个人介绍:

邓兴旺，博士，教授，博士生导师，美国科学院院士。曾任耶鲁大学冠名终身教授（Daniel C. Eaton Professor）。1989年于美国加州大学伯克利分校获得博士学位，1992年开始在美国耶鲁大学建立实验室，任助理教授；1995年起任该校副教授，2001年起任该校终身正教授。其领导的研究团队迄今在《细胞》、《科学》和《自然》顶级刊物上发表14篇论文，在国际刊物上共发表304篇学术论文。2003年成为国际植物分子生物学会Kumho奖的唯一获奖者。2000年起担任js33333金沙线路检测-耶鲁大学植物分子遗传及农业生物技术联合中心主任，2013年入选美国科学院院士，2014年全职回js33333金沙线路检测工作。

教育经历:

1985.9-1989.4： 博士(Ph.D.)，美国，加州大学伯克利分校，植物生物学
1982.9-1985.7： 硕士(MS)，中国，js33333金沙线路检测，植物生理学
1978.9-1982.7： 学士(BS)，中国，js33333金沙线路检测，生物学

工作经历:

2014.10-至今： 筹备小组组长，中国，js33333金沙线路检测现代农学院(筹)
2014.7.1-至今： 讲席教授(University Endowed Professor)，中国，js33333金沙线路检测
2003.5-2014.6.30： 冠名终身教授(Daniel C. Eaton Professor)，美国，耶鲁大学分子细胞和发育生物学系
2001.7-2014.6.30： 终身教授(Full Professor)，美国，耶鲁大学分子细胞和发育生物学系
2000.10-至今： 主任(兼职) (Director)，中国，北大-耶鲁植物遗传学和农业生物技术联合研究中心
2003-2008： 共同所长(兼职) (Director)，中国，北京生命科学研究所
1998.7-2001.6： 终身职副教授(Associate Professor with tenure)，美国，耶鲁大学分子细胞和发育生物学系
1995.7-1998.6： 副教授(Associate Professor with term)，美国，耶鲁大学分子细胞和发育生物学系
1992.1-1995.6： 助理教授(Assistant Professor)，美国，耶鲁大学分子细胞和发育生物学系
1989.5-1991.12： 博士后(Postdoc)，美国，加州大学伯克利分校、美国农业部植物基因研究中心，植物分子生物学

社会服务工作:

美国植物生理学家协会(American Society of Plant Physiologists)会员
美国科学发展促进会 (American Society for the Advancement of Science)会士

荣誉奖励:

2013年： 当选为“美国科学院院士”( Elected member of US National Academy of Sciences)
2013年： 当选为“美国科学促进协会会士”(Elected fellow of American Association for Advancement of Science)
2003年： 获国际植物分子生物学学会(ISPMB)最重要奖项“The Kumho Science International Award”(2003)
1995年： 获“美国总统青年教师奖”(Presidential Faculty Fellow Award)

学术任职:

2011年植物光生物学国际研讨会(The 2011 International Symposium of Plant Photobiology)组织者
第18届国际拟南芥研究大会(The 18th International Conference on Arabidopsis Research)组织者、主席(2007年)
The Arabidopsis Information Research (TAIR) 顾问委员会成员(2006-2008年)
Multinational Arabidopsis Research Committee主席(2007-2008年)
Multinational Arabidopsis Research Committee共同主席(2006-2007年)
North American Arabidopsis Research Steering Committee主席(2007-2008年)
North American Arabidopsis Research Steering Committee成员(2004-2008年)
Ohio State Arabidopsis Stock Center科学顾问委员会成员(2003-2006年)
MPI(德国马普研究院)for Plant Breeding Research科学顾问委员会成员(2003-2008年)
Scientific Review Group Member for Samsbury Laboratory成员(2003年)

杂志任职:

“Plant Cell” 期刊编委(2008年至2014年) “Annual Review of Plant Biology” 期刊编委(2010-2012年) “Plant Journal” 期刊编委(2000-2005年) “Molecular Plant” 期刊顾问委员会成员(2006年至今) “Journal of Integrated Plant Biology” 期刊编委(2004年至今) “Plant Molecular Biology” 期刊编委(1998年至今) “Genes to Cell” 期刊编委(2000年至今)

书籍编撰:

(I) 专著 1. Karplus, V. J., and Deng, X.W. (2007). Agricultural Biotechnology in China: Origins and Prospects (a book with 10 chapters). Forwarded by Norman E. Borlaug. Published December 7, 2007 by Springer. (II) 书籍章节 13. He, G., and Deng X.W. (2013). Chromatin and gene expression mechanisms in hybrids. Chapter 20 in Hybrid and Polyploid Genomics. John Wiley & Sons, Inc.: 323-333. 12. Li, J., Li, G., Wang, H., and Deng, X.W. (2011). Phytochrome signaling mechanisms. Arabidopsis Book 9: e0148. 11. Yanagawa, Y., Feng, S., and Deng, X.W. (2005). Light control of plant development: a role of the ubiquitin/proteasome-mediated proteolysis. Chapter 29 in Light Sensing in Plants, pp. 253-260. Eds: Wada, M., Shimazaki, K., and Lino, M. Springer. 10. Li, L., Wang, X., Li, X., Su, N., Stolc, V., Han, B., Li, J., Xue, Y., Wang, J., and Deng, X.W. (2004). Toward genome-wide transcriptional analysis in rice using MAS oligonucleotide tiling-path microarrays. In Rice Is Life: Scientific Perspectives For The 21st Century. Eds: Toriyama K., Heong, K. L. and Hardy, B. Proceedings of the World Rice Research Conference. 9. Wang, H., and Deng, X.W. (2002). Phytochrome signaling mechanisms. In The Arabidopsis Book, Eds. Somerville, C. R., and Meyerowitz, E. M., American Society of Plant Biologists. 8. Schwechheimer, C., and Deng, X.W. (2002). FPLC Gel Filtration. In Arabidopsis-A Laboratory Manual pp. 226-228, Eds: Weigel, D., and Glazebrook, J. Cold Spring Harbor Laboratory Press. 7. Schwechheimer, C., and Deng, X.W. (2002). Studying protein-protein interactions with the yeast two-hybid system. Chapter 9 in Molecular Plant Biology: A practical Approach, volume II, pp. 173-198. Eds: Philip M. G. and Chris B. Oxford University Press. 6. Habashi, J., and Deng, X.W. (2002). Nondenaturing Gel Electrophoresis of Proteins. In Arabidopsis-A Laboratory Manual. pp. 228-233, Eds: Weigel, D., and Glazebrook, J. Cold Spring Harbor Laboratory Press. 5. Chamovitz, D.A., and Deng, X.W. (1998). Molecular approaches to biochemical purification: the COP9 complex paradigm. NATO ASI series, vol. H104, 83-91. 4. Kwok, S. F., and Deng, X.W. (1996). The role of he pleiotropic Arabidopsis COP/DET/FUS genes in repression of photomorphogenic development in darkness. In Current Topics in Plant Physiology: an american Society of Plant Physiologists Series on [regulation of plant growth and development by light] vol. 17 pg.134-143 3. Deng, X.W., and Gruissem, W. (1994). Chloroplast run-on transcription: determination of the transcription activity of chloroplast genes. A chapter on a published laboratory manual based on a COLD SPRING HARBOR COURSE. 2. Melis, A., and Deng, X.W. (1987). The physiological significance of thylakoid membrane protein phosphorylation. In Progress in Photosynthesis Research, Eds: Biggins, J. Vol. II (2):257 260. Springer. 1. Gruissem, W., Deng, X.W., Jones, H., Stern, D, Tonkyn, J., and Zurawski, G. (1987). Transcriptional and post transcriptional regulation of chloroplast gene expression. In Structure and Function of Plant Genome, pp.135 148, Eds: Von Wettstein D., Chua, N. H. Plenum Press, New York. (III) 书籍中译本 2. Published in Chinese in June 2006. Mechanisms in Plant Development. Eds: Ottoline Leyser, and Stephen Day. Wiley-Blackwell, Oxford. 2002 version. 1. Published in Chinese in February 2004. Biochemistry & Molecular Biology of Plants. Eds: Bob Buchanan, Wilhelm Gruissem, and Russell Jones. American Society of Plant Physiologists, Rockville, MD, USA. 2002 version.

