Chen, X.X., Ding, Y.L., Yang, Y.Q., Song, C.P., Wang, B.S., Yang, S.H., Guo, Y., and Gong, Z.Z. (2021). Protein kinases in plant responses to drought, salt, and cold stress. J. Integr. Plant Biol. 63: 53–78.

Gong, Z.Z. (2020). Flowering phenology as a core domestication trait in soybean. J. Integr. Plant Biol. 62: 546–549.

Li, S.F., Wang, Y., Zhao, Y.H., Zhao, X.J., Chen, X.M., and Gong, Z.Z. (2020a). Global Co-transcriptional Splicing in Arabidopsis and the Correlation with Splicing Regulation in Mature RNAs. Mol.Plant 13: 266–277.

Wang, L.S., Wang, C.L., Liu, X.Y., Cheng, J.K., Li, S.F., Zhu, J.K., and Gong, Z.Z. (2019a). Peroxisomal beta-oxidation regulates histone acetylation and DNA methylation in Arabidopsis. Proc. Natl. Acad. Sci. USA 116: 10576–10585.

Gong, Z.Z. (2019). A SUVH-DNAJ/SDJ protein complex activates the expression of promoter-methylated genes in Arabidopsis. J. Integr. Plant Biol. 61: 90–92.

Ding, Y.L., Lv, J., Shi, Y.T., Gao, J.P., Hua, J., Song, C.P., Gong, Z.Z., and Yang, S.H. (2019). EGR2 phosphatase regulates OST1 kinase activity and freezing tolerance in Arabidopsis. EMBO. J. 38:e99819.

Qi, J.S., Song, C.P., Wang, B.S., Zhou, J.M., Kangasjarvi, J., Zhu, J.K., and Gong, Z.Z. (2018). Reactive oxygen species signaling and stomatal movement in plant responses to drought stress and pathogen attack. J. Integr. Plant Biol. 60: 805–826.

Wang, K., He, J.N., Zhao, Y., Wu, T., Zhou, X.F., Ding, Y.L., Kong, L.Y., Wang, X.J., Wang, Y., Li, J.G., et al. (2018). EAR1 Negatively Regulates ABA Signaling by Enhancing 2C Protein Phosphatase Activity. Plant Cell 30: 815–834.

Meng, J.J., Wang, L.S., Wang, J.Y., Zhao, X.W., Cheng, J.K., Yu, W.X., Jin, D., Li, Q., and Gong, Z.Z. (2018). METHIONINE ADENOSYLTRANSFERASE4 mediates DNA and histone methylation. Plant Physiol.177: 652–670.

Lang, Z.B., and Gong, Z.Z. (2018). A role of OsROS1 in aleurone development and nutrient improvement in rice. Proc. Natl. Acad. Sci. USA. 115: 11659–11660.

Ding, Y.L., Jia, Y.X., Shi, Y.T., Zhang, X.Y., Song, C.P., Gong, Z.Z., and Yang, S.H. (2018). OST1-mediated BTF3L phosphorylation positively regulates CBFs during plant cold responses. EMBO. J. 37: e98228.

Li, H., Ding, Y.L., Shi, Y.T., Zhang, X.Y., Zhang, S.Q., Gong, Z.Z., and Yang, S.H. (2017). MPK3-and MPK6-mediated ICE1 phosphorylation negatively regulates ICE1 stability and freezing tolerance in Arabidopsis. Dev. Cell 43: 630–642.

Qi, J.S., Wang, J.L., Gong, Z.Z., and Zhou, J.M. (2017). Apoplastic ROS signaling in plant immunity. Curr. Opin. Plant Biol. 38: 92–100.

Liu, Z.Y., Jia, Y.X., Ding, Y.L., Shi, Y.T., Li, Z., Guo, Y., Gong, Z.Z., and Yang, S.H. (2017b). Plasma membrane CRPK1-mediated phosphorylation of 14-3-3 proteins induces their nuclear import to fine-tune CBF signaling during cold response. Mol. Cell 66: 117–128.

Promchuea, S., Zhu, Y.J., Chen, Z.Z., Zhang, J., and Gong, Z.Z. (2017). ARF2 coordinates with PLETHORAs and PINs to orchestrate ABA-mediated root meristem activity in Arabidopsis. J. Integr. Plant Biol. 59: 30–43.

Liu, L., Yan, X.J., Kong, X.X., Zhao, Y.Q., Gong, Z.Z., Jin, J.B., and Guo, Y. (2017a). Transcriptional Gene Silencing Maintained by OTS1 SUMO Protease Requires a DNA-Dependent Polymerase V-Dependent Pathway. Plant Physiol.173: 655–667.

