Detecting and responding to environmental perturbations are important for all living organisms. One of the most important distinguishing features of plants is that they are sessile and thus have to endure environmental challenges. Our lab is interested in the molecular mechanisms underlying plant responses to harsh environments such as soil salinity, drought and cold temperatures. In addition, we are interested in the mechanisms of transcriptional gene silencing and in the role of epigenetic gene regulation in stress adaptation. We use a combination of genetic, biochemical, genomic and proteomic approaches to analyze various levels of gene regulation (chromatin level/epigenetic, transcriptional, posttranscriptional, and protein activity) and to understand stress signaling and stress tolerance. Our long-term goals are to elucidate the signaling pathways used by plants in responding to environmental stresses and to identify key genes for modifying the responses of crops to environmental stresses which ultimately will lead to major contributions to agriculture and the environment.
Yan J, Zhao C, Zhou J, Yang Y, Wang P, Zhu X, Tang G, Bressan RA, Zhu JK. 2016. The miR165/166 Mediated Regulatory Module Plays Critical Roles in ABA Homeostasis and Response in Arabidopsis thaliana. PLoS Genet. 12:e1006416
Tang K, Lang Z, Zhang H, Zhu JK. 2016. The DNA demethylase ROS1 targets genomic regions with distinct chromatin modifications. Nat Plants. 2:16169
Wang L, Li H, Zhao C, Li S, Kong L, Wu W, Kong W, Liu Y, Wei Y, Zhu JK, Zhang H. 2016. The inhibition of protein translation mediated by AtGCN1 is essential for cold tolerance in Arabidopsis thaliana. Plant Cell Environ. In press. doi: 10.1111/pce.12826
Lang Z, Xie S, Zhu JK. 2016. The 1001 Arabidopsis DNA methylomes: An important resource for studying natural genetic, epigenetic, and phenotypic variation. Trends Plant Sci. 21:906-908.
Wang Z, Wang F, Hong Y, Huang J, Shi H, Zhu JK. 2016. Two chloroplast proteins suppress drought resistance by affecting ROS production in guard cells. Plant Physiol. 172:2491-2503.
Zhu JK. 2016. Abiotic stress signaling and responses in plants. Cell. 167:313-324.
Wang Y, Xue X, Zhu JK, Dong J. 2016. Demethylation of ERECTA receptor genes by IBM1 histone demethylase affects stomatal development. Development. 146:4452-4461.
Mao Y, Botella JR, Zhu JK. 2016. Heritability of targeted gene modifications induced by plant-optimized CRISPR systems. Cell Mol Life Sci. In press. doi:10.1007/s00018-016-2380-1
Yang Y, La H, Tang K, Miki D, Yang L, Wang B, Duan CG, Nie W, Wang X, Wang S, Pan Y, Tran EJ, An L, Zhang H, Zhu JK. 2016. SAC3B, a central component of the mRNA export complex TREX-2, is required for prevention of epigenetic gene silencing in Arabidopsis. Nucleic Acids Res. In Press. doi: 10.1093/nar/gkw850.
Ma J, Wang D, She J, Li J, Zhu JK, She YM. 2016. Endoplasmic reticulum-associated N-glycan degradation of cold-upregulated glycoproteins in response to chilling stress in Arabidopsis. New Phytol. 212:282-96.
Zhang Q, Li Y, Xu T, Srivastava AK, Wang D, Zeng L, Yang L, He L, Zhang H, Zheng Z, Yang DL, Zhao C, Dong J, Gong Z, Liu R, Zhu JK. 2016. The chromatin remodeler DDM1 promotes hybrid vigor by regulating salicylic acid metabolism. Cell Discov. 2:16027
Zhao C, Zhu JK.. 2016. The broad roles of CBF genes: from development to abiotic stress. Plant Signal Behav. 11:e1215794
Zhang Q, Wang D, Lang Z, He L, Yang L, Zeng L, Li Y, Zhao C, Huang H, Zhang H, Zhang H, Zhu JK.. 2016. Methylation interactions in Arabidopsis hybrids require RNA-directed DNA methylation and are influenced by genetic variation. Proc Natl Acad Sci U S A. 113:E4248-56.
