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Han R#, Ma L#, Lv Y, Qi L, Peng J, Li H, Zhou Y, Song P, Duan J, Li J, Li Z, Terzaghi W, Guo Y, Li J* (2023). SALT OVERLY SENSITIVE2 stabilizes phytochrome-interacting factors PIF4 and PIF5 to promote Arabidopsis shade avoidance. Plant Cell doi: 10.1093/plcell/koad119.
Ma L#, Han R#, Yang Y, Liu X, Li H, Zhao X, Li J, Fu H, Huo Y, Sun L, Yan Y, Zhang H, Li Z, Tian F, Li J*, Guo Y* (2023). Phytochromes enhance SOS2-mediated PIF1 and PIF3 phosphorylation and degradation to promote Arabidopsis salt tolerance. Plant Cell doi: 10.1093/plcell/koad117.
Song P#, Yang Z#, Guo C, Han R, Wang H, Dong J, Kang D, Guo Y, Yang S, Li J* (2023). 14-3-3 proteins regulate photomorphogenesis by facilitating light-induced degradation of PIF3. New Phytol 237:140-159.
Lin X, Dong L, Tang Y, Li H, Cheng Q, Li H, Zhang T, Ma L, Xiang H, Chen L, Nan H, Fang C, Lu S, Li J, Liu B, Kong F (2022). Novel and multifaceted regulations of photoperiodic flowering by phytochrome A in soybean. Proc Natl Acad Sci USA 119:e2208708119.
Li T, Li H, Lian H, Song P, Wang Y, Duan J, Song Z, Cao Y, Xu D, Li J, Zhang H (2022). SICKLE represses photomorphogenic development of Arabidopsis seedlings via HY5- and PIF4-mediated signaling. J Integr Plant Biol 64:1706-1723.
Wang Y, Su C, Yu Y, He Y, Wei H, Li N, Li H, Duan J, Li B, Li J, Davis SJ, Wang L (2022). TIME FOR COFFEE regulates phytochrome A-mediated hypocotyl growth through dawn-phased signaling. Plant Cell 34:2907-2924.
Peng J, Wang M, Wang X, Qi L, Guo C, Li H, Li C, Yan Y, Zhou Y, Terzaghi W, Li Z, Song CP, Qin F, Gong Z, Li J* (2022). COP1 positively regulates ABA signaling during Arabidopsis seedling growth in darkness by mediating ABA-induced ABI5 accumulation. Plant Cell 34:2286-2308.
Qi L#, Shi Y#, Terzaghi W, Yang S*, Li J* (2022). Integration of light and temperature signaling pathways in plants. J Integr Plant Biol 64:393-411.
Li C#, Qi L#, Zhang S, Dong X, Jing Y, Cheng J, Feng Z, Peng J, Li H, Zhou Y, Wang X, Han R, Duan J, Terzaghi W, Lin R, Li J* (2022). Mutual upregulation of HY5 and TZP in mediating phytochrome A signaling. Plant Cell 34:633-654.
Li Y, Shi Y, Li M, Fu D, Wu S, Li J, Gong Z, Liu H, Yang S (2021). The CRY2-COP1-HY5-BBX7/8 module regulates blue light-dependent cold acclimation in Arabidopsis. Plant Cell 33:3555-3573.
Liu S, Yang L, Li J, Tang W, Li J, Lin R (2021). FHY3 interacts with phytochrome B and regulates seed dormancy and germination. Plant Physiol 187:289-302.
Li J*, Hiltbrunner A* (2021). Is the Pr form of phytochrome biologically active in the nucleus? Mol Plant 14:535-537.
Li H, Qin X, Song P, Han R, Li J* (2021). A LexA-based yeast two-hybrid system for studying light-switchable interactions of phytochromes with their interacting partners. aBIOTECH 2:105–116.
Song P, Zhang S, Li J* (2021). Co-immunoprecipitation assays to detect in vivo association of phytochromes with their interacting partners. Methods Mol Biol 2297:75-82.
Pan W, Lin B, Yang X, Liu L, Xia R, Li J, Wu Y, Xie Q (2020). The UBC27-AIRP3 ubiquitination complex modulates ABA signaling by promoting the degradation of ABI1 in Arabidopsis. Proc Natl Acad Sci USA 117:27694-27702.
Gong Z, Xiong L, Shi H, Yang S, Herrera-Estrella LR, Xu G, Chao DY, Li J, Wang PY, Qin F, Li J, Ding Y, Shi Y, Wang Y, Yang Y, Guo Y, Zhu JK (2020). Plant abiotic stress response and nutrient use efficiency. Sci China Life Sci 63:635-674.