Meng, Z., Ruberti, C., Gong, Z.Z., and Brandizzi, F. (2017). CPR5 modulates salicylic acid and the unfolded protein response to manage tradeoffs between plant growth and stress responses. Plant J. 89: 486–501.

Huang, X.Z., Zhang, X.Y., Gong, Z.Z., Yang, S.H., and Shi, Y.T. (2017). ABI4 represses the expression of type-A ARRs to inhibit seed germination in Arabidopsis. Plant J. 89: 354–365.

Zhang, Q.Z., Li, Y.Q., Xu, T., Srivastava, A.K., Wang, D., Zeng, L., Yang, L., He, L., Zhang, H., Zheng, Z.M., et al. (2016c). The chromatin remodeler DDM1 promotes hybrid vigor by regulating salicylic acid metabolism. Cell Discov. 2 16027.

Jia, Y.X., Ding, Y.L., Shi, Y.T., Zhang, X.Y., Gong, Z.Z., and Yang, S.H. (2016). The cbfs triple mutants reveal the essential functions of CBFs in cold acclimation and allow the definition of CBF regulons in Arabidopsis. New Phytol. 212: 345–353.

Lang, Z.B., and Gong, Z.Z. (2016). SMALL RNA BIOGENESIS Novel roles of an RNase III enzyme. Nat. Plants 2.

Zhang, J.X., Xie, S.J., Cheng, J.K., Lai, J.S., Zhu, J.K., and Gong, Z.Z. (2016a). The second subunit of DNA polymerase delta is required for genomic stability and epigenetic regulation. Plant Physiol. 171: 1192–1208.

Zhang, J.X., Xie, S.J., Zhu, J.K., and Gong, Z.Z. (2016b). Requirement for flap endonuclease 1 (FEN1) to maintain genomic stability and transcriptional gene silencing in Arabidopsis. Plant Journal 87: 629–640.

Kong, L.Y., Cheng, J.K., Zhu, Y.J., Ding, Y.L., Meng, J.J., Chen, Z.Z., Xie, Q., Guo, Y., Li, J.G., Yang, S.H., et al. (2015). Degradation of the ABA co-receptor ABI1 by PUB12/13 U-box E3 ligases. Nature Commun. 6.

Zheng, Z.M., Yu, H.S., Miki, D., Jin, D., Zhang, Q.Z., Ren, Z.H., Gong, Z.Z., Zhang, H., and Zhu, J.K. (2015). Involvement of multiple gene-silencing pathways in a paramutation-like phenomenon in Arabidopsis. Cell Reports 11: 1160–1167.

Ding, Y.L., Li, H., Zhang, X.Y., Xie, Q., Gong, Z.Z., and Yang, S.H. (2015). OST1 kinase modulates freezing tolerance by enhancing ICE1 stability in Arabidopsis. Dev.Cell 32: 278–289.

Shi, Y.T., and Gong, Z.Z. (2015). One SNP in COLD1 Determines cold tolerance during rice domestication. J. Genet. Genomics. 42: 133–134.

Lang, Z., Lei, M., Wang, X., Tang, K., Miki, D., Zhang, H., Mangrauthia, S.K., Liu, W., Nie, W., Ma, G., Yan, J., Duan, C.G., Hsu, C.C., Wang, C., Tao, W.A., Gong, Z., Zhu, J.K. (2015). The methyl-CpG-binding protein MBD7 facilitates active DNA demethylation to limit DNA hyper-methylation and transcriptional gene silencing. Mol. Cell 57: 971–983.

Wang, C.L., Dong, X.M., Jin, D., Zhao, Y.S., Xie, S.J., Li, X.J., He, X.J., Lang, Z.B., Lai, J.S., Zhu, J.K., et al. (2015). Methyl-CpG-binding domain protein MBD7 is required for active DNA demethylation in Arabidopsis. Plant Physiol. 167: 905–914.

Yang, L., Zhang, J., He, J.N., Qin, Y.Y., Hua, D.P., Duan, Y., Chen, Z.Z., and Gong, Z.Z. (2014).ABA-mediated ROS in mitochondria regulate root meristem activity by controlling PLETHORA expression in Arabidopsis. PLoS Genet. 10: e1004791.