Xing L, Zhao Y, Gao J, Xiang C, Zhu JK.. 2016. The ABA receptor PYL9 together with PYL8 plays an important role in regulating lateral root growth. Sci Rep. 6:27177.
Zhao C, Zhang Z, Xie S, Si T, Li Y, Zhu JK.. 2016. Mutational Evidence for the Critical Role of CBF Transcription Factors in Cold Acclimation in Arabidopsis.Plant Physiol. 171:2744-59.
Zhang J, Xie S, Zhu JK, Gong Z.. 2016. Requirement for flap endonuclease 1 (FEN1) to maintain genomic stability and transcriptional gene silencing in Arabidopsis. Plant J. 87:629-640.
Zhang J, Xie S, Cheng J, Lai J, Zhu JK, Gong Z.. 2016. The Second Subunit of DNA Polymerase Delta Is Required for Genomic Stability and Epigenetic Regulation. Plant Physiol. 171:1192-208.
Wang S, Bai G, Wang S, Yang L, Yang F, Wang Y, Zhu JK, Hua J.. 2016. Chloroplast RNA-Binding Protein RBD1 Promotes Chilling Tolerance through 23S rRNA Processing in Arabidopsis. PLoS Genet. 12:e1006027.
Zhan X, Yang L, Wang D, Zhu JK, Lang Z. 2016. De novo assembly and analysis of the transcriptome of Ocimum americanum var. pilosum under cold stress. BMC Genomics. 17:209.
Hou YJ, Zhu Y, Wang P, Zhao Y, Xie S, Batelli G, Wang B, Duan CG, Wang X, Xing L, Lei M, Yan J, Zhu X, Zhu JK. 2016. Type One Protein Phosphatase 1 and Its Regulatory Protein Inhibitor 2 Negatively Regulate ABA Signaling. PLoS Genet. 12:e1005835.
Zhao Y, Chan Z, Gao J, Xing L, Cao M, Yu C, Hu Y, You J, Shi H, Zhu Y, Gong Y, Mu Z, Wang H, Deng X, Wang P, Bressan RA, Zhu JK. 2016. ABA receptor PYL9 promotes drought resistance and leaf senescence. Proc Natl Acad Sci U S A. 113:1949-54.
Yang DL, Zhang G, Tang K, Li J, Yang L, Huang H, Zhang H, Zhu JK. 2016. Dicer-independent RNA-directed DNA methylation in Arabidopsis. Cell Res. 26:66-82
Wang P, Zhu JK. 2016. Assessing Kinase Activity in Plants with In-Gel Kinase Assays. Methods Mol Biol. 1363:189-97. (pdf)
Chan Z, Wang Y, Cao M, Gong Y, Mu Z, Wang H, Hu Y, Deng X, He XJ, Zhu JK. 2016. RDM4 modulates cold stress resistance in Arabidopsis partially through the CBF-mediated pathway. New Phytol. 209:1527-39.
Yamamuro C, Zhu JK, Yang Z. 2016. Epigenetic Modifications and Plant Hormone Action. Mol Plant. 9:57-70.
Zhang H, Gou F, Zhang J, Liu W, Li Q, Mao Y, Botella JR, Zhu JK. 2016. TALEN-mediated targeted mutagenesis produces a large variety of heritable mutations in rice. Plant Biotechnol J. 14:186-94.
Mao Y, Zhang Z, Feng Z, Wei P, Zhang H, Botella JR, Zhu JK. 2015. Development of germ-line-specific CRISPR-Cas9 systems to improve the production of heritable gene modifications in Arabidopsis. Plant Biotechnol J. 14:519-32.
Duan CG, Wang X, Tang K, Zhang H, Mangrauthia SK, Lei M, Hsu CC, Hou YJ, Wang C, Li Y, Tao WA, Zhu JK. 2015. MET18 Connects the Cytosolic Iron-Sulfur Cluster Assembly Pathway to Active DNA Demethylation in Arabidopsis. PLoS Genet. 11:e1005559.