执教课程:

舌尖上的植物学

      邓兴旺课题组以拟南芥、水稻等为研究对象，主要从事植物光信号转导、非编码RNA、植物杂种优势分子机理和分子设计育种领域的研究工作。本课题组目前有教授1人，副研究员4人，博士后、技术员和博士研究生多名，实验室建有配套齐全的植物基因组学、分子生物学、生物信息学等研究平台，具有长期的植物基因组学及分子生物学研究经验。实验室具体研究方向如下：
　　1. 植物光形态建成的分子机理
　　光是对于植物发育最重要也是最基本的生长信号。本实验室多年来以拟南芥为模式植物，通过遗传筛选获得了一系列光形态建成的抑制因子COP/DET/FUS。它们的突变体在暗中可以完成不同程度的光形态建成。多年的研究结果表明，这些因子在植物体内可以形成三个复合体并通过参与或调节泛素化途径来调控光信号传导。目前，在此基础上，我们将继续综合运用遗传学、生物化学、分子生物学、细胞生物学等实验手段，进一步解析光形态建成中的信号传导通路。
　　2. 植物非编码RNA功能分析
　　非编码RNA是直接以RNA形式行使生物学功能的核糖核酸群体的总称。本实验室通过独特的分离方式以及深度测序技术，在拟南芥和水稻全基因组中对50-300核苷酸长度的非编码RNA进行了注释，并结合分子生物学，生物化学及细胞生物学等手段，探讨：小核仁RNA在拟南芥生长发育中的作用机理；非编码RNA参与拟南芥光形态建成中的分子机理；由较长非编码RNA产生的小分子RNA在拟南芥及水稻发育调控中的作用机理。
　　3. 植物杂种优势形成的分子机理
　　杂种优势是自然界普遍存在的一种复杂生物学现象，在农业生产中得到了广泛的应用。但是，对于杂种优势形成的分子遗传机理迄今尚未阐述清楚。本实验室以水稻、玉米和拟南芥为研究对象，采用高通量测序技术，对具有不同优势程度的杂交组合进行全基因组基因差异表达分析，进一步分析造成这种差异表达的基于顺、反式调控的遗传机制，以及基于DNA甲基化、组蛋白修饰和非编码RNA的表观遗传机制。并通过整合杂种优势的经典遗传学假说，在分子水平上解析杂种优势形成的机理，为在农业生产上更好地应用杂种优势现象进行杂交育种提供理论指导。
　　4. 水稻功能基因组与分子设计育种
　　传统水稻育种依赖于育种家的经验，需要从大量的水稻杂交后代中挑选优良水稻株系，效率较低。随着基因组学与分子生物学技术的进步，在育种过程中对调控特定性状的基因位点进行跟踪成为了可能。我们通过利 用大量的水稻全基因组重测序信息，创制了水稻高密度单核苷酸多态性(SNP)芯片，并将其应用于水稻育种，从而使得水稻育种成为可以精确设计与控制的过程。我们创制的芯片及相应的设计流程大大提高了水稻育种效率，加快了培育高产、优质、多抗水稻品种的进程。