Zhao, Y.S., Xie, S.J., Li, X.J., Wang, C.L., Chen, Z.Z., Lai, J.S., and Gong, Z.Z. (2014). Repressor of silencing5 encodes a member of the small heat shock protein family and is required for DNA demethylation in Arabidopsis. Plant Cell 26: 2660–2675.

Luo, X.J., Chen, Z.Z., Gao, J.P., and Gong, Z.Z. (2014) Abscisic acid inhibits root growth in Arabidopsis through ethylene biosynthesis. Plant J. 79: 44–55.

Yao, T.X., Jin, D., Liu, Q., and Gong, Z.Z. (2013). Abscisic acid suppresses the highly occurred somatic homologous recombination in Arabidopsis rfc1 mutant. J. Genet. Genomics. 40: 465–471.

Wang, Y.X., Cheng, Z.H., Huang, J.Y., Shi, Q., Hong, Y., Copenhaver, G.P., Gong, Z.Z., and Ma, H. (2012). The DNA replication factor RFC1 is required for interference-sensitive meiotic crossovers in Arabidopsis thaliana. PloS Genet. 8: e1003039.

Li, X.J., Qian, W.Q., Zhao, Y.S., Wang, C.L., Shen, J., Zhu, J.K., and Gong, Z.Z. (2012). Antisilencing role of the RNA-directed DNA methylation pathway and a histone acetyltransferase in Arabidopsis. Proc. Natl. Acad. Sci. USA. 109: 11425–11430.

Qian, W.Q., Miki, D., Zhang, H., Liu, Y.H., Zhang, X., Tang, K., Kan, Y.C., La, H.G., Li, X.J., Li, S.F., Zhu, X., Shi, X., Zhang, K., Pontes, O., Chen, X., Liu, R., Gong, Z., Zhu, J.K. (2012). A histone acetyltransferase regulates active DNA demethylation in Arabidopsis. Science 336: 1445–1448.

Hua, D.P., Wang, C., He, J.N., Liao, H., Duan, Y., Zhu, Z.Q., Guo, Y., Chen, Z.Z., and Gong, Z.Z. (2012). A plasma membrane receptor kinase, GHR1, mediates ABA- and H2O2-regulated stomatal movement in Arabidopsis. Plant Cell 24: 2546–2561.

He, J.N., Duan, Y., Hua, D.P., Fan, G.J., Wang, L., Liu, Y., Chen, Z.Z., Han, L.H., Qu, L.J., and Gong, Z.Z. (2012). DEXH-box RNA helicase-mediated mitochondrial ROS production in Arabidopsis mediates cross-talk between abscisic acid and auxin signalling. Plant Cell 24: 1815–1833.

Zhang, X.L., Zhang, Q., Xin, Q., Yu, L., Wang, Z., Wu, W., Jiang, L., Wang, G.Q., Tian, W.L., Deng, Z.Q., Wang, Y., Liu, Z., Long, J., Gong, Z., Chen, Z. (2012). Complex structures of the abscisic acid receptor PYL3/RCAR13 reveal a unique regulatory mechanism. Structure 20: 780–790.

Gong, Z.Z., and Zhu, J.K. (2011).Active DNA demethylation by oxidation and repair. Cell Res. 21: 1649–1651.

Wang, L., Hua, D.P., He, J.N., Duan, Y., Chen, Z.Z., Hong, X.H., and Gong, Z.Z. (2011). Auxin response factor2 (ARF2) and its regulated homeodomain gene HB33 mediate abscisic acid response in Arabidopsis. PLoS Genet. 7: e1002172.

Liu, Q., and Gong, Z.Z. (2011).The coupling of epigenome replication with DNA replication. Curr. Opin. Plant Biol. 14: 187–194.

Liu, Q.A., Wang, J.G., Miki, D., Xia, R., Yu, W.X., He, J.N., Zheng, Z.M., Zhu, J.K., and Gong, Z.Z. (2010). DNA replication factor C1 mediates genomic stability and transcriptional gene silencing in Arabidopsis. Plant Cell 22: 2336–2352.

Liu, Y., He, J.N., Chen, Z.Z., Ren, X.Z., Hong, X.H., and Gong, Z.Z. (2010). ABA Overly-Sensitive5 (ABO5), encoding a pentatricopeptide repeat protein required for cis-splicing of mitochondrial nad2 intron 3, is involved in abscisic acid response in Arabidopsis. Plant J. 63: 749–765.

Ren, X.Z., Chen, Z.Z., Liu, Y., Zhang, H.R., Zhang, M., Liu, Q.A., Hong, X.H., Zhu, J.K., and Gong, Z.Z. (2010). ABO3, a WRKY transcription factor, mediates plant responses to abscisic acid and drought tolerance in Arabidopsis. Plant J. 63: 417–429.

