​植物科學研究所

Shih Y-H, Hung F-Y, Lin P-Y, Yang S and Wu K* (2024).Lysine acetylation regulates the subcellular localization and function of WRKY63. Plant Physiol. (accepted).

Hsieh JA, Yen MR, Hung FY, Wu K*, Chen PY* (2024)  Epigenetic-driven synergistic and antagonistic regulation on transposable elements by HDA6 and LDL1/LDL2 in Arabidopsis. Plant Physiol. doi: 10.1093/plphys/kiae392.

Li Z, Zeng J, Zhou Y, Ding X, Jiang G, Wu K, Jiang Y, Duan X (2024). Histone H3K27 demethylase SlJMJ3 modulates fruit ripening in tomato. Plant Physiol. 195:2727-2742. doi: 10.1093/plphys/kiae233.

Wang M, Zhong Z, Gallego-Bartolomé J, Feng S, Shih YH, Liu M, Zhou J, Richey JC, Ng C, Jami-Alahmadi Y, Wohlschlegel J, Wu K, Jacobsen SE. (2023) Arabidopsis TRB proteins function in H3K4me3 demethylation by recruiting JMJ14. Nat Commun.14:1736. doi: 10.1038/s41467-023-37263-9.

Hung FY, Feng YR, Hsin KT, Shih YH, Chang CH, Zhong W, Lai YC, Xu Y, Yang S, Sugimoto K, Cheng YS, Wu K*. (2023) Arabidopsis histone H3 lysine 9 methyltransferases KYP/SUVH5/6 are involved in leaf development by interacting with AS1-AS2 to repress KNAT1 and KNAT2. Commun Biol. 6:219. doi: 10.1038/s42003-023-04607-6.

Chen CY, Chang CH, Wu CH, Tu YT, Wu K* (2022) Arabidopsis Cyclin-Dependent Kinase C2 interacts with HDA15 and is involved in far-red light-mediated hypocotyl cell elongation. Plant J. 112:1462-1472

Hung F-Y, Shih Y-H, Lin P-Y, Feng Y-Ru, Li C and Wu K* (2022) WRKY63 transcriptional activation of COOLAIR and COLDAIR regulates vernalization-induced flowering. Plant Physiol. 190: 532–547.

Tu Y-T, Chen C-Y, Huang Y-S, Chang C-H, Yen M-R, Hsieh J-W A, Chen P-Y, Wu K* (2022) HISTONE DEACETYLASE 15 and MOS4-Associated Complex subunits 3A/3B coregulate intron retention of ABA-responsive genes. Plant Physiol. 190: 882–897.

Hung F.Y., Lai Y.C., Wang J., Feng Y.R., Shih Y.H., Chen J.H., Sun H.C., Yang S.*, Li C.*, Wu K.* (2021) The Arabidopsis histone demethylase JMJ28 regulates CONSTANS by interacting with FBH transcription factors. Plant Cell, koab014.

Hung, F.-Y., Chen, C., Yen, M.-R., Hsieh, J.-W.A., Li, C., Shih, Y.-H., Chen, F.-F., Chen, P.-Y., Cui, Y., and Wu, K.* (2020). The expression of long non-coding RNAs is associated with H3Ac and H3K4me2 changes regulated by the HDA6-LDL1/2 histone modification complex in Arabidopsis. NAR Genomics and Bioinformatics 2.

Chen, C.-Y., Tu, Y.-T., Hsu, J.-C., Hung, H.-C., Liu, T.-C., Lee, Y.-H., Chou, C.-C., Cheng, Y.-S., and Wu, K.* (2020). Structure of Arabidopsis HISTONE DEACETYLASE15. Plant Physiol., pp.00604.02020.

Lin, J., Hung, F.-Y., Ye, C., Hong, L., Shih, Y.-H., Wu, K.*, and Li, Q.Q. (2020). HDA6 dependent chromatin deacetylation orchestrates mRNA polyadenylation. Genome Res., gr. 255232.255119.

Hung, F.‐Y., Chen, J.‐H., Feng, Y.‐R., Lai, Y.‐C., Yang, S. and Wu, K.*, Arabidopsis JMJ29 is involved in trichome development by regulating the core trichome initiation gene GLABRA3 . Plant J. May 2020.