304 Ling, J.J., Li, J., Zhu, D. and Deng, X.W. (2017). Noncanonical role of Arabidopsis COP1/SPA complex in repressing BIN2-mediated PIF3 phosphorylation and degradation in darkness. Proc Natl Acad Sci U S A doi:10.1073/pnas.1700850114.
303 Zhu, P., Wang, Y., Qin, N., Wang, F., Wang, J., Deng, X.W., and Zhu, D. (2016). Arabidopsis small nucleolar RNA monitors the efficient pre-rRNA processing during ribosome biogenesis. Proc Natl Acad Sci U S A 113, 11967-11972.
302 Chang, Z., Chen, Z., Wang, N., Xie, G., Lu, J., Yan, W., Zhou, J., Tang, X., and Deng, X.W. (2016). Construction of a male sterility system for hybrid rice breeding and seed production using a nuclear male sterility gene. Proc Natl Acad Sci U S A 113, 14145-14150.
301 Li, K., Yu, R., Fan, L.M., Wei, N., Chen, H., and Deng, X.W. (2016). DELLA-mediated PIF degradation contributes to coordination of light and gibberellin signalling in Arabidopsis. Nat Commun 7, 11868.
300 Shi, H., Shen, X., Liu, R., Xue, C., Wei, N., Deng, X.W., and Zhong, S. (2016). The Red Light Receptor Phytochrome B Directly Enhances Substrate-E3 Ligase Interactions to Attenuate Ethylene Responses. Dev Cell 39, 597-610.
299 Xu, D., Jiang, Y., Li, J., Lin, F., Holm, M., and Deng, X.W. (2016). BBX21, an Arabidopsis B-box protein, directly activates HY5 and is targeted by COP1 for 26S proteasome-mediated degradation. Proc Natl Acad Sci U S A 113, 7655-7660.
298 Yan, W., Chen, Z., Lu, J., Xu, C., Xie, G., Li, Y., Deng, X.W., He, H., and Tang, X. (2016). Simultaneous Identification of Multiple Causal Mutations in Rice. Frontiers in plant science 7, 2055.
297 Yu, R., Yan, W., Liang, M., Dai, X., Chen, H., Sun, Y., Deng, X.W., Chen, X., He, H., and Chen, L. (2016). Exploring the genetic characteristics of 93-11 and Nipponbare recombination inbred lines based on the GoldenGate SNP assay. Sci China Life Sci 59, 700-708.
296 Sun, N., Wang, J., Gao, Z., Dong, J., He, H., Terzaghi, W., Wei, N., Deng, X.W. and Chen H. (2016). Arabidopsis SAURs are critical for differential light regulation of the development of various organs. Proc Natl Acad Sci U S A pii: 201604782.
295 Yan, J., Lv, S., Hu, M., Gao, Z., He, H., Ma, Q., Deng, X.W., Zhu Z. and Wang X. (2016). Single-Molecule Sequencing Assists Genome Assembly Improvement and Structural Variation Inference. Mol Plant doi: 10.1016/j.molp.2016.04.002.
294 Yang, M., Huang, H., Zhang, C., Wang, Z., Su, Y., Zhu, P., Guo, Y. and Deng, X.W. (2016). Arabidopsis atypical kinase ABC1K1 is involved in red light-mediated development. Plant Cell Rep 35(6): 1213-1220.
293 Xu, D., Zhu, D. and Deng, X.W. (2016). The role of COP1 in repression of photoperiodic flowering. F1000Res 5.
292 Yu, Y., Wang, J., Shi, H., Gu, J., Dong, J., Deng, X.W. and Huang R. (2016). Salt stress and ethylene antagonistically regulate nucleocytoplasmic partitioning of COP1 to control seed germination. Plant Physiol pii: pp.01724.2015.
291 Shi, H., Liu, R., Xue, C., Shen, X., Wei, N., Deng, X.W. and Zhong S. (2016). Seedlings Transduce the Depth and Mechanical Pressure of Covering Soil Using COP1 and Ethylene to Regulate EBF1/EBF2 for Soil Emergence. Curr Biol 26(2): 139-149.
290 Ma, L., Tian, T., Lin, R., Deng, X.W., Wang H. and Li G. (2016). Arabidopsis FHY3 and FAR1 Regulate Light-Induced myo-Inositol Biosynthesis and Oxidative Stress Responses by Transcriptional Activation of MIPS1. Mol Plant 9(4): 541-557.
289 Yang, M., Wang, X., Huang, H., Ren, D., Su, Y., Zhu, P., Zhu, D., Fan, L., Chen, L., He, G. and Deng, X.W. (2016). Natural variation of H3K27me3 modification in two Arabidopsis accessions and their hybrid. J Integr Plant Biol 58(5): 466-474.
288 Dutilleul, C., Ribeiro, I., Blanc, N., Nezames, C. D., Deng, X.W., Zglobicki, P., Palacio Barrera, A. M., Atehortua, L., Courtois, M., Labas, V., Giglioli-Guivarc'h, N. and Ducos, E. (2016). ASG2 is a farnesylated DWD protein that acts as ABA negative regulator in Arabidopsis. Plant Cell Environ 39(1): 185-198.
287 Zhou, D., Chen, W., Lin, Z., Chen, H., Wang, C., Li, H., Yu, R., Zhang, F., Zhen, G., Yi, J., Li, K., Liu, Y., Terzaghi, W., Tang, X., He, H., Zhou, S. and Deng, X.W. (2016). Pedigree-based analysis of derivation of genome segments of an elite rice reveals key regions during its breeding. Plant Biotechnol J 14(2): 638-648.
286 Huang, L., Zhang, H., Zhang, H., Deng, X.W. and Wei, N. (2015). HY5 regulates nitrite reductase 1 (NIR1) and ammonium transporter1;2 (AMT1;2) in Arabidopsis seedlings. Plant Sci 238: 330-339.
285 Xu, D., Lin, F., Jiang, Y., Ling, J., Hettiarachchi, C., Tellgren-Roth, C., Holm, M., Wei, N. and Deng, X.W. (2015). Arabidopsis COP1 SUPPRESSOR 2 Represses COP1 E3 Ubiquitin Ligase Activity through Their Coiled-Coil Domains Association. PLoS Genet 11(12): e1005747.
284 Zhu, L., Bu, Q., Xu, X., Paik, I., Huang, X., Hoecker, U., Deng, X.W. and Huq, E. (2015). CUL4 forms an E3 ligase with COP1 and SPA to promote light-induced degradation of PIF1. Nat Commun 6: 7245.
283 Dong, J., Terzaghi, W., Deng, X.W. and Chen H. (2015). Multiple photomorphogenic repressors work in concert to regulate Arabidopsis seedling development. Plant Signal Behav 10(3): e1011934.
282 Huang, H., Yang, M., Su, Y., Qu, L., and Deng, X.W. (2015). Arabidopsis Atypical Kinases ABC1K1 and ABC1K3 Act Oppositely to Cope with Photodamage Under Red Light. Mol Plant 8, 1122-1124.
281 Yang, L., Li, B., Zheng, X.Y., Li, J., Yang, M., Dong, X., He, G., An, C., and Deng, X.W. (2015). Salicylic acid biosynthesis is enhanced and contributes to increased biotrophic pathogen resistance in Arabidopsis hybrids. Nat Commun 6, 7309.
280 Li, K., Gao, Z., He, H., Terzaghi, W., Fan, L.M., Deng, X.W., and Chen, H. (2015). Arabidopsis DET1 Represses Photomorphogenesis in Part by Negatively Regulating DELLA Protein Abundance in Darkness. Mol Plant 8, 622-630.
279 Shi, H., Wang, X., Mo, X., Tang, C., Zhong, S., and Deng, X.W. (2015). Arabidopsis DET1 degrades HFR1 but stabilizes PIF1 to precisely regulate seed germination. Proc Natl Acad Sci U S A. 112, 3817-3822.
278 Zhang, H., Zhao, X., Li, J., Cai, H., Deng, X.W., and Li, L. (2014). MicroRNA408 is critical for the HY5-SPL7 gene network that mediates the coordinated response to light and copper. Plant Cell 26, 4933-4953.
277 Kim, S. H., Kim, H., Seo, K. I., Kim, S. H., Chung, S., Huang, X., Yang, P., Deng, X. W., and Lee, J. H. (2014). DWD HYPERSENSITIVE TO UV-B 1 is negatively involved in UV-B mediated cellular responses in Arabidopsis. Plant Mol Biol 86, 571-583.
276 Kim, S. H., Lee, J. H., Seo, K. I., Ryu, B., Sung, Y., Chung, T., Deng, X. W., and Lee, J. H (2014). Characterization of a Novel DWD Protein that Participates in Heat Stress Response in Arabidopsis. Mol Cells 37, 833-840.
275 Dong, J., Tang, D., Gao, Z., Yu, R., Li, K., He, H., Terzaghi, W., Deng, X. W. and Chen, H. (2014). Arabidopsis DE-ETIOLATED1 Represses Photomorphogenesis by Positively Regulating Phytochrome-Interacting Factors in the Dark. Plant Cell 26, 3630-3645.