Zhang Z, Mao Y, Ha S, Liu W, Botella JR, Zhu JK. 2015. A multiplex CRISPR/Cas9 platform for fast and efficient editing of multiple genes in Arabidopsis. Plant Cell Rep. 35:1519-33
Zhang S, Zhan X, Xu X, Cui P, Zhu JK, Xia Y, Xiong L. 2015. Two domain-disrupted hda6 alleles have opposite epigenetic effects on transgenes and some endogenous targets. Sci Rep. 5:17832
Zhao C, Lang Z, Zhu JK. 2015. Cold responsive gene transcription becomes more complex. Trends Plant Sci. 20:466-8.
Zhan X, Qian B, Cao F, Wu W, Yang L, Guan Q, Gu X, Wang P, Okusolubo TA, Dunn SL, Zhu JK, Zhu J.. 2015. An Arabidopsis PWI and RRM motif-containing protein is critical for pre-mRNA splicing and ABA responses. Nat Commun. 6:8139.
Wang P, Zhu JK, Lang Z. 2015. Nitric oxide suppresses the inhibitory effect of abscisic acid on seed germination by S-nitrosylation of SnRK2 proteins. Plant Signal Behav. 10:e1031939.
Zheng Z, Yu H, Miki D, Jin D, Zhang Q, Ren Z, Gong Z, Zhang H, Zhu JK. 2015. Involvement of Multiple Gene-Silencing Pathways in a Paramutation-like Phenomenon in Arabidopsis. Cell Rep. 11:1160-1167.
Li Y, Duan CG, Zhu X, Qian W, Zhu JK. 2015. A DNA ligase required for active DNA demethylation and genomic imprinting in Arabidopsis. Cell Res. 25:757-760.
Xiao L, Yang G, Zhang L, Yang X, Zhao S, Ji Z, Zhou Q, Hu M, Wang Y, Chen M, Xu Y, Jin H, Xiao X, Hu G, Bao F, Hu Y, Wan P, Li L, Deng X, Kuang T, Xiang C, Zhu JK, Oliver MJ, He Y. 2015. The resurrection genome of Boea hygrometrica: A blueprint for survival of dehydration. Proc Natl Acad Sci U S A. 112:5833-5837.
Zhang Y, Wang P, Shao W, Zhu JK, Dong J. 2015. The BASL Polarity Protein Controls a MAPK Signaling Feedback Loop in Asymmetric Cell Division. Dev Cell 33:136-149.
Lind C, Dreyer I, López-Sanjurjo EJ, von Meyer K, Ishizaki K, Kohchi T, Lang D, Zhao Y, Kreuzer I, Al-Rasheid KA, Ronne H, Reski R, Zhu JK, Geiger D, Hedrich R. 2015. Stomatal guard cells co-opted an ancient ABA-dependent desiccation survival system to regulate stomatal closure. Curr Biol. 25:928-935.
Lei M, Zhang H, Julian R, Tang K, Xie S, Zhu JK. 2015. Regulatory link between DNA methylation and active demethylation in Arabidopsis. Proc Natl Acad Sci U S A. 112:3553-3557.
Lang Z, Lei M, Wang X, Tang K, Miki D, Zhang H, Mangrauthia SK, Liu W, Nie W, Ma G, Yan J, Duan CG, Hsu CC, Wang C, Tao WA, Gong Z, Zhu JK. 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.
Zhan X, Zhu JK, Lang Z. 2015. Increasing freezing tolerance: kinase regulation of ICE1. Dev Cell. 32:257-258.
Wang B, Duan CG, Wang X, Hou YJ, Yan J, Gao C, Kim JH, Zhang H, Zhu JK. 2015. HOS1 regulates Argonaute1 by promoting transcription of the microRNA gene MIR168b in Arabidopsis. Plant J. 81:861-870.
Wang C, Dong X, Jin D, Zhao Y, Xie S, Li X, He X, Lang Z, Lai J, Zhu JK, Gong Z. 2015. Methyl-CpG-binding domain protein MBD7 is required for active DNA demethylation in Arabidopsis. Plant Physiol. 167:905-914.
Li Y, Córdoba-Cañero D, Qian W, Zhu X, Tang K, Zhang H, Ariza RR, Roldán-Arjona T, Zhu JK. 2015. An AP endonuclease functions in active DNA dimethylation and gene imprinting in arabidopsis. PLoS Genet. 11:e1004905.