Yang, J., Yuan, L., Yen, M.‐R., Zheng, F., Ji, R., Peng, T., Gu, D., Yang, S., Cui, Y., Chen, P.‐Y., Wu, K.* and Liu, X., SWI3B and HDA6 interact and are required for transposon silencing in Arabidopsis . Plant J, 102: 809-822. 2020.

Li, Z., Jiang, G., Liu, X., Ding, X., Zhang, D., Wang, X., Zhou, Y., Yan, H., Li, T., Wu, K.*, Jiang, Y. and Duan, X. (2020), Histone demethylase SlJMJ6 promotes fruit ripening by removing H3K27 methylation of ripening‐related genes in tomato. New Phytol, 227: 1138-1156. doi:10.1111/nph.16590

Linmao Zhao, Tao Peng, Chia-Yang Chen, Rujun Ji, Dachuan Gu, Tingting Li, Dongdong Zhang, Yi-Tsung Tu, Keqiang Wu*, Xuncheng Liu. HY5 Interacts with the Histone Deacetylase HDA15 to Repress Hypocotyl Cell Elongation in Photomorphogenesis. Plant Phtsiology 180 (1) 
May 2019

Fu-Yu Hung, Fang-Fang Chen, Chenlong Li, Chen Chen, Jian-Hao Chen, Yuhai Cui* and Keqiang Wu* The LDL1/2-HDA6 Histone Modification Complex Interacts With TOC1 and Regulates the Core Circadian Clock Components in Arabidopsis. Front. Plant Sci., 26 February 2019

Hung, F.-Y., F.-F. Chen, C. Li, C. Chen, Y.-C. Lai, J.-H. Chen, Y. Cui and K. Wu. (2018). The Arabidopsis LDL1/2-HDA6 histone modification complex is functionally associated with CCA1/LHY in regulation of circadian clock genes. NAR 46: 10669-10681.

F.-Y. Hung, F.-F. Chen, C. Li, C. Chen, Y.-C. Lai, J.-H. Chen, Y. Cui, K.Wu*.​​The Arabidopsis LDL1/2-HDA6 histone modification complex is functionally associated with CCA1/LHY in regulation of circadian clock genes.Nucleic Acids Res. (2018) August; gky749-gky49. doi:10.1093/nar/gky749.

Yu CW, Tai R, Wang SC, Yang P, Luo M, Yang S, Cheng K, Wang WC, Cheng YS and Wu K * (2017) HISTONE DEACETYLASE6 Acts in Concert with Histone Methyltransferases SUVH4, SUVH5, and SUVH6 to Regulate Transposon Silencing. Plant Cell. pii: tpc.00570.2016. doi: 10.1105/tpc.16.00570. [Epub ahead of print]

Gu D, Chen CY, Zhao M, Zhao L, Duan X, Duan J*, Wu K * and Liu X* (2017) Identification of HDA15-PIF1 as a key repression module directing the transcriptional network of seed germination in the dark. Nucleic Acids Res. doi: 10.1093/nar/gkx283. [Epub ahead of print]

Liu X, Luo M, Yang S and Wu K * (2015) Role of Epigenetic Modifications in Plant Responses to Environmental Stresses. In “Nuclear Functions in Plant Transcription and Signaling”, O. Pontes and H. Jin eds., Springer Science+Business Media, New York, pp., 81-92.

Yang S, Li C, Zhao L, Gao S, Lu J, Zhao M, Chen C, Liu X, Luo M, Cui Yu, Yang C and Wu K *  (2015) Arabidopsis  SWI2 / SNF2 chromatin remodeling ATPase BRAHMA targets directly to pins and is required for root stem cell niche maintenance. Plant Cell 27:1670-1680.

Luo M, Tai R, Yu CW, Yang S, Chen C, Lin WD, Wolfgan S and Wu K * (2015) Regulation of flowering time by the histone deacetylase HDA5 in Arabidopsis. Plant J 82:925-936.