274 Wang, L., Li, J., Zhou, Q., Yang, G., Ding, X. L., Li, X., Cai, C. X., Zhang, Z., Wei, H. Y., Lu, T. H., Deng, X. W. and Huang, X. H. (2014). Rare earth elements activate endocytosis in plant cells. Proc Natl Acad Sci U S A. 111, 12936-12941.
273 Chen, F., Li, B., Demone, J., Charron, J.B., Shi, X., and Deng, X.W. (2014). Photoreceptor partner FHY1 has an independent role in gene modulation and plant development under far-red light. Proc Natl Acad Sci U S A 111, 11888-11893.
272 Huang, X., Ouyang, X., and Deng, X.W. (2014). Beyond repression of photomorphogenesis: role switching of COP/DET/FUS in light signaling. Curr Opin Plant Biol 21C, 96-103.
271 Ouyang, X., Huang, X., Jin, X., Chen, Z., Yang, P., Ge, H., Li, S., and Deng, X.W. (2014). Coordinated photomorphogenic UV-B signaling network captured by mathematical modeling. Proc Natl Acad Sci U S A 111, 11539-11544.
270 Wang, Y., Fan, X., Lin, F., He, G., Terzaghi, W., Zhu, D., and Deng, X.W. (2014). Arabidopsis noncoding RNA mediates control of photomorphogenesis by red light. Proc Natl Acad Sci U S A 111, 10359-10364.
269 Xu, D., Lin, F., Jiang, Y., Huang, X., Li, J., Ling, J., Hettiarachchi, C., Tellgren-Roth, C., Holm, M., and Deng, X.W. (2014). The RING-Finger E3 Ubiquitin Ligase COP1 SUPPRESSOR1 Negatively Regulates COP1 Abundance in Maintaining COP1 Homeostasis in Dark-Grown Arabidopsis Seedlings. Plant Cell 26, 1981-1991.
268 Chen, F., Li, B., Li, G., Charron, J.B., Dai, M., Shi, X., and Deng, X.W. (2014). Arabidopsis Phytochrome A Directly Targets Numerous Promoters for Individualized Modulation of Genes in a Wide Range of Pathways. Plant Cell 26, 1949-1966.
267 Jin, D., Li, B., Deng, X.W., and Wei, N. (2014). Plant COP9 signalosome subunit 5, CSN5. Plant Sci 224, 54-61.
266 Huang, X., Yang, P., Ouyang, X., Chen, L., and Deng, X.W. (2014). Photoactivated UVR8-COP1 module determines photomorphogenic UV-B signaling output in Arabidopsis. PLoS Genet 10, e1004218.
265 Zhong, S., Shi, H., Xue, C., Wei, N., Guo, H., and Deng, X.W. (2014). Ethylene-orchestrated circuitry coordinates a seedling's response to soil cover and etiolated growth. Proc Natl Acad Sci U S A 111, 3913-3920.
264 Xu, D., Li, J., Gangappa, S.N., Hettiarachchi, C., Lin, F., Andersson, M.X., Jiang, Y., Deng, X.W., and Holm, M. (2014). Convergence of Light and ABA signaling on the ABI5 promoter. PLoS Genet 10, e1004197.
263 Xu, X., Paik, I., Zhu, L., Bu, Q., Huang, X., Deng, X.W., and Huq, E. (2014). PHYTOCHROME INTERACTING FACTOR1 Enhances the E3 Ligase Activity of CONSTITUTIVE PHOTOMORPHOGENIC1 to Synergistically Repress Photomorphogenesis in Arabidopsis. Plant Cell 26, 1992-2006.
262 Wang, Y., Wang, X., Deng, W., Fan, X., Liu, T.T., He, G., Chen, R., Terzaghi, W., Zhu, D., and Deng, X.W. (2014). Genomic features and regulatory roles of intermediate-sized non-coding RNAs in Arabidopsis. Mol Plant 7, 514-527.
261 Seo, K.I., Lee, J.H., Nezames, C.D., Zhong, S., Song, E., Byun, M.O., and Deng, X.W. (2014). ABD1 is an Arabidopsis DCAF substrate receptor for CUL4-DDB1-based E3 ligases that acts as a negative regulator of abscisic acid signaling. Plant Cell 26, 695-711.
260 Irigoyen, M.L., Iniesto, E., Rodriguez, L., Puga, M.I., Yanagawa, Y., Pick, E., Strickland, E., Paz-Ares, J., Wei, N., De Jaeger, G., Rodriguez, P.L., Deng, X.W., and Rubio, V. (2014). Targeted degradation of abscisic acid receptors is mediated by the ubiquitin ligase substrate adaptor DDA1 in Arabidopsis. Plant Cell 26, 712-728.
259 Chen, W., Chen, H., Zheng, T., Yu, R., Terzaghi, W.B., Li, Z., Deng, X.W., Xu, J., and He, H. (2014). Highly efficient genotyping of rice biparental populations by GoldenGate assays based on parental resequencing. Theor Appl Genet 127, 297-307.
258 Chen, S., He, H., and Deng, X.W. (2014). Allele-specific DNA methylation analyses associated with siRNAs in Arabidopsis hybrids. Science China. Life sciences.
257 Chen, H., Xie, W., He, H., Yu, H., Chen, W., Li, J., Yu, R., Yao, Y., Zhang, W., He, Y., Tang, X., Zhou, F., Deng, X.W., and Zhang, Q. (2014). A high-density SNP genotyping array for rice biology and molecular breeding. Mol Plant 7, 541-553.
256 Zhang, H., Deng, X.W., and Li, L. (2013). Analysis of allele-specific gene expression using a target-oriented tiling microarray assay. Methods in molecular biology (Clifton, N.J.) 1067, 65-76.
255 Yu, Y., Wang, J., Zhang, Z., Quan, R., Zhang, H., Deng, X.W., Ma, L., and Huang, R. (2013). Ethylene promotes hypocotyl growth and HY5 degradation by enhancing the movement of COP1 to the nucleus in the light. PLoS Genet 9, e1004025.
254 Wang, J., Yu, Y., Zhang, Z., Quan, R., Zhang, H., Ma, L., Deng, X.W., and Huang, R. (2013). Arabidopsis CSN5B interacts with VTC1 and modulates ascorbic acid synthesis. Plant Cell 25, 625-636.
253 Shi, H., Zhong, S., Mo, X., Liu, N., Nezames, C.D., and Deng, X.W. (2013). HFR1 sequesters PIF1 to govern the transcriptional network underlying light-initiated seed germination in Arabidopsis. Plant Cell 25, 3770-3784.
252 Liu, T.T., Zhu, D., Chen, W., Deng, W., He, H., He, G., Bai, B., Qi, Y., Chen, R., and Deng, X.W. (2013). A global identification and analysis of small nucleolar RNAs and possible intermediate-sized non-coding RNAs in Oryza sativa. Mol Plant 6, 830-846.
251 Liu, C., Guo, L.Q., Menon, S., Jin, D., Pick, E., Wang, X., Deng, X.W., and Wei, N. (2013). COP9 signalosome subunit Csn8 is involved in maintaining proper duration of the G1 phase. J Biol Chem 288, 20443-20452.
250 Li, J., Yang, L., Jin, D., Nezames, C.D., Terzaghi, W., and Deng, X.W. (2013). UV-B-induced photomorphogenesis in Arabidopsis. Protein & cell 4, 485-492.
249 Li, B., Duan, H., Li, J., Deng, X.W., Yin, W., and Xia, X. (2013). Global identification of miRNAs and targets in Populus euphratica under salt stress. Plant Mol Biol 81, 525-539.
248 Huang, X., Ouyang, X., Yang, P., Lau, O.S., Chen, L., Wei, N., and Deng, X.W. (2013). Conversion from CUL4-based COP1-SPA E3 apparatus to UVR8-COP1-SPA complexes underlies a distinct biochemical function of COP1 under UV-B. Proc Natl Acad Sci U S A 110, 16669-16674.
247 Huang, X., and Deng, X.W. (2013). Organization of protein complexes under photomorphogenic UV-B in Arabidopsis. Plant Signal Behav 8.
246 He, G., He, H., and Deng, X.W. (2013). Epigenetic variations in plant hybrids and their potential roles in heterosis. J Genet Genomics 40, 205-210.
245 He, G., Chen, B., Wang, X., Li, X., Li, J., He, H., Yang, M., Lu, L., Qi, Y., and Deng, X.W. (2013). Conservation and divergence of transcriptomic and epigenomic variation in maize hybrids. Genome Biol 14, R57.
244 Guo, L., Nezames, C.D., Sheng, L., Deng, X.W., and Wei, N. (2013). Cullin-RING ubiquitin ligase family in plant abiotic stress pathways(F). J Integr Plant Biol 55, 21-30.
243 Franciosini, A., Lombardi, B., Iafrate, S., Pecce, V., Mele, G., Lupacchini, L., Rinaldi, G., Kondou, Y., Gusmaroli, G., Aki, S., Tsuge, T., Deng, X.W., Matsui, M., Vittorioso, P., Costantino, P., and Serino, G. (2013). The Arabidopsis COP9 SIGNALOSOME INTERACTING F-BOX KELCH 1 protein forms an SCF ubiquitin ligase and regulates hypocotyl elongation. Mol Plant 6, 1616-1629.