Wang P, Du Y, Hou YJ, Zhao Y, Hsu CC, Yuan F, Zhu X, Tao WA, Song CP, Zhu JK. 2015. Nitric oxide negatively regulates abscisic acid signaling in guard cells by S-nitrosylation of OST1. Proc Natl Acad Sci U S A. 112:613-618.
Duan CG, Zhang H, Tang K, Zhu X, Qian W, Hou YJ, Wang B, Lang Z, Zhao Y, Wang X, Wang P, Zhou J, Liang G, Liu N, Wang C, Zhu JK. 2015. Specific but interdependent functions for Arabidopsis AGO4 and AGO6 in RNA-directed DNA methylation. EMBO J. 34:581-592.
Ban T, Zhu JK, Melcher K, Xu HE. 2015. Structural mechanisms of RNA recognition: sequence-specific and non-specific RNA-binding proteins and the Cas9-RNA-DNA complex. Cell Mol Life Sci. 72:1045-1058.
Wang ZY, Gehring C, Zhu J, Li FM, Zhu JK, Xiong L. 2015. The Arabidopsis Vacuolar Sorting Receptor1 is required for osmotic stress-induced abscisic acid biosynthesis. Plant Physiol. 167:137-152.
Sridharamurthy M, Kovach A, Zhao Y, Zhu JK, Xu HE, Swaminathan K, Melcher K. 2014. H2O2 inhibits ABA-signaling protein phosphatase HAB1. PLoS One. 9:e113643.
Han YF, Dou K, Ma ZY, Zhang SW, Huang HW, Li L, Cai T, Chen S, Zhu JK, He XJ. 2014. SUVR2 is involved in transcriptional gene silencing by associating with SNF2-related chromatin-remodeling proteins in Arabidopsis. Cell Res 24:1445-1465.
Zhu Y, Schluttenhoffer CM, Wang P, Fu F, Thimmapuram J, Zhu JK, Lee SY, Yun DJ, Mengiste T. 2014. CYCLIN-DEPENDENT KINASE8 differentially regulates plant immunity to fungal pathogens through kinase-dependent and -independent functions in Arabidopsis. Plant Cell 26:4149-4170.
Zhu X, Taylor A, Zhang S, Zhang D, Feng Y, Liang G, Zhu JK. 2014. Measuring spatial and temporal Ca2+ signals in Arabidopsis plants. J Vis Exp. e51945.
Zhang H, Zhu JK. 2014. Emerging roles of RNA processing factors in regulating long non-coding RNAs. RNA Biol. 11:793-797.
Xue L, Wang P, Cao P, Zhu JK, Tao WA. 2014. Identification of ERK1 Direct Substrates using Stable Isotope Labeled Kinase Assay-Linked Phosphoproteomics.. Mol Cell Proteomics. 13:3199-3210.
Qian W, Miki D, Lei M, Zhu X, Zhang H, Liu Y, Li Y, Lang Z, Wang J, Tang K, Liu R, Zhu JK. 2014. Regulation of Active DNA Demethylation by an α-Crystallin Domain Protein in Arabidopsis. Mol Cell. 55:361-371.
Zhang H, Tang K, Wang B, Duan CG, Lang Z, Zhu JK. 2014. Protocol: a beginner's guide to the analysis of RNA-directed DNA methylation in plants. Plant Methods. 10:18.
Yamamuro C, Miki D, Zheng Z, Ma J, Wang J, Yang Z, Dong J, Zhu JK. 2014. Overproduction of stomatal lineage cells in Arabidopsis mutants defective in active DNA demethylation. Nat Commun. 5:4062.
Zhao Y, Xing L, Wang X, Hou YJ, Gao J, Wang P, Duan CG, Zhu X, Zhu JK.. 2014. The ABA receptor PYL8 promotes lateral root growth by enhancing MYB77-dependent transcription of auxin-responsive genes. Sci Signal. 7:ra53.
Shi H, Ye T, Zhu JK, Chan Z. 2014. Constitutive production of nitric oxide leads to enhanced drought stress resistance and extensive transcriptional reprogramming in Arabidopsis. J Exp Bot. 65:4119-4131.