Liu, J., Ren, X.Z., Yin, H.B., Wang, Y., Xia, R., Wang, Y.Q., and Gong, Z.Z. (2010). Mutation in the catalytic subunit of DNA polymerase alpha influences transcriptional gene silencing and homologous recombination in Arabidopsis. Plant J. 61: 36–45.

Zhang, M., Henquet, M., Chen, Z.Z., Zhang, H.R., Zhang, Y., Ren, X.Z., van der Krol, S., Gonneau, M., Bosch, D., and Gong, Z.Z. (2009). LEW3 encoding a putative alpha-1, 2-mannosyltransferase (ALG11) in N-linked glycoprotein plays vital roles in cell wall biosynthesis and abiotic stress response in Arabidopsis. Plant J. 60: 983–999.

Shen, J., Ren, X.Z., Cao, R., Liu, J., and Gong, Z.Z. (2009). Transcriptional gene silencing mediated by a plastid inner envelope phosphoenolpyruvate/phosphate translocator CUE1 in Arabidopsis. Plant Physiol. 150: 1990–1996.

Zhou, X.F., Hua, D.P., Chen, Z.Z., Zhou, Z.J., and Gong, Z.Z. (2009). Elongator mediates ABA responses, oxidative stress resistance, and anthocyanin biosynthesis in Arabidopsis. Plant J. 60: 79–90.

Yin, H.B., Zhang, X., Liu, J., Wang, Y.Q., He, J.N., Yang, T., Hong, X.H., Yang, Q., and Gong, Z.Z. (2009). Epigenetic regulation, somatic homologous recombination, and abscisic acid signaling are influenced by DNA polymerase epsilon mutation in Arabidopsis. Plant Cell 21: 386–402.

Yang, Q., Chen, Z.Z., Zhou, X.F., Yin, H.B., Li, X., Xin, X.F., Hong, X.H., Zhu, J.K., and Gong, Z.Z. (2009). Overexpression of SOS (Salt Overly Sensitive) genes increases the salt tolerance in transgenic Arabidopsis. Mol. Plant 2: 22–31.

Chinnusamy, V., Gong, Z., and Zhu, J.K. (2008a). Nuclear RNA export and its importance in abiotic stress responses of plants. Curr. Top Microbiol. Immunol. 326: 235–255.

Chinnusamy, V., Gong, Z.Z., and Zhu, J.K. (2008b). Abscisic acid-mediated epigenetic processes in plant development and stress responses. J. Integr. Plant Biol. 50: 1187–1195.

Zhang, H.R., Ohyama, K., Boudet, J., Chen, Z.Z., Yang, J.L., Zhang, M., Muranaka, T., Maurel, C., Zhu, J.K., and Gong, Z.Z. (2008). Dolichol biosynthesis and its effects on the unfolded protein response and abiotic stress resistance in Arabidopsis. Plant Cell 20: 1879–1898.

Zhao, J.F., Zhang, W.H., Zhao, Y., Gong, X.M., Guo, L., Zhu, G.L., Wang, X.C., Gong, Z.Z., Schumaker, K.S., and Guo, Y. (2007). SAD2, an importin-like protein, is required for UV-B response in Arabidopsis by mediating MYB4 nuclear trafficking. Plant Cell 19: 3805–3818.

Wang, Y., Liu, J., Xia, R., Wang, J.G., Shen, J., Cao, R., Hong, X.H., Zhu, J.K., and Gong, Z.Z. (2007). The protein kinase TOUSLED is required for maintenance of transcriptional gene silencing in Arabidopsis. EMBO Rep. 8: 77–83.

Chen, Z., Zhang, H., Jablonowski, D., Zhou, X., Ren, X., Hong, X., Schaffrath, R., Zhu, J.K., and Gong, Z. (2006). Mutations in ABO1/ELO2, a subunit of holo-elongator, increase ABA sensitivity and drought tolerance in Arabidopsis. Mol. Cell Biol. 26: 6902–6912.

Xia, R., Wang, J.G., Liu, C.Y., Wang, Y., Wang, Y.Q., Zhai, J.X., Liu, J., Hong, X.H., Cao, X.F., Zhu, J.K., and Gong, Z. (2006) ROR1/RPA2A, a putative replication protein A2, functions in epigenetic gene silencing and in regulation of meristem development in Arabidopsis. Plant Cell 18: 85–103.