242 Dai, M., Xue, Q., McCray, T., Margavage, K., Chen, F., Lee, J.H., Nezames, C.D., Guo, L., Terzaghi, W., Wan, J., Deng, X.W., and Wang, H. (2013). The PP6 Phosphatase Regulates ABI5 Phosphorylation and Abscisic Acid Signaling in Arabidopsis. Plant Cell 25, 517-534.
241 Chen, H., He, H., Zhou, F., Yu, H., and Deng, X.W. (2013). Development of genomics-based genotyping platforms and their applications in rice breeding. Curr Opin Plant Biol 16, 247-254.
240 Bowler, C., Botto, J., and Deng, X.W. (2013). Photomorphogenesis, B-Box transcription factors, and the legacy of Magnus Holm. Plant Cell 25, 1192-1195.
239 Zhu, D., and Deng, X.W. (2012). A non-coding RNA locus mediates environment-conditioned male sterility in rice. Cell Res 22, 791-792.
238 Zhou, H., Zhao, J., Yang, Y., Chen, C., Liu, Y., Jin, X., Chen, L., Li, X., Deng, X.W., Schumaker, K.S., and Guo, Y. (2012). Ubiquitin-specific protease16 modulates salt tolerance in Arabidopsis by regulating Na(+)/H(+) antiport activity and serine hydroxymethyltransferase stability. Plant Cell 24, 5106-5122.
237 Zhong, S., Shi, H., Xue, C., Wang, L., Xi, Y., Li, J., Quail, P.H., Deng, X.W., and Guo, H. (2012). A molecular framework of light-controlled phytohormone action in Arabidopsis. Curr Biol 22, 1530-1535.
236 Zhao, J., Huang, X., Ouyang, X., Chen, W., Du, A., Zhu, L., Wang, S., Deng, X.W., and Li, S. (2012). OsELF3-1, an ortholog of Arabidopsis early flowering 3, regulates rice circadian rhythm and photoperiodic flowering. PLoS One 7, e43705.
235 Yang, D.L., Yao, J., Mei, C.S., Tong, X.H., Zeng, L.J., Li, Q., Xiao, L.T., Sun, T.P., Li, J., Deng, X.W., Lee, C.M., Thomashow, M.F., Yang, Y., He, Z., and He, S.Y. (2012). Plant hormone jasmonate prioritizes defense over growth by interfering with gibberellin signaling cascade. Proc Natl Acad Sci U S A 109, E1192-1200.
234 Wu, D., Hu, Q., Yan, Z., Chen, W., Yan, C., Huang, X., Zhang, J., Yang, P., Deng, H., Wang, J., Deng, X.W., and Shi, Y. (2012). Structural basis of ultraviolet-B perception by UVR8. Nature 484, 214-219.
233 Shen, H., He, H., Li, J., Chen, W., Wang, X., Guo, L., Peng, Z., He, G., Zhong, S., Qi, Y., Terzaghi, W., and Deng, X.W. (2012). Genome-wide analysis of DNA methylation and gene expression changes in two Arabidopsis ecotypes and their reciprocal hybrids. Plant Cell 24, 875-892.
232 Nezames, C.D., and Deng, X.W. (2012). The COP9 signalosome: its regulation of cullin-based E3 ubiquitin ligases and role in photomorphogenesis. Plant Physiol 160, 38-46.
231 Li, J., Terzaghi, W., and Deng, X.W. (2012). Genomic basis for light control of plant development. Protein & cell 3, 106-116.
230 Lau, O.S., and Deng, X.W. (2012). The photomorphogenic repressors COP1 and DET1: 20 years later. Trends Plant Sci 17, 584-593.
229 Huang, X., Ouyang, X., Yang, P., Lau, O.S., Li, G., Li, J., Chen, H., and Deng, X.W. (2012). Arabidopsis FHY3 and HY5 positively mediate induction of COP1 transcription in response to photomorphogenic UV-B light. Plant Cell 24, 4590-4606.
228 Fan, D., Dai, Y., Wang, X., Wang, Z., He, H., Yang, H., Cao, Y., Deng, X.W., and Ma, L. (2012). IBM1, a JmjC domain-containing histone demethylase, is involved in the regulation of RNA-directed DNA methylation through the epigenetic control of RDR2 and DCL3 expression in Arabidopsis. Nucleic Acids Res 40, 8905-8916.
227 Dai, M., Zhang, C., Kania, U., Chen, F., Xue, Q., McCray, T., Li, G., Qin, G., Wakeley, M., Terzaghi, W., Wan, J., Zhao, Y., Xu, J., Friml, J., Deng, X.W., and Wang, H. (2012). A PP6-type phosphatase holoenzyme directly regulates PIN phosphorylation and auxin efflux in Arabidopsis. Plant Cell 24, 2497-2514.
226 Chen, H., Chen, W., Zhou, J., He, H., Chen, L., and Deng, X.W. (2012). Basic leucine zipper transcription factor OsbZIP16 positively regulates drought resistance in rice. Plant Sci 193-194, 8-17.
225 Chen, F., Shi, X., Chen, L., Dai, M., Zhou, Z., Shen, Y., Li, J., Li, G., Wei, N., and Deng, X.W. (2012). Phosphorylation of FAR-RED ELONGATED HYPOCOTYL1 is a key mechanism defining signaling dynamics of phytochrome A under red and far-red light in Arabidopsis. Plant Cell 24, 1907-1920.
224 Zhang, H., He, H., Wang, X., Yang, X., Li, L., and Deng, X.W. (2011). Genome-wide mapping of the HY5-mediated gene networks in Arabidopsis that involve both transcriptional and post-transcriptional regulation. Plant J 65, 346-358.
223 Zang, B., Li, H., Li, W., Deng, X.W., and Wang, X. (2011). Analysis of trehalose-6-phosphate synthase (TPS) gene family suggests the formation of TPS complexes in rice. Plant Mol Biol 76, 507-522.
222 Wang, F., and Deng, X.W. (2011). Plant ubiquitin-proteasome pathway and its role in gibberellin signaling. Cell Res 21, 1286-1294.
221 Ouyang, X., Li, J., Li, G., Li, B., Chen, B., Shen, H., Huang, X., Mo, X., Wan, X., Lin, R., Li, S., Wang, H., and Deng, X.W. (2011). Genome-wide binding site analysis of FAR-RED ELONGATED HYPOCOTYL3 reveals its novel function in Arabidopsis development. Plant Cell 23, 2514-2535.
220 Lozano-Duran, R., Rosas-Diaz, T., Gusmaroli, G., Luna, A.P., Taconnat, L., Deng, X.W., and Bejarano, E.R. (2011). Geminiviruses subvert ubiquitination by altering CSN-mediated derubylation of SCF E3 ligase complexes and inhibit jasmonate signaling in Arabidopsis thaliana. Plant Cell 23, 1014-1032.
219 Li, W., Zang, B., Liu, C., Lu, L., Wei, N., Cao, K., Deng, X.W., and Wang, X. (2011). TSA1 interacts with CSN1/CSN and may be functionally involved in Arabidopsis seedling development in darkness. J Genet Genomics 38, 539-546.
218 Li, H.W., Zang, B.S., Deng, X.W., and Wang, X.P. (2011). Overexpression of the trehalose-6-phosphate synthase gene OsTPS1 enhances abiotic stress tolerance in rice. Planta 234, 1007-1018.
217 Li, G., Siddiqui, H., Teng, Y., Lin, R., Wan, X.Y., Li, J., Lau, O.S., Ouyang, X., Dai, M., Wan, J., Devlin, P.F., Deng, X.W., and Wang, H. (2011). Coordinated transcriptional regulation underlying the circadian clock in Arabidopsis. Nat Cell Biol 13, 616-622.
216 Lee, J.H., Terzaghi, W., and Deng, X.W. (2011). DWA3, an Arabidopsis DWD protein, acts as a negative regulator in ABA signal transduction. Plant Sci 180, 352-357.
215 Lau, O.S., Huang, X., Charron, J.B., Lee, J.H., Li, G., and Deng, X.W. (2011). Interaction of Arabidopsis DET1 with CCA1 and LHY in mediating transcriptional repression in the plant circadian clock. Mol Cell 43, 703-712.
214 He, G., Elling, A.A., and Deng, X.W. (2011). The epigenome and plant development. Annu Rev Plant Biol 62, 411-435.
213 Cui, H., Hao, Y., Kovtun, M., Stolc, V., Deng, X.W., Sakakibara, H., and Kojima, M. (2011). Genome-wide direct target analysis reveals a role for SHORT-ROOT in root vascular patterning through cytokinin homeostasis. Plant Physiol 157, 1221-1231.
212 Chen, H., He, H., Zou, Y., Chen, W., Yu, R., Liu, X., Yang, Y., Gao, Y.M., Xu, J.L., Fan, L.M., Li, Y., Li, Z.K., and Deng, X.W. (2011). Development and application of a set of breeder-friendly SNP markers for genetic analyses and molecular breeding of rice (Oryza sativa L.). Theor Appl Genet 123, 869-879.