Wang D, Qu Z, Adelson DL, Zhu JK, Timmis JN. 2014. Transcription of nuclear organellar DNA in a model plant system. Genome Biol Evol. 6:1327-1334.
Zhang H, Zhang J, Wei P, Zhang B, Gou F, Feng Z, Mao Y, Yang L, Zhang H, Xu N, Zhu JK. 2014. The CRISPR/Cas9 system produces specific and homozygous targeted gene editing in rice in one generation. Plant Biotechnol J. 12:797-807.
Huang CF, Zhu JK. 2014. RNA splicing factors and RNA-directed DNA methylation. Biology (Basel). 3:243-254.
Zhang H, Tang K, Qian W, Duan CG, Wang B, Zhang H, Wang P, Zhu X, Lang Z, Yang Y, Zhu JK.. 2014. An Rrp6-like protein positively regulates noncoding RNA levels and DNA methylation in Arabidopsis. Mol Cell. 54:418-430.
Khan A, Garbelli A, Grossi S, Florentin A, Batelli G, Acuna T, Zolla G, Kaye Y, Paul LK, Zhu JK, Maga G, Grafi G, Barak S.. 2014. 12. The Arabidopsis STRESS RESPONSE SUPPRESSOR DEAD-box RNA helicases are nucleolar- and chromocenter-localized proteins that undergo stress-mediated relocalization and are involved in epigenetic gene silencing. Plant J. 79:28-43.
Feng Z, Mao Y, Xu N, Zhang B, Wei P, Yang DL, Wang Z, Zhang Z, Zheng R, Yang L, Zeng L, Liu X, Zhu JK.. 2014. Multigeneration analysis reveals the inheritance, specificity, and patterns of CRISPR/Cas-induced gene modifications in Arabidopsis. Proc Natl Acad Sci U S A. 111:4632-4637.
Cao MJ, Wang Z, Zhao Q, Mao JL, Speiser A, Wirtz M, Hell R, Zhu JK, Xiang CB.. 2014. Sulfate availability affects ABA levels and germination response to ABA and salt stress in Arabidopsis thaliana. Plant J. 77:604-615.
Lei M, La H, Lu K, Wang P, Miki D, Ren Z, Duan CG, Wang X, Tang K, Zeng L, Yang L, Zhang H, Nie W, Liu P, Zhou J, Liu R, Zhong Y, Liu D, Zhu JK. 2014. Arabidopsis EDM2 promotes IBM1 distal polyadenylation and regulates genome DNA methylation patterns. Proc Natl Acad Sci U S A. 111:527-532.
Zhang H, He X, Zhu JK. 2013. RNA-directed DNA methylation in plants: Where to start? RNA Biol. 10:1593-1596.(pdf)
Zhao Y, Chan Z, Xing L, Liu X, Hou YJ, Chinnusamy V, Wang P, Duan C, Zhu JK.. 2013. The unique mode of action of a divergent member of the ABA-receptor protein family in ABA and stress signaling. Cell Res.23:1380-1395.
Ke J, Chen RZ, Ban T, Zhou XE, Gu X, Tan MH, Chen C, Kang Y, Brunzelle JS, Zhu JK, Melcher K, Xu HE.. 2013. Structural basis for RNA recognition by a dimeric PPR-protein complex. Nat Struct Mol Biol. 20:1377-1382.
Yin P, Li Q, Yan C, Liu Y, Liu J, Yu F, Wang Z, Long J, He J, Wang HW, Wang J, Zhu JK, Shi Y, Yan N.. 2013. Structural basis for the modular recognition of single-stranded RNA by PPR proteins. Nature. 504:168-171.
Huang CF, Miki D, Tang K, Zhou HR, Zheng Z, Chen W, Ma ZY, Yang L, Zhang H, Liu R, He XJ, Zhu JK.. 2013. A Pre-mRNA-splicing factor is required for RNA-directed DNA methylation in Arabidopsis. PLoS Genet. 9:e1003779.
Batelli G, Oh DH, D'Urzo MP, Orsini F, Dassanayake M, Zhu JK, Bohnert HJ, Bressan RA, Maggio A.. 2013. Using Arabidopsis-related model species (ARMS): growth, genetic transformation, and comparative genomics. Methods Mol Biol. 1062:27-51.