Zhao M, Yang S, Chen C, Li C, Shan W, Lu W, Cui Yu, Liu X, and Wu K * (2015) Arabidopsis BREVIPEDICELLUS interacts with the SWI2/SNF2 chromatin remodeling ATPase BRAHMA to regulate KNAT2 and KNAT6 expression in control of inflorescence architecture. PLoS Genet. 11: e1005125.

Zhao M, Yang S, Liu X, and Wu K * (2015) Arabidopsis histone demethylases LDL1 and LDL2 control primary seed dormancy by regulating the DELAY OF GERMINATION 1 and ABA signaling-related genes. Front. Plant Sci. 6:159. doi: 10.3389/fpls.2015.00159.

Li C, Chen C, Gao L, Yang S, Nguyen V, Shi X, Siminovitch K, Kohalmi SE, Huang S, Wu K, Chen X, Cui Y (2015) The Arabidopsis SWI2/SNF2 chromatin remodeler BRAHMA regulates polycomb function during vegetative development and directly activates the flowering repressor gene SVP. PLoS Genet.11: e1004944.

Zhao L, Lu J, Zhang J, Wu P, Yang S, Wu K *(2015)Identification and characterization of histone deacetylases in tomato (Solanum Lycopersicum). Front. Plant Sci. 5:760. doi: 10.3389/fpls.2014.00760)

Hsu C, Wu P, Chen T, Yu C, Tsai W, Wu K, Wu W, Chen W, and Chen H (2014) Histone acetylation accompanied with promoter sequences displaying differential expression profiles of B-class MADS-box genes for Phalaenopsis floral morphogenesis. PLoS ONE (accepted)

Singh P, Yekondi S, Chen PW, Tsai CH, Yu CW, Wu K, Zimmerli L* (2014) Environmental history modulates Arabidopsis pattern-triggered immunity in a HISTONE ACETYLTRANSFERASE1-dependent manner. Plant Cell 26:2676-2688.

Liu X, Yang S, Zhao M, Luo M, Yu CW, Chen C, Tai R, and Wu K* (2014) Transcriptional repression by histone deacetylases in plants. Mol Plant 7, 764–772.

Luo M, Hung F, Yang S, Liu X, and Wu K* (2014) Histone lysine demethylases and their functions in plants. Plant Mol Biol Rep 32:558–565.

Yuan L, Liu X, Luo M, Yang S, and Wu K* (2013) Involvement of histone modifications in plant abiotic stress responses. J Integr Plant Biol 55: 892-901.

Liu X, Chen C, Wang K, Luo M, Tai R, Yuan L, Zhao M, Yang S, Tian G, Cui Y, Hsieh H and Wu K* (2013) PHYTOCHROME INTERACTING FACTOR3associates with the Histone Deacetylase HDA15 in repression of chlorophyll biosynthesis and photosynthesis in etiolated Arabidopsis seedlings. Plant Cell 25: 1258–1273.

Zhou Y, Tan B, Luo M, Lin Y, Liu C, Chen C, Yu C-Wu, Yang S, Dong S, Ruan J, Yuan L, Zhang Z, Zhao L, Li C, Chen H, Cui Y,Wu K*and Huang S* (2013) HISTONE DEACETYLASE19 interacts with HSL1 and participates in the repression of seed maturation genes in Arabidopsis seedlings. Plant Cell 25: 134–148.

Luo M, Yu C-W, Chen F-F, Zhao L, Tian G, Liu X, Cui Y, Yang J-Y, and Wu K* (2012) Histone Deacetylase HDA6 Is Functionally Associated with AS1 in Repression of KNOX Genes in Arabidopsis. PLoS Genet 8(12): e1003114. doi:10.1371/journal.pgen.1003114

Luo M, Wang YY, Liu X, Yang S, Lu Q, Cui Y, and Wu K* (2012) HD2C interacts with HDA6 and is involved in ABA and salt stress response in Arabidopsis. J. Exp. Bot. 63: 3297-3306.