211 Zhou, J., Wang, X., He, K., Charron, J.B., Elling, A.A., and Deng, X.W. (2010). Genome-wide profiling of histone H3 lysine 9 acetylation and dimethylation in Arabidopsis reveals correlation between multiple histone marks and gene expression. Plant Mol Biol 72, 585-595.
210 Yang, Y., Qin, Y., Xie, C., Zhao, F., Zhao, J., Liu, D., Chen, S., Fuglsang, A.T., Palmgren, M.G., Schumaker, K.S., Deng, X.W., and Guo, Y. (2010). The Arabidopsis chaperone J3 regulates the plasma membrane H+-ATPase through interaction with the PKS5 kinase. Plant Cell 22, 1313-1332.
209 Li, J., Li, G., Gao, S., Martinez, C., He, G., Zhou, Z., Huang, X., Lee, J.H., Zhang, H., Shen, Y., Wang, H., and Deng, X.W. (2010). Arabidopsis transcription factor ELONGATED HYPOCOTYL5 plays a role in the feedback regulation of phytochrome A signaling. Plant Cell 22, 3634-3649.
208 Lee, J.H., Yoon, H.J., Terzaghi, W., Martinez, C., Dai, M., Li, J., Byun, M.O., and Deng, X.W. (2010). DWA1 and DWA2, two Arabidopsis DWD protein components of CUL4-based E3 ligases, act together as negative regulators in ABA signal transduction. Plant Cell 22, 1716-1732.
207 Lau, O.S., and Deng, X.W. (2010). Plant hormone signaling lightens up: integrators of light and hormones. Curr Opin Plant Biol 13, 571-577.
206 Kong, Y.M., Elling, A. A., Chen, B., and Deng, X.W. (2010). Differential Expression of microRNAs in Maize Inbred and Hybrid Lines During Salt and Drought Stress. Am J Plant Sci 1, 69-76.
205 He, H., Zhang, H., Wang, X., Wu, N., Yang, X., Chen, R., Li, Y., Deng, X.W., and Li, L. (2010). Development of a versatile, target-oriented tiling microarray assay for measuring allele-specific gene expression. Genomics 96, 308-315.
204 He, G., Zhu, X., Elling, A.A., Chen, L., Wang, X., Guo, L., Liang, M., He, H., Zhang, H., Chen, F., Qi, Y., Chen, R., and Deng, X.W. (2010). Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids. Plant Cell 22, 17-33.
203 Chen, H., Huang, X., Gusmaroli, G., Terzaghi, W., Lau, O.S., Yanagawa, Y., Zhang, Y., Li, J., Lee, J.H., Zhu, D., and Deng, X.W. (2010). Arabidopsis CULLIN4-damaged DNA binding protein 1 interacts with CONSTITUTIVELY PHOTOMORPHOGENIC1-SUPPRESSOR OF PHYA complexes to regulate photomorphogenesis and flowering time. Plant Cell 22, 108-123.
202 Chen, F., He, G., He, H., Chen, W., Zhu, X., Liang, M., Chen, L., and Deng, X.W. (2010). Expression analysis of miRNAs and highly-expressed small RNAs in two rice subspecies and their reciprocal hybrids. J Integr Plant Biol 52, 971-980.
201 Bai, S., Zhao, J., Zhang, Y., Huang, W., Xu, S., Chen, H., Fan, L.M., Chen, Y., and Deng, X.W. (2010). Rapid and reliable detection of 11 food-borne pathogens using thin-film biosensor chips. Appl Microbiol Biotechnol 86, 983-990.
200 Xie, C.G., Lin, H., Deng, X.W., and Guo, Y. (2009). Roles of SCaBP8 in salt stress response. Plant Signal Behav 4, 956-958.
199 Wang, X., Yu, Z., Yang, X., Deng, X.W., and Li, L. (2009). Transcriptionally active gene fragments derived from potentially fast-evolving donor genes in the rice genome. Bioinformatics 25, 1215-1218.
198 Wang, X., Li, W., Piqueras, R., Cao, K., Deng, X.W., and Wei, N. (2009). Regulation of COP1 nuclear localization by the COP9 signalosome via direct interaction with CSN1. Plant J 58, 655-667.
197 Wang, X., Elling, A.A., Li, X., Li, N., Peng, Z., He, G., Sun, H., Qi, Y., Liu, X.S., and Deng, X.W. (2009). Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize. Plant Cell 21, 1053-1069.
196 Wang, F., Zhu, D., Huang, X., Li, S., Gong, Y., Yao, Q., Fu, X., Fan, L.M., and Deng, X.W. (2009). Biochemical insights on degradation of Arabidopsis DELLA proteins gained from a cell-free assay system. Plant Cell 21, 2378-2390.
195 Shen, Y., Zhou, Z., Feng, S., Li, J., Tan-Wilson, A., Qu, L.J., Wang, H., and Deng, X.W. (2009). Phytochrome A mediates rapid red light-induced phosphorylation of Arabidopsis FAR-RED ELONGATED HYPOCOTYL1 in a low fluence response. Plant Cell 21, 494-506.
194 Rubio, V., and Deng, X.W. (2009). The dark side of clock-controlled flowering. F1000 Biol Rep 1, 57.
193 Peng, Z.Y., Zhang, H., Liu, T., Dzikiewicz, K.M., Li, S., Wang, X., Hu, G., Zhu, Z., Wei, X., Zhu, Q.H., Sun, Z., Ge, S., Ma, L., Li, L., and Deng, X.W. (2009). Characterization of the genome expression trends in the heading-stage panicle of six rice lineages. Genomics 93, 169-178.
192 Lau, O.S., and Deng, X.W. (2009). Effect of Arabidopsis COP10 ubiquitin E2 enhancement activity across E2 families and functional conservation among its canonical homologues. Biochem J 418, 683-690.
191 Jiao, Y., Tausta, S.L., Gandotra, N., Sun, N., Liu, T., Clay, N.K., Ceserani, T., Chen, M., Ma, L., Holford, M., Zhang, H.Y., Zhao, H., Deng, X.W., and Nelson, T. (2009). A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies. Nat Genet 41, 258-263.
190 He, K., Li, X., Zhou, J., Deng, X.W., Zhao, H., and Luo, J. (2009). NTAP: for NimbleGen tiling array ChIP-chip data analysis. Bioinformatics 25, 1838-1840.
189 Elling, A.A., and Deng, X.W. (2009). Next-generation sequencing reveals complex relationships between the epigenome and transcriptome in maize. Plant Signal Behav 4, 760-762.
188 Charron, J.B., He, H., Elling, A.A., and Deng, X.W. (2009). Dynamic landscapes of four histone modifications during deetiolation in Arabidopsis. Plant Cell 21, 3732-3748.
187 Zhu, D., Maier, A., Lee, J.H., Laubinger, S., Saijo, Y., Wang, H., Qu, L.J., Hoecker, U., and Deng, X.W. (2008). Biochemical characterization of Arabidopsis complexes containing CONSTITUTIVELY PHOTOMORPHOGENIC1 and SUPPRESSOR OF PHYA proteins in light control of plant development. Plant Cell 20, 2307-2323.
186 Zhang, Y., Xu, W., Li, Z., Deng, X.W., Wu, W., and Xue, Y. (2008). F-box protein DOR functions as a novel inhibitory factor for abscisic acid-induced stomatal closure under drought stress in Arabidopsis. Plant Physiol 148, 2121-2133.
185 Zhang, Y., Feng, S., Chen, F., Chen, H., Wang, J., McCall, C., Xiong, Y., and Deng, X.W. (2008). Arabidopsis DDB1-CUL4 ASSOCIATED FACTOR1 forms a nuclear E3 ubiquitin ligase with DDB1 and CUL4 that is involved in multiple plant developmental processes. Plant Cell 20, 1437-1455.
184 Zhang, Q., Li, J., Xue, Y., Han, B., and Deng, X.W. (2008). Rice 2020: a call for an international coordinated effort in rice functional genomics. Mol Plant 1, 715-719.
183 Zhang, H.Y., He, H., Chen, L.B., Li, L., Liang, M.Z., Wang, X.F., Liu, X.G., He, G.M., Chen, R.S., Ma, L.G., and Deng, X.W. (2008). A genome-wide transcription analysis reveals a close correlation of promoter INDEL polymorphism and heterotic gene expression in rice hybrids. Mol Plant 1, 720-731.
182 Yu, J.W., Rubio, V., Lee, N.Y., Bai, S., Lee, S.Y., Kim, S.S., Liu, L., Zhang, Y., Irigoyen, M.L., Sullivan, J.A., Lee, I., Xie, Q., Paek, N.C., and Deng, X.W. (2008). COP1 and ELF3 control circadian function and photoperiodic flowering by regulating GI stability. Mol Cell 32, 617-630.