Ban T, Ke J, Chen R, Gu X, Tan MH, Zhou XE, Kang Y, Melcher K, Zhu JK, Xu HE.. 2013. Structure of a PLS-class Pentatricopeptide Repeat Protein Provides Insights into Mechanism of RNA Recognition. J Biol Chem. 288:31540-31548.
Wang X, Duan CG, Tang K, Wang B, Zhang H, Lei M, Lu K, Mangrauthia SK, Wang P, Zhu G, Zhao Y, Zhu JK.. 2013. RNA-binding protein regulates plant DNA methylation by controlling mRNA processing at the intronic heterochromatin-containing gene IBM1. Proc Natl Acad Sci U S A. 110:15467-15472.
Mao Y, Zhang H, Xu N, Zhang B, Gou F, Zhu JK.. 2013. Application of the CRISPR-Cas System for Efficient Genome Engineering in Plants. Mol Plant. 6:2008-2011.
Feng Z, Zhang B, Ding W, Liu X, Yang DL, Wei P, Cao F, Zhu S, Zhang F, Mao Y, Zhu JK.. 2013. Efficient genome editing in plants using a CRISPR/Cas system. Cell Res. 23:1229-1232.
Bai G, Yang DH, Zhao Y, Ha S, Yang F, Ma J, Gao XS, Wang ZM, Zhu JK.. 2013. Interactions between soybean ABA receptors and type 2C protein phosphatases. Plant Mol Biol. 83:651-664.
Wang Y, Yang L, Zheng Z, Grumet R, Loescher W, Zhu JK, Yang P, Hu Y, Chan Z.. 2013. Transcriptomic and physiological variations of three Arabidopsis ecotypes in response to salt stress. PLoS One. 8:e69036.
Zhou HR, Zhang FF, Ma ZY, Huang HW, Jiang L, Cai T, Zhu JK, Zhang C, He XJ.. 2013. Folate polyglutamylation is involved in chromatin silencing by maintaining global DNA methylation and histone H3K9 dimethylation in Arabidopsis. Plant Cell. 25:2545-2559.
Dou K, Huang CF, Ma ZY, Zhang CJ, Zhou JX, Huang HW, Cai T, Tang K, Zhu JK, He XJ.. 2013. The PRP6-like splicing factor STA1 is involved in RNA-directed DNA methylation by facilitating the production of Pol V-dependent scaffold RNAs. Nucleic Acids Res. 41:8489-8502.
Zhang H, Wang B, Duan CG, Zhu JK. 2013. Chemical probes in plant epigenetics studies. Plant Signal Behav. 8(9).
Cao M, Liu X, Zhang Y, Xue X, Zhou XE, Melcher K, Gao P, Wang F, Zeng L, Zhao Y, Zhao Y, Deng P, Zhong D, Zhu JK, Xu HE, Xu Y.. 2013. An ABA-mimicking ligand that reduces water loss and promotes drought resistance in plants. Cell Res. 23:1043-1054.
Wang P, Xue L, Batelli G, Lee S, Hou YJ, Van Oosten MJ, Zhang H, Tao WA, Zhu JK. 2013. Quantitative phosphoproteomics identifies SnRK2 protein kinase substrates and reveals the effectors of abscisic acid action. Proc Natl Acad Aci U S A. 110:11205-11210.
Zhu X, Zhu JK.. 2013. Double repression in jasmonate-mediated plant defense. Mol Cell. 50:459-460.
Xue L, Wang P, Wang L, Renzi E, Radivojac P, Tang H, Arnold R, Zhu JK, Tao WA.. 2013. Quantitative measurement of phosphoproteome response to osmotic stress in Arabidopsis based on Library-Assisted eXtracted Ion Chromatogram (LAXIC). Mol Cell Proteomics. 12:2354-2369.
Zhang H, Ma ZY, Zeng L, Tanaka K, Zhang CJ, Ma J, Bai G, Wang P, Zhang SW, Liu ZW, Cai T, Tang K, Liu R, Shi X, He XJ, Zhu JK.. 2013. DTF1 is a core component of RNA-directed DNA methylation and may assist in the recruitment of Pol IV. Proc Natl Acad Sci U S A. 110:8290-8295.