Dong X, Yan Y, Jiang B, Shi Y, Jia Y, Cheng J, Shi Y, Kang J, Li H, Zhang D, Qi L, Han R, Zhang S, Zhou Y, Wang X, Terzaghi W, Gu H, Kang D*, Yang S*, Li J* (2020). The cold response regulator CBF1 promotes Arabidopsis hypocotyl growth at ambient temperatures. EMBO J 39:e103630.
Yan Y, Li C, Dong X, Li H, Zhang D, Zhou Y, Jiang B, Peng J, Qin X, Cheng J, Wang X, Song P, Qi L, Zheng Y, Li B, Terzaghi W, Yang S, Guo Y, Li J* (2020). MYB30 is a key negative regulator of Arabidopsis photomorphogenic development that promotes PIF4 and PIF5 protein accumulation in the light. Plant Cell 32:2196-2215.
This paper was featured in: Bertoni G. MYB30 regulates photomorphogenesis via interactions with active phytochromes and PIFs. Plant Cell 32: 2065–2066.
Jiang B, Shi Y, Peng Y, Jia Y, Yan Y, Dong X, Li H, Dong J, Li J, Gong Z, Thomashow MF, Yang S (2020). Cold-Induced CBF-PIF3 interaction enhances freezing tolerance by stabilizing the phyB thermosensor in Arabidopsis. Mol Plant 13:894-906.
Qu GP, Li H, Lin XL, Kong X, Hu ZL, Jin YH, Liu Y, Song HL, Kim DH, Lin R, Li J, Jin JB (2020). Reversible SUMOylation of FHY1 regulates phytochrome A signaling in Arabidopsis. Mol Plant 13:879-893.
Qi L, Liu S, Li C, Fu J, Jing Y, Cheng J, Li H, Zhang D, Wang X, Dong X, Han R, Li B, Zhang Y, Li Z, Terzaghi W, Song CP, Lin R, Gong Z, Li J* (2020). PHYTOCHROME-INTERACTING FACTORS interact with the ABA receptors PYL8 and PYL9 to orchestrate ABA signaling in darkness. Mol Plant 13:414-430.
Zhang H, Zhang Q, Zhai H, Gao S, Yang L, Wang Z, Xu Y, Huo J, Ren Z, Zhao N, Wang X, Li J, Liu Q, He S (2020). IbBBX24 promotes the jasmonic acid pathway and enhances fusarium wilt resistance in sweet potato. Plant Cell 32:1102-1123.
Qin N, Xu D, Li J, Deng XW (2020). COP9 signalosome: Discovery, conservation, activity, and function. J Integr Plant Biol 62:90-103.
Wen C, Zhao W, Liu W, Yang L, Wang Y, Liu X, Xu Y, Ren H, Guo Y, Li C, Li J, Weng Y, Zhang X (2019). CsTFL1 inhibits determinate growth and terminal flower formation through interaction with CsNOT2a in cucumber. Development 146:dev180166.
Wang L, Cheng M, Yang Q, Li J, Wang X, Zhou Q, Nagawa S, Xia B, Xu T, Huang R, He J, Li C, Fu Y, Liu Y, Bao J, Wei H, Li H, Tan L, Gu Z, Xia A, Huang X, Yang Z, Deng XW (2019). Arabinogalactan protein-rare earth element complexes activate plant endocytosis. Proc Natl Acad Sci USA 116:14349-14357.
Zhang H, Gao X, Zhi Y, Li X, Zhang Q, Niu J, Wang J, Zhai H, Zhao N, Li J, Liu Q, He S (2019). A non-tandem CCCH-type zinc-finger protein, IbC3H18, functions as a nuclear transcriptional activator and enhances abiotic stress tolerance in sweet potato. New Phytol 223:1918-1936.
Du XQ, Wang FL, Li H, Jing S, Yu M, Li J, Wu WH, Kudla J, Wang Y (2019). The transcription factor MYB59 regulates K+/NO3- translocation in the Arabidopsis response to low K+ stress. Plant Cell 31:699-714.
Zhang L, Zhang X, Wang X, Xu J, Wang M, Li L, Bai G, Fang H, Hu S, Li J, Yan J, Li J, Yang X (2019). SEED CAROTENOID DEFICIENT functions in isoprenoid biosynthesis via the plastid MEP pathway. Plant Physiol 179:1723-1738.