Alinsug MV, Chen FF, Luo M, Tai R, Jiang L, and Wu K* (2012) Subcellular Localization of Class II HDAs in Arabidopsis thaliana: Nucleocytoplasmic Shuttling of HDA15 Is Driven by Light. PLoS ONE 7(2): e30846. doi:10.1371/journal.pone.0030846

Liu X, Yu CW, Dun J, Luo M, Wang K, Tian G, Cui Y, and Wu K* (2012) HDA6 directly interacts with DNA methyltransferase MET1 and maintains transposable elements silencing in Arabidopsis. Plant Physiol. 158: 119-129

Liu X, Luo M, Zhang W, Zhao J, Zhang J, Wu K*, Tian L* and Duan J* (2012) Histone acetyltransferases in rice (Oryza sativa L.): phylogenetic analysis, subcellular localization and expression. BMC Plant Biology 12:145. doi:10.1186/1471-2229-12-145

Gao Y, Yang S, Yuan L, Cui Y, and Wu K* (2012) Comparative analysis of SWIRM domain-containing proteins in plants. Comp. Funct. Genomics 2012:310402.

Luo M, Wang Y, Liu X, Yang S, Wu K*, (2012) HD2 proteins interact with RPD3-type histone deacetylases. Plant Signal Behav. 7: 608 – 610.

Liu X, Luo M, and Wu K* (2012) Epigenetic interplay of histone modifications and DNA methylation mediated by HDA6. Plant Signal Behav. 7: 633 – 635

Luo M, Liu X, Singh P, Cui Y, Zimmerli L, and Wu K* (2011) Chromatin modifications and remodeling in plant abiotic stress responses. Biochim. Biophys. Acta. – Gen. Regul. 1819: 129-136.

Zhou Y, Chu P, Chen H, Li Y,Liu J,Ding Y,Tsang EW, Jiang L, Wu K, and Huang S. (2012) Overexpression of Nelumbo nucifera metallothioneins 2a and 3 enhances seed germination vigor in Arabidopsis.Planta (2012) 235:523–537

Yu CW, Liu X, Luo M, Chen C, Lin X, Tian G, Lu Q, Cui Y, and Wu K* (2011) Histone Deacetylase6 interacts with Flower Locus D and regulates flowering in Arabidopsis. Plant Physiol. 156: 173-184.

Chen L, and Wu K* (2010) Role of histone deacetylases HDA6 and HDA19 in ABA and abiotic stress response. Plant Signal Behav. 5: 1318-1320.

Chen L, Luo M, Wang Y, and Wu K* (2010) Involvement of Arabidopsis histone deacetylase HDA6 in ABA and salt stress response. J. Exp. Bot. 61: 3345-3353.

Song Y, Wu K, Dhaubhade S, An L and Tian L (2010) Arabidopsis DNA methyltransferase AtDNMT2 associates with histone deacetylase AtHD2s activity. Biochem. Biophys. Res. Commun. 396:187-192.

Fu G, Zhong Y, Li C, Li Y , Lin X, Liao B, Tsang E WT, Wu K* , and Huang S (2010) Epigenetic regulation of peanut allergen gene Ara h 3 in developing embryos. Planta 231: 1049-1060.

Li C, Wu K, Fu G, Li Y, Zhong Y, Lin X, Zhou Y, and Huang S (2009) Regulation of oleosin expression in developing peanut embryos through nucleosome loss and histone modifications. J. Exp. Bot. 60: 4371-4382.

Alinsug MV, Yu C-W and Wu K* (2009) Phylogenetic analysis, subcellular localization, and expression patterns of RPD3/HDA1 family histone deacetylases in plants. BMC Plant Biol. 9: 37.

Wu K* , Zhang L, Zhou C, Yu C, and Chaikam V (2008) HDA6 is required for jasmonate response, senescence and flowering in Arabidopsis. J. Exp. Bot.59: 225–234.

Liu Z, Zhou C and Wu K (2008) Creation and analysis of a novel chimeric promoter for the complete containment of pollen- and seed-mediated gene flow. Plant Cell Rep. 27:995–1004

Ciou C, Wu K. and Yeh K. (2008) Characterization and promoter activity of chromoplast specific carotenoid associated gene (CHRC) from Oncidium gower ramsey. Biotechnology Letters 30:1861-1866.

Fu W., Wu K. and Duan J. (2007) Sequence and expression analysis of histone deacetylases in rice. Biochem. Biophys. Res. Commun. 356：843-850.