Zhang CJ, Zhou JX, Liu J, Ma ZY, Zhang SW, Dou K, Huang HW, Cai T, Liu R, Zhu JK, He XJ.. 2013. The splicing machinery promotes RNA-directed DNA methylation and transcriptional silencing in Arabidopsis. EMBO J. 32:1128-1140.
Luhua S, Hegie A, Suzuki N, Shulaev E, Luo X, Cenariu D, Ma V, Kao S, Lim J, Gunay MB, Oosumi T, Lee SC, Harper J, Cushman J, Gollery M, Girke T, Bailey-Serres J, Stevenson RA, Zhu JK, Mittler R.. 2013. Linking genes of unknown function with abiotic stress responses by high-throughput phenotype screening. Physiol Plant. 148:322-333.
Zhang X, Lii Y, Wu Z, Polishko A, Zhang H, Chinnusamy V, Lonardi S, Zhu JK, Liu R, Jin H.. 2013. Mechanisms of small RNA generation from cis-NATs in response to environmental and developmental cues. Mol Plant. 6:704-715.
Zhu X, Feng Y, Liang G, Liu N, Zhu JK. 2013. Aequorin-based luminescence imaging reveals stimulus- and tissue-specific Ca2+ dynamics in Arabidopsis plants. Mol Plant. 6:444-455.
Arisz SA, van Wijk R, Roels W, Zhu JK, Haring MA, Munnik T. 2013. Rapid phosphatidic acid accumulation in response to low temperature stress in Arabidopsis is generated through diaclglycerol kinase. Front Plant Sci. 4:1.
Li L, Atef A, Piatek A, Ali Z, Piatek M, Aouida M, Sharakou A, Mahjoub A, Wang G, Khan S, Fedoroff NV, Zhu JK, Mahfouz M. 2013. Characterization and DNA-binding specificities of Ralstonia TAL-like effectors. Mol Plant. 6:1318-1330.
Chaabane SB, Liu R, Chinnusamy V, Kwon Y, Park JH, Kim SY, Zhu JK, Yang SW, Lee BH. 2013. STA1, an Arabidopsis pre-mRNA processing factor 6 homolog, is a new player involved in miRNA biogenesis. Nucleic Acids Res. 41:1984-1997.
Soon FF, Ng LM, Zhou XE, West GM, Kovach A, Tan MH, Suino-Powell KM, He Y, Xu Y, Chalmers MJ, Brunzelle JS, Zhang H, Yang H, Jiang H, Li J, Yong EL, Cutler S, Zhu JK, Griffin PR, Melcher K, Xu HE. 2012. Molecular mimicry regulates ABA signaling by SnRK2 kinases and PP2C phosphatases. Science 335:85-88
Mahfouz MM, Li L, Piatek M, Fang X, Mansour H, Bangarusamy DK, Zhu JK. 2012. Targeted transcriptional repression using a chimeric TALE-SRDX repressor protein. Plant Mol Biol. 78:311-321.
Deng D, Yan C, Pan X, Mahfouz M, Wang J, Zhu JK, Shi Y, Yan N. 2012. Structural basis for sequence-specific recognition of DNA by TAL effectors. Science 335:720-723
Li Z, Li Z, Gao X, Chinnusamy V, Bressan R, Wang ZX, Zhu JK, Wu JW, Liu D. 2012. ROP11 GTPase negatively regulates ABA signaling by protecting ABI1 phosphatase activity from inhibition by the ABA receptor RCAR1/PYL9 in Arabidopsis. J Integr Plant Biol. 54:180-188.
Li L, Piatek MJ, Atef A, Piatek A, Wibowo A, Fang X, Sabir JS, Zhu JK, Mahfouz MM. 2012. Rapid and highly efficient construction of TALE-based transcriptional regulators and nucleases for genome modification. Plant Mol Biol. 78:407-416.
