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2009
Zhu JK. 2009 Active DNA Demethylation Mediated by DNA Glycosylases. Annu Rev Genet. in press doi: 10.1146/annurev-genet-102108-134205 [pdf]
Rohila JS, Chen M, Chen S, Chen J, Cerny RL, Dardick C, Canlas P, Fujii H, Gribskov M, Kanrar S, Knoflicek L, Stevenson B, Xie M, Xu X, Zheng X, Zhu JK, Ronald P, Fromm ME. 2009 Protein-protein interactions of tandem affinity purified protein kinases from rice. PLoS One. 4:e6685.
He XJ, Hsu YF, Zhu S, Wierzbicki AT, Pontes O, Pikaard CS, Liu HL, Wang CS, Jin H, Zhu JK. 2009. An effector of RNA-directed DNA methylation in Arabidopsis is an ARGONAUTE 4-and RNA-binding protein. Cell 137:498-508. [pdf]
Park SY, Fung P, Nishimura N, Jensen DR, Fujii H, Zhao Y, Lumba S, Santiago J, Rodrigues A, Chow TF, Alfred SE, Bonetta D, Finkelstein R, Provart NJ, Desveaux D, Rodriquez PL, McCourt P, Zhu JK, Schroeder JI, Volkman BR, Cutler SR. 2009. Abscisic acid inhibits type 2C protein phosphatases via the PYR/PYL family of ABA binding START proteins. 324:1068-1071.
Fujii H, Zhu JK. 2009. Arabidopsis mutant deficient in three abscisic acid-activated protein kinases reveals critical roles in growth, reproduction and stress. Proc. Natl. Acad. Sci. U S A 106:8380-8385. [pdf]
Bertorello AM, Zhu JK. 2009. SIK1/SOS2 networks: decoding sodium signals via calcium-responsive protein kinase pathways. Pflugers Arch. 324:1068-1071.[pdf]
Iida K, Jin H, Zhu JK. 2009. Bioinformatics analysis suggests base modifications of tRNAs and miRNAs in Arabidopsis thanliana. BMC Genomics 10:155. [pdf]
Chinnusamy V, Zhu JK. 2009. RNA-directed DNA methylation and demethylation in plants. Sci. China C Life Sci. 52:331-343. [pdf]
He XJ, Hsu YF, Pontes O, Zhu J, Lu J, Bressan RA, Pikaard C, Wang CS, Zhu JK. 2009. NRPD4, a protein related to the RPB4 subunit of RNA polymerase II, is a component of RNA polymerase IV and V and is required for RNA-dicrected DNA methylation. Genes Dev. 23:318-330. [pdf]
Chinnusamy V, Zhu JK. 2009. Epigenetic regulation of stress responses in plants. Curr. Opin. Plant Biol. 12:133-139 [pdf]
Fujii H, Zhu JK. 2009. An autophosphorylation site of the protein kinase SOS2 is important for salt tolerance in Arabidopsis. Mol. Plant. 2:183-190. [pdf]
Dong CH, Zolman BK, Bartel B, Lee BH, Stevenson B, Agarwal M, Zhu JK. 2009. Disruption of Arabidopsis CHY1 reveals an important role of metabolic status in plant cold stress signaling. Mol. Plant. 2:59-72. [pdf]
Bressan R, Bohnert H, Zhu JK. 2009. Abiotic stress tolerance: from gene discovery in model organisms to crop improvement. Mol. Plant. 2:1-2. [pdf]
Ream TS, Haag JR, Wierzbicki AT, Nicora CD, Norbeck A, Zhu JK, Hagen G, Guilfoyle TJ, Pasa-Tolic L, Pikaard CS. 2008. Subunit compositions of the RNA-silencing enzymes Pol IV and Pol V reveal their origins as specialized forms of RNA polymerase II. Mol. Cell. 33:192-203.
Ding X, Richter T, Chen M, Fujii H, Seo YS, Xie M, Zheng X, Kanrar S, Stevenson RA, Dardick C, Li Y, Jiang H, Zhang Y, Yu F, Bartley LE, Chern M, Bart R, Chen X, Zhu L, Farmerie WG, Gribskov M, Zhu JK, Fromm ME, Ronald PC, Song WY. 2009. A rice kinase-protein interaction map. Plant Physiol. 149:1478-1492.