Wang X, Guo C#, Peng J#, Li C#, Wan F#, Zhang S, Zhou Y, Yan Y, Qi L, Sun K, Yang S, Gong Z, Li J* (2019). ABRE-BINDING FACTORS play a role in the feedback regulation of ABA signaling by mediating rapid ABA induction of ABA co-receptor genes. New Phytol 221:341-355.
Zhou Y#, Yang L#, Duan J, Cheng J, Shen Y, Wang X, Han R, Li H, Li Z, Wang L, Terzaghi W, Zhu D, Chen H, Deng XW*, Li J* (2018). Hinge region of Arabidopsis phyA plays an important role in regulating phyA function. Proc Natl Acad Sci USA 115:E11864-E11873.
Wang Q, Qu GP, Kong X, Yan Y, Li J, Jin JB (2018). Arabidopsis small ubiquitin-related modifier protease ASP1 positively regulates abscisic acid signaling during early seedling development. J Integr Plant Biol 60:924-937.
Wang K, He J, Zhao Y, Wu T, Zhou X, Ding Y, Kong L, Wang X, Wang Y, Li J, Song CP, Wang B, Yang S, Zhu JK, Gong Z (2018). EAR1 negatively regulates ABA signaling by enhancing 2C protein phosphatase activity. Plant Cell 30:815-834.
Zhang S#, Li C#, Zhou Y, Wang X, Li H, Feng Z, Chen H, Qin G, Jin D, Terzaghi W, Gu H, Qu LJ, Kang D*, Deng XW, Li J* (2018). TANDEM ZINC-FINGER/PLUS3 is a key component of phytochrome A signaling. Plant Cell 30:835-852.
This paper was featured in: Salomé PA. Developmental timing is everything: TZP and phytochrome signaling. Plant Cell 30:741-742.
Jin D, Wu M, Li B, Bücker B, Keil P, Zhang S, Li J, Kang D, Liu J, Dong J, Deng XW, Irish V, Wei N (2018). The COP9 Signalosome regulates seed germination by facilitating protein degradation of RGL2 and ABI5. PLoS Genet 14:e1007237.
Xin X, Chen W, Wang B, Zhu F, Li Y, Yang H, Li J, Ren D (2018). Arabidopsis MKK10-MPK6 mediates red-light-regulated opening of seedling cotyledons through phosphorylation of PIF3. J Exp Bot 69:423-439.
Wang Z, Wang J, Li N, Li J, Trail F, Dunlap JC, Townsend JP (2018). Light sensing by opsins and fungal ecology: NOP-1 modulates entry into sexual reproduction in response to environmental cues. Mol Ecol 27:216-232.
Lian N#, Liu X#, Wang X#, Zhou Y, Li H, Li J*, Mao T* (2017). COP1 mediates dark-specific degradation of microtubule-associated protein WDL3 in regulating Arabidopsis hypocotyl elongation. Proc Natl Acad Sci USA 114:12321-12326.
Jiang B#, Shi Y#, Zhang X, Xin X, Qi L, Guo H, Li J*, Yang S* (2017). PIF3 is a negative regulator of the CBF pathway and freezing tolerance in Arabidopsis. Proc Natl Acad Sci USA 114:E6695-E6702.
Li J, Wu Y, Xie Q, Gong Z (2017) Abscisic acid. In: Li J, Li C, Smith SM (Eds.), Hormone Metabolism and Signaling in Plants. Academic Press, United States of America, 161-202.
Wang L, He J, Yang Q, Lv X, Li J, Chen DDY, Ding X, Huang X, Zhou Q (2017) Abnormal pinocytosis and valence-variable behaviors of cerium suggested a cellular mechanism for plant yield reduction induced by environmental cerium. Environ Pollut 230:902-910.
Xu D, Jiang Y, Li J, Lin F, Holm M, Deng XW (2016). BBX21, an Arabidopsis B-box protein, directly activates HY5 and is targeted by COP1 for 26S proteasome-mediated degradation. Proc Natl Acad Sci USA 113:7655-7660.
Wang Z, Li N, Li J, Dunlap JC, Trail F, Townsend JP (2016). The fast-evolving phy-2 gene modulates sexual development in response to light in the model fungus Neurospora crassa. MBio 7:e02148-15.
Kong L, Cheng J, Zhu Y, Ding Y, Meng J, Chen Z, Xie Q, Guo Y, Li J, Yang S, Gong Z (2015). Degradation of the ABA co-receptor ABI1 by PUB12/13 U-box E3 ligases. Nat Commun 6:8630.