181 Yin, B.L., Guo, L., Zhang, D.F., Terzaghi, W., Wang, X.F., Liu, T.T., He, H., Cheng, Z.K., and Deng, X.W. (2008). Integration of cytological features with molecular and epigenetic properties of rice chromosome 4. Mol Plant 1, 816-829.
180 Wei, N., Serino, G., and Deng, X.W. (2008). The COP9 signalosome: more than a protease. Trends Biochem Sci 33, 592-600.
179 Saijo, Y., Zhu, D., Li, J., Rubio, V., Zhou, Z., Shen, Y., Hoecker, U., Wang, H., and Deng, X.W. (2008). Arabidopsis COP1/SPA1 complex and FHY1/FHY3 associate with distinct phosphorylated forms of phytochrome A in balancing light signaling. Mol Cell 31, 607-613.
178 Liu, Y., Wang, F., Zhang, H., He, H., Ma, L., and Deng, X.W. (2008). Functional characterization of the Arabidopsis ubiquitin-specific protease gene family reveals specific role and redundancy of individual members in development. Plant J 55, 844-856.
177 Li, X., Wang, X., He, K., Ma, Y., Su, N., He, H., Stolc, V., Tongprasit, W., Jin, W., Jiang, J., Terzaghi, W., Li, S., and Deng, X.W. (2008). High-resolution mapping of epigenetic modifications of the rice genome uncovers interplay between DNA methylation, histone methylation, and gene expression. Plant Cell 20, 259-276.
176 Li, L., He, H., Zhang, J., Wang, X., Bai, S., Stolc, V., Tongprasit, W., Young, N.D., Yu, O., and Deng, X.W. (2008). Transcriptional analysis of highly syntenic regions between Medicago truncatula and Glycine max using tiling microarrays. Genome Biol 9, R57.
175 Lee, J.H., Terzaghi, W., Gusmaroli, G., Charron, J.B., Yoon, H.J., Chen, H., He, Y.J., Xiong, Y., and Deng, X.W. (2008). Characterization of Arabidopsis and rice DWD proteins and their roles as substrate receptors for CUL4-RING E3 ubiquitin ligases. Plant Cell 20, 152-167.
174 Jang, S., Marchal, V., Panigrahi, K.C., Wenkel, S., Soppe, W., Deng, X.W., Valverde, F., and Coupland, G. (2008). Arabidopsis COP1 shapes the temporal pattern of CO accumulation conferring a photoperiodic flowering response. EMBO J 27, 1277-1288.
173 Guo, L., Zhou, J., Elling, A.A., Charron, J.B., and Deng, X.W. (2008). Histone modifications and expression of light-regulated genes in Arabidopsis are cooperatively influenced by changing light conditions. Plant Physiol 147, 2070-2083.
172 Gong, W., He, K., Covington, M., Dinesh-Kumar, S.P., Snyder, M., Harmer, S.L., Zhu, Y.X., and Deng, X.W. (2008). The development of protein microarrays and their applications in DNA-protein and protein-protein interaction analyses of Arabidopsis transcription factors. Mol Plant 1, 27-41.
171 Feng, S., Martinez, C., Gusmaroli, G., Wang, Y., Zhou, J., Wang, F., Chen, L., Yu, L., Iglesias-Pedraz, J.M., Kircher, S., Schafer, E., Fu, X., Fan, L.M., and Deng, X.W. (2008). Coordinated regulation of Arabidopsis thaliana development by light and gibberellins. Nature 451, 475-479.
170 Chen, H., Zhang, J., Neff, M.M., Hong, S.W., Zhang, H., Deng, X.W., and Xiong, L. (2008). Integration of light and abscisic acid signaling during seed germination and early seedling development. Proc Natl Acad Sci U S A 105, 4495-4500.
169 Alabadi, D., Gallego-Bartolome, J., Orlando, L., Garcia-Carcel, L., Rubio, V., Martinez, C., Frigerio, M., Iglesias-Pedraz, J.M., Espinosa, A., Deng, X.W., and Blazquez, M.A. (2008). Gibberellins modulate light signaling pathways to prevent Arabidopsis seedling de-etiolation in darkness. Plant J 53, 324-335.
168 Zhou, J., Wang, X., Jiao, Y., Qin, Y., Liu, X., He, K., Chen, C., Ma, L., Wang, J., Xiong, L., Zhang, Q., Fan, L., and Deng, X.W. (2007). Global genome expression analysis of rice in response to drought and high-salinity stresses in shoot, flag leaf, and panicle. Plant Mol Biol 63, 591-608.
167 Su, N., He, K., Jiao, Y., Chen, C., Zhou, J., Li, L., Bai, S., Li, X., and Deng, X.W. (2007). Distinct reorganization of the genome transcription associates with organogenesis of somatic embryo, shoots, and roots in rice. Plant Mol Biol 63, 337-349.
166 Serino, G., and Deng, X.W. (2007). Protein coimmunoprecipitation in Arabidopsis. CSH Protoc 2007, pdb prot4683.
165 Rubio, V., and Deng, X.W. (2007). Standing on the shoulders of GIGANTEA. Science 318, 206-207.
164 Qin, G., Gu, H., Ma, L., Peng, Y., Deng, X.W., Chen, Z., and Qu, L.J. (2007). Disruption of phytoene desaturase gene results in albino and dwarf phenotypes in Arabidopsis by impairing chlorophyll, carotenoid, and gibberellin biosynthesis. Cell Res 17, 471-482.
163 Pick, E., Lau, O.S., Tsuge, T., Menon, S., Tong, Y., Dohmae, N., Plafker, S.M., Deng, X.W., and Wei, N. (2007). Mammalian DET1 regulates Cul4A activity and forms stable complexes with E2 ubiquitin-conjugating enzymes. Mol Cell Biol 27, 4708-4719.
162 Menon, S., Chi, H., Zhang, H., Deng, X.W., Flavell, R.A., and Wei, N. (2007). COP9 signalosome subunit 8 is essential for peripheral T cell homeostasis and antigen receptor-induced entry into the cell cycle from quiescence. Nat Immunol 8, 1236-1245.
161 Li, L., Wang, X., Sasidharan, R., Stolc, V., Deng, W., He, H., Korbel, J., Chen, X., Tongprasit, W., Ronald, P., Chen, R., Gerstein, M., and Deng, X.W. (2007). Global identification and characterization of transcriptionally active regions in the rice genome. PLoS One 2, e294.
160 Lee, J., He, K., Stolc, V., Lee, H., Figueroa, P., Gao, Y., Tongprasit, W., Zhao, H., Lee, I., and Deng, X.W. (2007). Analysis of transcription factor HY5 genomic binding sites revealed its hierarchical role in light regulation of development. Plant Cell 19, 731-749.
159 Jiao, Y., Lau, O.S., and Deng, X.W. (2007). Light-regulated transcriptional networks in higher plants. Nat Rev Genet 8, 217-230.
158 Jiao, Y., and Deng, X.W. (2007). A genome-wide transcriptional activity survey of rice transposable element-related genes. Genome Biol 8, R28.
157 Han, B., Xue, Y., Li, J., Deng, X.W., and Zhang, Q. (2007). Rice functional genomics research in China. Philos Trans R Soc Lond B Biol Sci 362, 1009-1021.
156 Gusmaroli, G., Figueroa, P., Serino, G., and Deng, X.W. (2007). Role of the MPN subunits in COP9 signalosome assembly and activity, and their regulatory interaction with Arabidopsis Cullin3-based E3 ligases. Plant Cell 19, 564-581.
155 Bai, S.L., Zhong, X., Ma, L., Zheng, W., Fan, L.M., Wei, N., and Deng, X.W. (2007). A simple and reliable assay for detecting specific nucleotide sequences in plants using optical thin-film biosensor chips. Plant J 49, 354-366.
154 Yi, C., Li, S., Wang, J., Wei, N., and Deng, X.W. (2006). Affinity purification reveals the association of WD40 protein constitutive photomorphogenic 1 with the hetero-oligomeric TCP-1 chaperonin complex in mammalian cells. Int J Biochem Cell Biol 38, 1076-1083.
153 Wang, X., He, H., Li, L., Chen, R., Deng, X.W., and Li, S. (2006). NMPP: a user-customized NimbleGen microarray data processing pipeline. Bioinformatics 22, 2955-2957.
152 Li, L., Wang, X., Stolc, V., Li, X., Zhang, D., Su, N., Tongprasit, W., Li, S., Cheng, Z., Wang, J., and Deng, X.W. (2006). Genome-wide transcription analyses in rice using tiling microarrays. Nat Genet 38, 124-129.
