2016) PCH1 integrates circadian and light-signaling pathways to control photoperiod-responsive growth in Arabidopsis. eLife 5:e13292.
– Qiu, Y.*, Li, M.*, Pasoreck, E.K., Long, L., Shi, Y., Galvão, R.M., Chou, C.L., Wang, H., Sun, A.Y., Zhang, Y.C., Jiang, A., Chen, M. (2015) HEMERA couples the proteolysis and transcriptional activity of Phytochrome-Interacting Factors in Arabidopsis photomorphogenesis. Plant Cell 27:1409-1427. 
– Van Buskirk, E.K., Reddy, A.K., Nagatani, A., Chen, M. (2014) Photobody localization of phytochrome B is tightly correlated with prolonged and light-dependent inhibition of hypocotyl elongation in the dark. Plant Physiol 165(2):595-607.
– Van Buskirk E.K., Decker, P.V., Chen, M. (2012) Photobodies in light signaling. Plant Physiol 158(1):52-60.
– Chen, M.*, Chory, J.* (2011). Phytochrome signaling mechanisms and the control of plant development. Trends Cell Biol 21(11):664-71 (* Corresponding author).
– Chen, M.*, Galvão, R.M., Li, M., Burger, B., Bugea, J., Bolado, J., Chory, J.* (2010). Arabidopsis HEMERA/pTAC12 initiates photomorphogenesis by phytochromes. Cell 141(7): 1230-1240 (* Corresponding author).
– Chen, M., Tao, Y., Lim, J., Shaw, A., Chory, J. (2005). Regulation of phytochrome B nuclear localization through light-dependent unmasking of nuclear localization signals. Curr Biol 15(7):637-42.
– Chen, M., Chory, J., Fankhauser, C. (2004). Light signal transduction in higher plants. Annu Rev Genet 38:87-117.
– Chen, M., Schwab, R., and Chory, J. (2003). Characterization of requirements for localization of phytochrome B to nuclear bodies. Proc Natl Acad Sci U S A 100(24):14493-14498.

Research Area #2: Daytime high-temperature signaling. 

Temperature sensing is essential for organismal survival. Beyond stress responses to extreme cold or heat, moderate increases in ambient growth temperature can trigger profound adaptive changes in plant development, growth, metabolism, and immunity—collectively termed thermomorphogenesis. In nature, plants often experience warm temperatures during the daytime, coinciding with high light intensity, yet the mechanisms underlying daytime thermosensing remain elusive. Our work has defined a multisensor high-temperature signaling framework in which multiple pathways converge on the abundance and activity of the central thermal regulator PIF4 to ensure robust daytime thermomorphogenic growth under sunlight. In this model, the multisensory network includes (i) phyB thermal reversion as a temperature-sensing input that becomes negligible under strong light, (ii) a chloroplast- and sucrose-dependent pathway that promotes PIF4 stability, and (iii) ELF3-mediated regulation of PIF4 transcription and PIF4 activity. In parallel, we discovered that microRNA-mediated regulation tunes thermomorphogenic growth by modulating temperature-responsive signaling and hormone sensitivity. We are now dissecting the molecular mechanisms of these pathways to understand how plants integrate temperature and light cues to optimize growth in fluctuating environments.

– Xiong H., Bajracharya A., Odari R., Bayer E.E., Stoner A., Wasti A., Xi J., Baerson S.R., Chen M., Qiu Y. (2026) Oligomerization-competent PIF4 drives thermomorphogenesis through functional redundancy in transactivation and DNA binding. Nat Commun https://doi.org/10.1038/s41467-026-70748-x.
– Fan D., Chen M. (2024) Dissection of daytime and nighttime thermoresponsive hypocotyl elongation in Arabidopsis. In: Chen, M. (eds) Thermomorphogenesis. Methods Mol Biol vol 2795, Humana, New York, NY. doi: https://doi.org/10.1007/978-1-0716-3814-9_2.
– Du J., Chen M. (2024) Characterization of thermoresponsive photobody dynamics. In: Chen, M. (eds) Thermomorphogenesis. Methods Mol Biol vol 2795, Humana, New York, NY. doi: https://doi.org/10.1007/978-1-0716-3814-9_10.
– Chen M. (eds) (2024) Thermomorphogenesis. Methods Mol Biol vol 2795, Humana, New York, NY. doi: https://doi.org/10.1007/978-1-0716-3814-9.
– Quint M, Delker C, Balasubramanian S, Balcerowicz M, Casal JJ, Castroverde CDM, Chen M, Chen X, De Smet I, Fankhauser C, Franklin KA, Halliday KJ, Hayes S, Jiang D, Jung JH, Kaiserli E, Kumar SV, Maag D, Oh E, Park CM, Penfield S, Perrella G, Prat S, Reis RS, Wigge PA, Willige BC, van Zanten M. (2023) 25 years of thermomorphogenesis research: milestones and perspectives. Trends Plant Sci. doi: 10.1016/j.tplants.2023.07.001.
– Sang Q, Fan L, Liu T, Qiu Y, Du J, Mo B, Chen M*, Chen X*. (2023) MicroRNA156 conditions auxin sensitivity to enable growth plasticity in response to environmental changes in Arabidopsis. Nat Commun  14:1449.
– Qiu, Y.*, Pasoreck, E.K., Yoo, C.Y., He, J., Wang, H., Li, M., Larsen, H.D., Cheung, S., Chen, M.* (2021) RCB initiates Arabidopsis thermomorphogenesis by stabilizing the thermoregulator PIF4 in the daytime. Nat Commun  12:2042.
– Hahm, J., Kim, K., Qiu, Y., Chen, M. (2020) Increasing ambient temperature progressively disassembles Arabidopsis phytochrome B from individual photobodies with distinct thermostabilities. Nat Commun 11:1660.
– Qiu, Y., Li, M., Kim, R.J., Moore, C.M., Chen, M. (2019) Daytime temperature is sensed by phytochrome B in Arabidopsis through a transcriptional activator HEMERA. Nat Commun 10:140. doi: 10.1038/s41467-018-08059-z.