Yang L, Li B, Zheng XY, Li J, Yang M, Dong X, He G, An C, Deng XW (2015). Salicylic acid biosynthesis is enhanced and contributes to increased biotrophic pathogen resistance in Arabidopsis hybrids. Nat Commun 6:7309.
Wang C, Zheng Y, Zhao Y, Zhao Y, Li J, Guo Y (2015). SCAB3 is required for reorganization of actin filaments during light quality changes. J Genet Genomics 42:161-168.
Zhang H, Zhao X, Li J, Cai H, Deng XW, Li L (2014). MicroRNA408 is critical for the HY5-SPL7 gene network that mediates the coordinated response to light and copper. Plant Cell 26:4933-4953.
Wang L#, Li J#, Zhou Q, Yang G, Ding XL, Li X, Cai CX, Zhang Z, Wei HY, Lu TH, Deng XW, Huang XH (2014). Rare earth elements activate endocytosis in plant cells. Proc Natl Acad Sci USA 111: 12936-12941. (# equal contribution)
Xu D, Lin F, Jiang Y, Huang X, Li J, Ling J, Hettiarachchi C, Tellgren-Roth C, Holm M, Deng XW (2014). The RING-finger E3 ubiquitin ligase COP1 SUPPRESSOR1 negatively regulates COP1 abundance in maintaining COP1 homeostasis in dark-grown Arabidopsis seedlings. Plant Cell 26:1981-1991.
Xu D#, Li J#, Gangappaa SN, Hettiarachchia C, Lin F, Andersson MX, Jiang Y, Deng XW, Holm M (2014). Convergence of light and ABA signaling on the ABI5 promoter. PLoS Genet 10:e1004197. (# equal contribution)
Zhu D, Wu Z, Cao G, Li J, Wei J, Tsuge T, Gu H, Aoyama T and Qu LJ (2014). TRANSLUCENT GREEN, an ERF family transcription factor, controls water balance in Arabidopsis by activating the expression of aquaporin genes. Mol Plant 7:601-615.
Li J, Yang L, Jin D, Nezames CD, Terzaghi W and Deng XW (2013). UV-B-induced photomorphogenesis in Arabidopsis. Protein Cell 7: 485–492.
He G#, Chen B#, Wang X#, Li X#, Li J#, He H, Yang M, Lu L, Qi Y, Wang X and Deng XW (2013). Conservation and divergence of transcriptomic and epigenomic variation in maize hybrids. Genome Biol 14:R57. (# equal contribution)
Li B, Duan H, Li J, Deng XW, Yin W and Xia X (2013). Global identification of miRNAs and targets in Populus euphratica under salt stress. Plant Mol Biol 81: 525-539.
Huang X, Ouyang X, Yang P, Lau OS, Li G, Li J, Chen H and Deng XW (2012). Arabidopsis FHY3 and HY5 positively mediate induction of COP1 transcription in response to photomorphogenic UV-B light. Plant Cell 24:4590-4606.
Zhong S, Shi H, Xue C, Wang L, Xi Y, Li J, Quail PH, Deng XW and Guo H (2012). A molecular framework of light-controlled phytohormone action in Arabidopsis. Curr Biol 22:1530-1535.
paper was featured in: Lorrain S and Fankhauser C. Plant development: should I stop or should I grow? Curr Biol 22: R645-647.
Chen F, Shi X, Chen L, Dai M, Zhou Z, Shen Y, Li J, Li G, Wei N and Deng XW (2012). Phosphorylation of FAR-RED ELONGATED HYPOCOTYL1 is a key mechanism defining signaling dynamics of phytochrome A under red and far-red light in Arabidopsis. Plant Cell 24:1907-1920.
Yang DL, Yao J, Mei CS, Tong XH, Zeng LJ, Li Q, Xiao LT, Sun TP, Li J, Deng XW, Lee CM, Thomashow MF, Yang Y, He Z and He SY (2012). Plant hormone jasmonate prioritizes defense over growth by interfering with gibberellin signaling cascade. Proc Natl Acad Sci USA 109:E1192-E1200.
Li J, Terzaghi W and Deng XW (2012). Genomic basis for light control of plant development. Protein Cell 3:106-116.
Shen H#, He H#, Li J#, Chen W, Wang X, Guo L, Peng Z, He G, Zhong S, Qi Y, Terzaghi W and Deng XW (2012). Genome-wide analysis of DNA methylation and gene expression changes in two Arabidopsis ecotypes and their reciprocal hybrids. Plant Cell 24:875-892. (# equal contribution)
This paper was featured in: Hofmann NR. A global view of hybrid vigor: DNA methylation, small RNAs, and gene expression. Plant Cell 24:841.
