Ke-Qiang Wu Professor
Ph.D., University of Saskatchewan, Canada
Specialty: Epigenetics, Plant Development, Plant Abiotic Stress
Laboratory: Life Science Building R1026
Current Research Interests
Epigenetics is the study of heritable changes in gene expression that occur without a change in DNA sequence. Much of today's epigenetic research focuses on the study of covalent and noncovalent modifications of DNA and histone proteins and the mechanisms by which such modifications influence overall chromatin structure. Recently, it has become evident that RNA, particularly noncoding RNAs, also play a role in controlling multiple epigenetic phenomena. Many important aspects of plant development are regulated by changes in gene expression that derive from modifications of chromatin structure. Histone modification is an important molecular mechanism of epigenetics. In particular, the reversible acetylation and deacetylation of specific lysine residues on core histones of chromatins regulate the accessibility of chromatins and gene activity. We have shown that reversible acetylation of core histones is involved in hormonal signaling and responses to biotic and abiotic stimuli in Arabidop sis. Given the importance of histone modification in the regulation of gene expression in plants, a better understanding of how histone modification modulates gene expression may provide a new insight into how plants response to the environment during plant development.
Epigenetics refers to changes in heritable gene expression due to non-gene sequence changes. The molecular mechanisms of epigenetics include methylation of DNA, modification of histones, and chromatin remodeling. Recent studies have shown that RNA, especially noncoding RNA, also plays an important role in epigenetic phenomena. Gene expression during plant growth and development is closely related to changes in chromatin structure, and as an important component of chromatin, protein modification on histones plays an important role in the regulation of gene expression. Group protein modifications include phosphorylation, methylation , acetylation, and ubiquitination. In general, if the degree of chromatin histone acetylation is higher, the structure of the site is looser, which is conducive to gene expression. On the other hand, if the degree of chromatin histone acetylation is low, the structure of the site is dense, which is not conducive to gene expression. Our study found that histone acetylation and deacetylation are involved in plant hormone signaling and plant response to stress. We are further studying the effects of histone modifications on plant gene expression and its role in plant growth and development. These studies will reveal the molecular mechanisms of signal transmission during plant growth and development and plant stress response.
Arabidopsis is a model plant widely used in molecular biology research. The flowering of Arabidopsis can be regulated by photoperiod.
The figure shows the different flowering times of wild type (A, B) and mutant (C, D) Arabidopsis thaliana grown under long day (A, C) or short day (B, D) conditions.
Hung FY, Lai YC, Wang J., Feng YR, Shih YH, Chen JH, Sun HC, 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.-WA, 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, QQ (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 Physiology 180 (1)
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 CW, Chen FF, Zhao L, Tian G, Liu X, Cui Y, Yang JY, 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 CW 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.
Biotechnology Core Experiment
Methods in Plant Molecular Biology Research
Discussion on Plant Biology Research