Research Area #3: Anterograde signaling for controlling plastid transcription. 

Our molecular genetic dissection of phytochrome signaling serendipitously uncovered a nucleus-to-plastid (anterograde) signaling pathway that links light perception in the nucleus to regulation of plastid gene expression during chloroplast biogenesis. We showed that phytochrome-triggered removal of nuclear repressors of chloroplast development—most notably PIF transcription factors—initiates light-dependent assembly and activation of the bacterial-type plastid RNA polymerase (PEP) to drive transcription of plastid-encoded photosynthesis genes. Unexpectedly, we found that this pathway is mediated by a set of dual-targeted signaling components, including HMR, RCB, and NCP, which coordinate information flow between the nucleus and plastids. Together, these advances provide a mechanistic framework for how light signaling controls chloroplast biogenesis and how nuclear and organellar gene expression programs are coordinated during the photoautotrophic developmental transition, and they establish a powerful genetic model for investigating how the nucleus controls organellar transcription.

– Flynn N., Chen X.*, Chen M.* (2024) Plastid transcription: A major regulatory point in chloroplast biogenesis. In: Burch-Smith T. (eds) Chloroplast Gene Expression: Regulation, Signaling and Biotechnology. Nucleic Acids & Mol Biol vol 37, Springer, Cham, Switzerland. (* Co-corresponding authors) doi:10.1007/978-3-031-70098-9_1.
– Hwang Y., Han S, Yoo C.Y., Hong L., You C., Le B.H., Shi H., Zhong S., Hoecker U., Chen X., Chen M. (2022) Anterograde signaling controls plastid transcription via sigma factors separately from nuclear photosynthesis genes. Nat Commun 13:7440.
– Yoo, C.Y., He, J., Sang, Q., Qiu, Y., Long, L., Kim, R.J., Chong, E., Hahm, J., Morffy, N., Zhou, P., Strader, L.C., Nagatani, A., Mo, B., Chen, X., Chen, M. (2021) Direct photoresponsive inhibition of a p53-like transcriptional activation domain in PIF3 by Arabidopsis phytochrome B. Nat Commun 12:5614.
– Qiu, Y.*, Pasoreck, E.K., Yoo, C.Y., He, J., Wang, H., Li, M., Larsen, H.D., Cheung, S., Chen, M.* (2021) RCB initiates Arabidopsis thermomorphogenesis by stabilizing the thermoregulator PIF4 in the daytime. Nat Commun 12:2042.
– Yoo CY, Han S, Chen M. (2020) Nucleus-to-plastid phytochrome signalling in controlling chloroplast biogenesis. Annu Plant Rev 3:251-280. doi: 10.1002/9781119312994.apr0615.
– Yang, E.M., Yoo, C.Y., Liu, J., Wang, H., Cao, J., Li, F-W, Pryer, K.M., Sun, T., Weigel, D., Zhou, P.*, Chen, M.* (2019) NCP activates chloroplast transcription by controlling phytochrome-dependent dual nuclear and plastidial switches. Nat Commun 10:2630. doi: 10.1038/s41467-019-10517-1.
– Yoo, C.Y., Pasoreck, E.K., Wang, H., Cao, J., Blaha, G.M., Weigel, D., Chen, M. (2019) Phytochrome activates the plastid-encoded RNA polymerase for chloroplast biogenesis via nucleus-to-plastid signaling. Nat Commun 10:2629. doi: 10.1038/s41467-019-10518-0.
– Nevarez P.A., Qiu, Y., Inoue, H., Yoo, C., Benfey, P.N., Schnell, D.J., Chen, M. (2017) Mechanism of dual-targeting of the phytochrome signaling component HEMERA/pTAC12 to plastids and the nucleus. Plant Physiol DOI:10.1104/pp.16.00116.
– Qiu, Y.*, Li, M.*, Pasoreck, E.K., Long, L., Shi, Y., Galvão, R.M., Chou, C.L., Wang, H., Sun, A.Y., Zhang, Y.C., Jiang, A., Chen, M. (2015) HEMERA couples the proteolysis and transcriptional activity of Phytochrome-Interacting Factors in Arabidopsis photomorphogenesis. Plant Cell 27:1409-1427.

Research Area #4: Spatial positioning of individual genes in plants.

A growing body of evidence from studies in yeast and metazoan models suggests that spatial positioning of individual genes plays an important role in transcriptional regulation. However, the mechanism controlling gene positioning is still poorly understood. We have shown that the light-inducible photosynthetic genes, such as the CAB1 locus, in Arabidopsis are rapidly relocated from the nuclear interior to the nuclear periphery during their transcriptional activation. The repositioning of CAB1 to the nuclear periphery is controlled by phytochromes and phytochrome signaling components. Our study of the positioning of the photosynthetic genes provides the initial evidence demonstrating the biological importance of gene positioning in plants. We currently use CAB1 as a model to investigate mechanisms of gene repositioning by cell signaling.

– Feng, C.-M., Qiu, Y., Van Buskirk, E.K., Yang, E.J., Chen, M. (2014) Light-regulated gene repositioning in Arabidopsis. Nat Commun 5:3027 doi: 10.1038/ncomms4027.