“Author Profile” could be found in: http://www.plantcell.org/content/24/3/875/suppl/DC2
Li J, Li G, Wang H and Deng XW (2011). Phytochrome signaling mechanisms. Arabidopsis Book 9:e148. doi: 10.1199/tab.0148.
Ouyang X#, Li J#, Li G#, Li B#, Chen B, Shen H, Huang X, Mo X, Wan X, Lin R, Li S, Wang H and Deng XW (2011). Genome-wide binding site analysis of FAR-RED ELONGATED HYPOCOTYL3 reveals its novel function in Arabidopsis development. Plant Cell 23:2514-2535. (# equal contribution)
Li G, Siddiqui H, Teng Y, Lin R, Wan X, Li J, Lau OS, Ouyang X, Dai M, Wan J, Devlin PF, Deng XW and Wang H (2011). Coordinated transcriptional regulation underlying the circadian clock in Arabidopsis. Nat Cell Biol 13:616-622.
Li J, Li G, Gao S, Martinez C, He G, Zhou Z, Huang X, Lee JH, Zhang H, Shen Y, Wang H and Deng XW (2010). Arabidopsis transcription factor ELONGATED HYPOCOTYL5 plays a role in the feedback regulation of phytochrome A signaling. Plant Cell 22:3634-3649.
Lee JH, Yoon HJ, Terzaghi W, Martinez C, Dai M, Li J, Byun MO and Deng XW (2010). DWA1 and DWA2, two Arabidopsis DWD protein components of CUL4-based E3 ligases, act together as negative regulators in ABA signal transduction. Plant Cell 22:1716-1732.
Chen H, Huang X, Gusmaroli G, Terzaghi W, Lau OS, Yanagawa Y, Zhang Y, Li J, Lee JH, Zhu D and Deng XW (2010). Arabidopsis CULLIN4-Damaged DNA Binding Protein 1 interacts with CONSTITUTIVELY PHOTOMORPHOGENIC1-SUPPRESSOR OF PHYA complexes to regulate photomorphogenesis and flowering time. Plant Cell 22:108-123.
Shen Y, Zhou Z, Feng S, Li J, Tan-Wilson A, Qu LJ, Wang H and Deng XW (2009). Phytochrome A mediates rapid red light–induced phosphorylation of Arabidopsis FAR-RED ELONGATED HYPOCOTYL1 in a low fluence response. Plant Cell 21:494-506.
Saijo Y, Zhu D, Li J, Rubio V, Zhou Z, Shen Y, Hoecker U, Wang H and Deng XW (2008). Arabidopsis COP1/SPA1 complex and FHY1/FHY3 associate with distinct phosphorylated forms of phytochrome A in balancing light signaling. Mol Cell 31:607-613.
Yang X, Li J, Pei M, Gu H, Chen Z and Qu LJ (2007). Over-expression of a flower-specific transcription factor gene AtMYB24 causes aberrant anther development. Plant Cell Rep 26:219-228.
Li J, Li X, Guo L, Lu F, Feng X, He K, Wei L, Chen Z, Qu LJ and Gu H (2006). A subgroup of MYB transcription factor genes undergoes highly conserved alternative splicing in Arabidopsis and rice. J Exp Bot 57:1263-1273.
Li J, Yang X, Wang Y, Li X, Gao Z, Pei M, Chen Z, Qu LJ and Gu H (2006). Two groups of MYB transcription factors share a motif which enhances trans-activation activity. Biochem Biophys Res Commun 341:1155-1163.
Chen Y, Yang X, He K, Liu M, Li J, Gao Z, Lin Z, Zhang Y, Wang X, Qiu X, Shen Y, Zhang L, Deng X, Luo J, Deng XW, Chen Z, Gu H and Qu LJ (2006). The MYB transcription factor superfamily of Arabidopsis: expression analysis and phylogenetic comparison with the rice MYB family. Plant Mol Biol 60:107-124.
Qin G, Kang D, Dong Y, Shen Y, Zhang L, Deng X, Zhang Y, Li S, Chen N, Niu W, Chen C, Liu P, Chen H, Li J, Ren Y, Gu H, Deng XW, Qu LJ and Chen Z (2003). Obtaining and analysis of flanking sequences from T-DNA transformants of Arabidopsis. Plant Sci 165:941-949.
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