Martínez-Macías MI, Qian W, Miki D, Pontes O, Liu Y, Tang K, Liu R, Morales-Ruiz T, Ariza RR, Roldán-Arjona T, Zhu JK. 2012. A DNA 3' phosphatase functions in active DNA demethylation in Arabidopsis. Mol Cell 45:357-370.
Zhang X, Xia J, Lii YE, Barrera-Figueroa BE, Zhou X, Gao S, Lu L, Niu D, Chen Z, Leung C, Wong T, Zhang H, Guo J, Li Y, Liu R, Liang W, Zhu JK, Zhang W, Jin H. 2012. Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function. Genome Biol. 13:R20.
Zhang H, Deng X, Miki D, Cutler S, La H, Hou YJ, Oh J, Zhu JK. 2012. Sulfamethazine suppresses epigenetic silencing in Arabidopsis by impairing folate synthesis. Plant Cell 24:1230-1241.
Kwon Y, Yu SI, Lee H, Yim JH, Zhu JK, Lee BH. 2012. Arabidopsis serine decarboxylase mutants implicate the roles of ethanolamine in plant growth and development. Int J Mol Sci. 13:3176-3188.
Zhou XE, Soon FF, Ng LM, Kovach A, Suino-Powell KM, Li J, Yong EL, Zhu JK, Xu HE, Melcher K. 2012. Catalytic mechanism and kinase interactions of ABA-signaling PP2C phosphatases. Plant Signal Behav. 7:581-588.
Qian W, Miki D, Zhang H, Liu Y, Zhang X, Tang K, Kan Y, La H, Li X, Li S, Zhu X, Shi X, Zhang K, Pontes O, Chen X, Liu R, Gong Z, Zhu JK. 2012. A histone acetyltransferase regulates active DNA demethylation in Arabidopsis. Science 336:1445-1448. .
Li X, Qian W, Zhao Y, Wang C, Shen J, Zhu JK, Gong Z. 2012. Antisilencing role of the RNA-directed DNA methylation pathway and a histone acetyltransferase in Arabidopsis. Proc Natl Acad Sci U S A 109:11425-11430
Wu HJ, Zhang Z, Wang JY, Oh DH, Dassanayake M, Liu B, Huang Q, Sun HX, Xia R, Wu Y, Wang YN, Yang Z, Liu Y, Zhang W, Zhang H, Chu J, Yan C, Fang S, Zhang J, Wang Y, Zhang F, Wang G, Lee SY, Cheeseman JM, Yang B, Li B, Min J, Yang L, Wang J, Chu C, Chen SY. 2012. Insights into salt tolerance from the genome of Thellungiella salsuginea. Proc Natl Acad Sci U S A 109:12219-12224
Fujii H, Zhu JK. 2012. Osmotic stress signaling via protein kinases. Cell Mol Life Sci. 69:3165-3173.
Batelli G, Massarelli I, Van Oosten M, Nurcate R, Vannini C, Raimondi G, Leone A, Zhu JK, Maggio A, Grillo S. 2012. Asg1 is a stress-inducible gene which increases stomatal resistance in salt stressed potato. J Plant Physiol. 169:1849-1857.
Barrera-Figueroa BE, Gao L, Wu Z, Zhou X, Zhu J, Jin H, Liu R, Zhu JK. 2012. High throughput sequencing reveals novel and abiotic stress-regulated mcroRNAs in the inflorescences of rice. BMC Plant Biol. 12:132.
Zhang H, Zhu JK. 2012. Seeing the forest for the trees: a wide perspective on RNA-directed DNA methylation. Genes Dev. 26:1769-1773.
Deng D, Yin P, Yan C, Pan X, Gong X, Qi S, Xie T, Mahfouz M, Zhu JK, Yan N, Shi Y. 2012. Recognition of methylated DNA by TAL effectors. Cell Res. 22:1502-1504.
Zhan X, Wang B, Li H, Liu R, Kalia RK, Zhu JK, Chinnusamy V. 2012. Arabidopsis proline-rich protein important for development and abiotic stress tolerance is involved in microRNA biogenesis. Proc Natl Acad Sci U S A. 109:18198-18203.
Zhang H, Zhu JK. 2012. Active DNA demethylation in plants and animals. Cold Spring Harb Symp Quant Biol. 77:161-173.