2008
Meyers BC, Axtell MJ, Bartel B, Bartel DP, Baulcombe D, Bowman JL, Cao X, Carrington JC, Chen X, Green PJ, Griffiths-Jones S, Jacobsen SE, Mallory AC, Martienssen RA, Poethig RS, Qi Y, Vaucheret H, Voinnet O, Watanabe Y, Weigel D, Zhu JK. 2008. Criteria for Annotation of Plant MicroRNAs. Plant Cell. 20:3186-3190.
Zheng X, Pontes O, Zhu J, Miki D, Zhang F, Li WX, Iida K, Kapoor A, Pikaard CS, Zhu JK. 2008. ROS3 is an RNA-binding protein required for DNA demethylation in Arabidopsis. Nature. 455:1259-1262. [pdf]
Zhu JK. 2008. Reconstituting plant miRNA biogenesis. Proc. Natl. Acad. Sci. USA 105:9851-9852. [pdf]
Kanaoka MM, Pillitteri LJ, Fujii H, Yoshida Y, Bogenschutz NL, Takabayashi J, Zhu JK, Torii KU. 2008. SCREAM/ICE1 and SCREAM2 Specify Three Cell-State Transitional Steps Leading to Arabidopsis Stomatal Differentiation. Plant Cell 20:1775-1785.
Li WX, Oono Y, Zhu J, He XJ, Wu JM, Iida K, Lu XY, Cui X, Jin H, Zhu JK. 2008. The Arabidopsis NFYA5 transcription factor is regulated transcriptionally and posttranscriptionally to promote drought resistance. Plant Cell. 20:2238.2251.[pdf]
Du J, Huang YP, Xi J, Cao MJ, Ni WS, Chen X, Zhu JK, Oliver DJ, Xiang CB. 2008. Functional Gene-mining for Salt Tolerance Genes with the Power of Arabidopsis. Plant J. 56:653-664.
Zhang H, Ohyama K, Boudet J, Chen Z, Yang J, Zhang M, Muranaka T, Maurel C, Zhu JK, Gong Z. 2008. Dolichol biosynthesis and its effects on the unfolded protein response and abiotic stress resistance in Arabidopsis. Plant Cell 20: 1879-1898.
Zhou X, Wang G, Sutoh K, Zhu JK, Zhang W. 2008. Identification of cold-inducible miroRNAs in plants by transcriptome analysis. Biochim. Biophys. Acta 1779:780-788.
Chinnusamy V, Gong Z, Zhu JK. 2008. Nuclear RNA export and its importance in abiotic stress responses of plants. Curr. Top. Microbiol. Immunol. 326:235-255. [pdf]
Yu H, Chen X, Hong YY, Wang Y, Xu P, Ke SD, Liu HY, Zhu JK, Oliver DJ, Xiang CB. 2008. Activated expression of an Arabidopsis HD-START protein confers drought tolerance with improved root system and reduced stomatal density. Plant Cell 20:1134-1151.
Zhu JK. 2008. Epigenome sequencing comes of age. Cell 133:395-397. [pdf]
Sunkar R, Zhou X, Zhang W, Zhu JK. 2008. Indentification of novel and candidate miRNAs in rice by high throughput sequencing. BMC Plant Biol. 8:25. [pdf]
Subramanian S, Fu Y, Sunkar R, Barbazuk BW, Zhu JK, Yu O. 2008. Novel and nodulation-regulated microRNAs in soybean roots. BMC Genomics. 9:160.
Jin H, Vacic V, Girke T, Lonardi S, Zhu JK. 2008. Small RNAs and the regulation of cis-natural antisense transcripts in Arabidopsis. BMC Mol. Biol. 9:6. [pdf]
Chung JS, Zhu JK, Bressan RA, Hasegawa PM, Shi H. 2008. Reactive oxygen species mediate Na+-induced SOS1 mRNA stability in Arabidopsis. Plant J. 53:554-565.
Zhu J, Jeong JC, Zhu Y, Sokolchik I, Miyazaki S, Zhu JK, Hasegawa PM, Bohnert HJ, Shi H, Yun DJ, Bressan RA. 2008. Involvement of Arabidopsis HOS15 in histone deacetylation and cold tolerance. Proc. Natl. Acad. Sci. USA. 105:4945-4950.
Horan K, Jang C, Bailey-Serres J, Mittler R, Shelton C, Harper JF, Zhu JK, Cushman JJ, Gollery M, Girke T. 2008. Annotating genes of known and unknown function by large-scale co-expression analysis. Plant Physiol. 147:41-57.