Kapoor, A., Agarwal, M., Andreucci, A., Zheng, X.W., Gong, Z.Z., Hasegawa, P.M., Bressan, R.A., and Zhu, J.K. (2005). Mutations in a conserved replication protein suppress transcriptional gene silencing in a DNA-methylation-independent manner in Arabidopsis. Curr. Biol. 15: 1912–1918.

Chen, Z.Z., Hong, X.H., Zhang, H.R., Wang, Y.Q., Li, X., Zhu, J.K., and Gong, Z.Z. (2005). Disruption of the cellulose synthase gene, AtCesA8/IRX1, enhances drought and osmotic stress tolerance in Arabidopsis. Plant J. 43: 273–283.

Gong, Z.Z., Dong, C.H., Lee, H., Zhu, J.H., Xiong, L.M., Gong, D.M., Stevenson, B., and Zhu, J.K. (2005). A DEAD box RNA helicase is essential for mRNA export and important for development and stress responses in Arabidopsis. Plant Cell 17: 256–267

Wang, Z.L., Li, P.H., Fredricksen, M., Gong, Z., Kim, C.S., Zhang, C., Bohnert, H.J., Zhu, J.K., Bressan, R.A., Hasegawa, P.M., Zhao, Y.X., and Zhang, H. (2004). Expressed seqeunce tags from Thellungiella halophila, a new model to study plant salt-tolerance. Plant Sci. 166: 609–616.

Gong, Z., Morales-Ruiz, T., Ariza, R. R., Rold¨¢n-Arjona, T., David, L., and Zhu, J.K. (2002). ROS1 a repressor of transcriptional gene silencing in Arabidopsis, encodes a DNA glycosylase/lyase. Cell 111: 803–814.

Zhu, J.H., Gong, Z.Z., Zhang, C.Q., Song, C.P., Damsz, B., Inan, G., Koiwa, H., Zhu, J.K., Hasegawa, P.M., and Bressan, R.A. (2002). OSM1/SYP61: A syntaxin protein in Arabidopsis controls abscisic acid-mediated and non-abscisic acid-mediated responses to abiotic stress. Plant Cell 14: 3009–3028.

Gong, D.M., Gong, Z.Z., Guo, Y., Chen, X.Y., and Zhu, J.K. (2002a). Constitutive activation and transgenic evaluation of the function of an Arabidopsis PKS protein kinase. J. Biol. Chem. 277: 42088–42096.

Gong, Z., Lee, H., Xiong, L., Jagendorf, A., Stevenson, B., and Zhu, J.K. (2002). RNA helicase-like protein as an early regulator of transcription factors for plant chilling and freezing tolerance. Proc. Natl. Acad. Sci. USA 99: 11507–11512.

Koiwa, H., Barb, A.W., Xiong, L.M., Li, F., McCully, M.G., Lee, B.H., Sokolchik, I., Zhu, J.H., Gong, Z.Z., Reddy, M., Sharkhuu, A., Manabe, Y., Yokoi, S., Zhu, J.K., Bressan, R.A., and Hasegawa, P.M. (2002). C-terminal domain phosphatase-like family members (AtCPLs) differentially regulate Arabidopsis thaliana abiotic stress signaling, growth, and development. Proc. Natl. Acad. Sci. USA 99: 10893–10898.

Yamazaki, M., Yamagishi, E., Gong, Z.Z., Fukuchi-Mizutani, M., Fukui, Y., Tanaka, Y., Kusumi, T., Yamaguchi, M., and Saito, K. (2002). Two flavonoid glucosyltransferases from Petunia hybrida: Molecular cloning, biochemical properties and developmentally regulated expression. Mol. Cell Biol. 26: 6902–6912.

Gong, D.M., Gong, Z.Z., Guo, Y., Chen, X.Y., and Zhu, J.K. (2002a). Biochemical and functional characterization of PKS11, a novel Arabidopsis protein kinase. Mol. Cell Biol. 277: 28340–28350.

Gong, D.M., Zhang, C.Q., Chen, X.Y., Gong, Z.Z., and Zhu, J.K. (2002b). Expression, activation and biochemical properties of a novel Arabidopsis protein kinase. Plant Physiol. 277: 28340-28350.

Kitada, C., Gong, Z.Z., Tanaka, Y., Yamazaki, M., and Saito, K. (2001). Differential expression of two cytochrome P450s involved in the biosynthesis of flavones and anthocyanins in chemo-varietal forms of Perilla frutescens. Plant Cell Physiol. 42: 1338–1344.