Publications

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 RJ*, 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. (* co-first authors).

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.

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.

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 (* Co-corresponding authors). The news release from UCR.

Hwang Y, Han S, Yoo CY, Hong L, You C, Le BH, 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. The news release from UCR.  

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 transcription activation domain in PIF3 by Arabidopsis phytochrome B. Nat Commun 12:5614. The news release from UCR. 

Willige, B.C., Zander, M., Yoo, C.Y., Phan, A., Garza, R.M., Trigg, S.A., He, Y., Nery, J.R., Chen, H., Chen, M., Ecker, J.R., Chory, J. (2021) PHYTOCHROME-INTERACTING FACTORs trigger environmentally responsive chromatin dynamics in plants. Nat Genet 53:955–961. 

Chen, M. (2021) Disengagement of light responses in Arabidopsis by localized developmental factors. Proc Natl Acad Sci U S A 118(21):e2106291118. 

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. doi: 10.1038/s41467-021-22313-x (*corresponding author). The news release from UCR. 

Yoo, C.Y., 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.

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. doi: 10.1038/s41467-020-15526-z. The news release from EurekAlert!

Yoo, C.Y., Williams, D., Chen, M. (2019) Quantitative analysis of photobodies. In: Hiltbrunner A. (eds) Phytochromes. Methods Mol Biol, vol 2026. Humana, New York, NY. doi: 10:1007/978-1-4939-9612-4_10.

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. The news release from Science Daily.

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. The news release from UCR  

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. The news releases from UCR and The New Food Economy  

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. UCR news release. 

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 173(4):1953-66. 

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.

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. 

Galvão, R.M., Li, M., Kothadia, S.M., Haskel, J.D., Decker, P.V., Van Buskirk, E.K., Chen, M. (2012) Photoactivated phytochromes interact with HEMERA and promote its accumulation to establish photomorphogenesis in Arabidopsis. Genes Dev 26:1851-63.

Van Buskirk, E.K., Decker, P.V., Chen, M. (2012) Photobodies in light signaling. Plant Physiol 158:52-60.

Chen, M.*, Chory, J.* (2011). Phytochrome signaling mechanisms and the control of plant development. Trends Cell Biol 21(11):664-671. (* 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):1230-40. (* Corresponding author) Read Duke and Salk news releases. 

Fankhauser C.*, Chen, M. (2008). Transposing phytochrome into the nucleus. Trends Plant Sci 13(11):596-601. (* Corresponding author)

Chen, M. (2008). Phytochrome nuclear body: an emerging model to study interphase nuclear dynamics and signaling. Curr Opin Plant Biol 11(5):503-8.

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.

Wang, Z.Y., Nakano, T., Gendron, J., He, J., Chen, M., Vafeados, D., Yang, Y., Fujioka, S., Yoshida, S., Asami, T., Chory, J. (2002). Nuclear-localized BZR1 mediates brassinosteroid-induced growth and feedback suppression of brassinosteroid biosynthesis. Dev Cell 2(4):505-513.

The Arabidopsis genome initiative (Chen, M. and Chory, J.). (2000). Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796-815.

Chen M., Choi, Y., Voytas, D.F., Rodermel, S.R. (2000). Mutations in the Arabidopsis VAR2 locus cause leaf variegation due to the loss of a chloroplast FtsH protease. Plant J 22(4):303-313.

Chen, M., Jensen, M., Rodermel, S.R. (1999). The yellow variegated mutant of Arabidopsis thaliana is plastid autonomous and delayed in chloroplast biogenesis. J Hered 90:207-14.

Martin, B.L., Luo, S., Kintanar, A., Chen, M., and Graves, D. J. (1998). Effect of citrulline for arginine replacement on the structure and turnover of phosphopeptide substrates of protein phosphatase-1. Arch Biochem Biophys 359:179-191.

Chen, M., Chen, L., and Fromm, H.J. (1994). Replacement of glutamic acid 29 with glutamine leads to a loss of cooperativity for AMP with porcine fructose-1,6-bisphosphatase. J Biol Chem 269:5554-58.

Chen, L., Hegde, R., Chen, M., and Fromm, H.J. (1993). Site-specific mutagenesis of the metal binding sites of porcine fructose-1,6-bisphosphatase. Arch Biochem Biophys 307:350-354.

Burton, V.A., Chen, M., Ong, W.C., Ling, T., Fromm, H.J., and Stayton, M.M. (1993). High-level expression of porcine fructose-1,6-bisphosphatase in E. Coli: purification and characterization of the enzyme. Biochem Biophys Res Commun 192:511-517.