Vacic V, Jin H, Zhu JK, Lonardi S. 2008. A probabilistic method for small RNA flowgram matching. Pac. Symp. Biocomput. 75-86.
2007
Sridhar VV, Kapoor A, Zhang K, Zhu J, Zhou T, Hasegawa PM, Bressan RA, Zhu JK. 2007. Control of DNA methylation and heterochromatic silencing by histone H2B deubiquitination. Nature. 447:735-738. [pdf]
Verslues PE, Batelli G, Grillo S, Agius F, Kim YS, Zhu J, Agarwal M, Katiyar-Agarwal S, Zhu JK. 2007. Interaction of SOS2 with nucleoside diphosphate kinase 2 and catalases reveals a point of connection between salt stress and H2O2 signaling in Arabidopsis thaliana. Mol. Cell. Biol. 27:7771-7780. [pdf]
Batelli G, Verslues PE, Agius F, Qiu Q, Fujii H, Pan S, Schumaker KS, Grillo S, Zhu JK. 2007. SOS2 promotes salt tolerance in part by interacting with the vaculoar H+-ATPase and upregulating its transport activity. Mol. Cell. Biol. 27:7781-7790. [pdf]
Zhang K, Sridhar VV, Zhu J, Kapoor A, Zhu JK. 2007. Distinctive core histone post-translational modification patterns in Arabidopsis thaliana. PLoS ONE. 2:e1210. [pdf]
Verslues PE, Zhu JK. 2007. New developments in abscisic acid perception and metabolism. Curr. Opin. Plant Biol. 10:447-452. [pdf]
Chinnusamy V, Zhu J, Zhu JK. 2007. Cold stress regulation of gene expression in plants. Trends Plant Sci. 12:444-451. [pdf]
Sunkar R, Chinnusamy V, Zhu J, Zhu JK. 2007. Small RNAs as big players in plant abiotic stress responses and nutrient deprivation. Trends Plant Sci. 12:301-309. [pdf]
Sunkar R, Zhu, JK. 2007. Micro RNAs and short-interfering RNAs in plants. J Integr Plant Biol. 49:817-826. [pdf]
Yao Y, Guo G, Ni Z, Sunkar R, Du J, Zhu JK, Sun Q. 2007. Cloning and characterization of microRNAs from wheat (Triticum aestivum L.). Genome Biol. 8:R96.
Zhu J, Dong CH, Zhu JK. 2007. Interplay between cold-responsive gene regulation, metabolism and RNA processing during plant cold acclimation. Curr Opin Plant Biol. 10:290-295. [pdf]
Fuglsang AT, Guo Y, Cuin TA, Qiu Q, Song CP, Kristiansen KA, Bych K, Schulz A, Shabala S, Schumaker KS, Palmgren MG, Zhu JK. 2007. Arabidopsis protein kinase PKS5 inhibits the plasma membrane H+-ATPase by preventing interaction with 14-3-3 protein. Plant Cell 19:1617-1634. [pdf]
Sanchez-Barrena MJ, Fujii H, Angulo I, Martinez-Ripoll M, Zhu JK, Albert A. 2007. The structure of the c-terminal domain of the protein kinase AtSOS2 bound to the calcium sensor AtSOS3. Mol Cell. 26:427-435.
Zhu J, Fu X, Koo YD, Zhu JK, Jenney FE Jr, Adams MW, Zhu Y, Shi H, Yun DJ, Hasegawa PM, Bressan RA. 2007. An enhancer mutant of Arabidopsis salt overly sensitive 3 mediates both ion homeostasis and the oxidative stress response. Mol Cell Biol. 27:5214-5224.
Zheng X, Zhu J, Kapoor A, Zhu JK. 2007. Role of Arabidopsis AGO6 in siRNA accumulation, DNA methylation and transcriptional gene silencing. EMBO J. 26:1691-1701. [pdf]
Verslues PE, Kim YS, Zhu JK. 2007. Altered ABA, proline and hydrogen peroxide in an Arabidopsis glutamate:glyoxylate aminotransferase mutant. Plant Mol Biol. 64:205-217. [pdf]
Fujii H, Verslues PE, Zhu JK. 2007. Identification of two protein kinases required for abscisic acid regulation of seed germination, root growth, and gene expression in Arabidopsis. Plant Cell. 19:485-494. [pdf]