151 Li, J., Zhu, S., Song, X., Shen, Y., Chen, H., Yu, J., Yi, K., Liu, Y., Karplus, V.J., Wu, P., and Deng, X.W. (2006). A rice glutamate receptor-like gene is critical for the division and survival of individual cells in the root apical meristem. Plant Cell 18, 340-349.
150 Lee, J.H., Deng, X.W., and Kim, W.T. (2006). Possible role of light in the maintenance of EIN3/EIL1 stability in Arabidopsis seedlings. Biochem Bioph Res Co 350, 484-491.
149 Han, Z., Guo, L., Wang, H., Shen, Y., Deng, X.W., and Chai, J. (2006). Structural basis for the specific recognition of methylated histone H3 lysine 4 by the WD-40 protein WDR5. Mol Cell 22, 137-144.
148 Guo, L., Yin, B., Zhou, J., Li, X., and Deng, X.W. (2006). Development of rabbit monoclonal and polyclonal antibodies for detection of site-specific histone modifications and their application in analyzing overall modification levels. Cell Res 16, 519-527.
147 Dong, L., Wang, L., Zhang, Y., Deng, X.W., and Xue, Y. (2006). An auxin-inducible F-box protein CEGENDUO negatively regulates auxin-mediated lateral root formation in Arabidopsis. Plant Mol Biol 60, 599-615.
146 Datta, S., Hettiarachchi, G.H., Deng, X.W., and Holm, M. (2006). Arabidopsis CONSTANS-LIKE3 is a positive regulator of red light signaling and root growth. Plant Cell 18, 70-84.
145 Chen, H., Shen, Y., Tang, X., Yu, L., Wang, J., Guo, L., Zhang, Y., Zhang, H., Feng, S., Strickland, E., Zheng, N., and Deng, X.W. (2006). Arabidopsis CULLIN4 Forms an E3 Ubiquitin Ligase with RBX1 and the CDD Complex in Mediating Light Control of Development. Plant Cell 18, 1991-2004.
144 Chen, H., Karplus, V.J., Ma, H., and Deng, X.W. (2006). Plant biology research comes of age in China. Plant Cell 18, 2855-2864.
143 Chen, Y., Yang, X., He, K., Liu, M., Li, J., Gao, Z., Lin, Z., Zhang, Y., Wang, X., Qiu, X., Shen, Y., Zhang, L., Deng, X., Luo, J., Deng, X.W., Chen, Z., Gu, H., and Qu, L.J. (2006). The MYB transcription factor superfamily of Arabidopsis: expression analysis and phylogenetic comparison with the rice MYB family. Plant Mol Biol 60, 107-124.
142 Zhang, S., Chen, C., Li, L., Meng, L., Singh, J., Jiang, N., Deng, X.W., He, Z.H., and Lemaux, P.G. (2005). Evolutionary expansion, gene structure, and expression of the rice wall-associated kinase gene family. Plant Physiol 139, 1107-1124.
141 Yi, C., Li, S., Chen, X., Wiemer, E.A., Wang, J., Wei, N., and Deng, X.W. (2005). Major vault protein, in concert with constitutively photomorphogenic 1, negatively regulates c-Jun-mediated activator protein 1 transcription in mammalian cells. Cancer Res 65, 5835-5840.
140 Yi, C., and Deng, X.W. (2005). COP1 - from plant photomorphogenesis to mammalian tumorigenesis. Trends Cell Biol 15, 618-625.
139 Yang, J., Lin, R., Sullivan, J., Hoecker, U., Liu, B., Xu, L., Deng, X.W., and Wang, H. (2005). Light regulates COP1-mediated degradation of HFR1, a transcription factor essential for light signaling in Arabidopsis. Plant Cell 17, 804-821.
138 Su, N., Sullivan, J.A., and Deng, X.W. (2005). Modulation of F1 hybrid stature without altering parent plants through trans-activated expression of a mutated rice GAI homologue. Plant Biotechnol J 3, 157-164.
137 Stolc, V., Li, L., Wang, X., Li, X., Su, N., Tongprasit, W., Han, B., Xue, Y., Li, J., Snyder, M., Gerstein, M., Wang, J., and Deng, X.W. (2005). A pilot study of transcription unit analysis in rice using oligonucleotide tiling-path microarray. Plant Mol Biol 59, 137-149.
136 Shen, Y., Feng, S., Ma, L., Lin, R., Qu, L.J., Chen, Z., Wang, H., and Deng, X.W. (2005). Arabidopsis FHY1 protein stability is regulated by light via phytochrome A and 26S proteasome. Plant Physiol 139, 1234-1243.
135 Sang, Y., Li, Q.H., Rubio, V., Zhang, Y.C., Mao, J., Deng, X.W., and Yang, H.Q. (2005). N-terminal domain-mediated homodimerization is required for photoreceptor activity of Arabidopsis CRYPTOCHROME 1. Plant Cell 17, 1569-1584.
134 Rubio, V., Shen, Y., Saijo, Y., Liu, Y., Gusmaroli, G., Dinesh-Kumar, S.P., and Deng, X.W. (2005). An alternative tandem affinity purification strategy applied to Arabidopsis protein complex isolation. Plant J 41, 767-778.
133 Rubio, V., and Deng, X.W. (2005). Phy tunes: phosphorylation status and phytochrome-mediated signaling. Cell 120, 290-292.
132 Menon, S., Rubio, V., Wang, X., Deng, X.W., and Wei, N. (2005). Purification of the COP9 signalosome from porcine spleen, human cell lines, and Arabidopsis thaliana plants. Methods Enzymol 398, 468-481.
131 Ma, L., Sun, N., Liu, X., Jiao, Y., Zhao, H., and Deng, X.W. (2005). Organ-specific expression of Arabidopsis genome during development. Plant Physiol 138, 80-91.
130 Ma, L., Chen, C., Liu, X., Jiao, Y., Su, N., Li, L., Wang, X., Cao, M., Sun, N., Zhang, X., Bao, J., Li, J., Pedersen, S., Bolund, L., Zhao, H., Yuan, L., Wong, G.K., Wang, J., and Deng, X.W. (2005). A microarray analysis of the rice transcriptome and its comparison to Arabidopsis. Genome Res 15, 1274-1283.
129 Li, L., Wang, X., Xia, M., Stolc, V., Su, N., Peng, Z., Li, S., Wang, J., and Deng, X.W. (2005). Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture. Genome Biol 6, R52.
128 Li, L., and Deng, X.W. (2005). It runs in the family: regulation of brassinosteroid signaling by the BZR1-BES1 class of transcription factors. Trends Plant Sci 10, 266-268.
127 Kraft, E., Stone, S.L., Ma, L., Su, N., Gao, Y., Lau, O.S., Deng, X.W., and Callis, J. (2005). Genome analysis and functional characterization of the E2 and RING-type E3 ligase ubiquitination enzymes of Arabidopsis. Plant Physiol 139, 1597-1611.
126 Jiao, Y., Ma, L., Strickland, E., and Deng, X.W. (2005). Conservation and divergence of light-regulated genome expression patterns during seedling development in rice and Arabidopsis. Plant Cell 17, 3239-3256.
125 Jiao, Y., Jia, P., Wang, X., Su, N., Yu, S., Zhang, D., Ma, L., Feng, Q., Jin, Z., Li, L., Xue, Y., Cheng, Z., Zhao, H., Han, B., and Deng, X.W. (2005). A tiling microarray expression analysis of rice chromosome 4 suggests a chromosome-level regulation of transcription. Plant Cell 17, 1641-1657.
124 Figueroa, P., Gusmaroli, G., Serino, G., Habashi, J., Ma, L., Shen, Y., Feng, S., Bostick, M., Callis, J., Hellmann, H., and Deng, X.W. (2005). Arabidopsis has two redundant Cullin3 proteins that are essential for embryo development and that interact with RBX1 and BTB proteins to form multisubunit E3 ubiquitin ligase complexes in vivo. Plant Cell 17, 1180-1195.
123 Feng, J.X., Liu, D., Pan, Y., Gong, W., Ma, L.G., Luo, J.C., Deng, X.W., and Zhu, Y.X. (2005). An annotation update via cDNA sequence analysis and comprehensive profiling of developmental, hormonal or environmental responsiveness of the Arabidopsis AP2/EREBP transcription factor gene family. Plant Mol Biol 59, 853-868.
122 Yanagawa, Y., Sullivan, J.A., Komatsu, S., Gusmaroli, G., Suzuki, G., Yin, J., Ishibashi, T., Saijo, Y., Rubio, V., Kimura, S., Wang, J., and Deng, X.W. (2004). Arabidopsis COP10 forms a complex with DDB1 and DET1 in vivo and enhances the activity of ubiquitin conjugating enzymes. Genes Dev 18, 2172-2181.
121 Wang, L., Dong, L., Zhang, Y., Wu, W., Deng, X.W., and Xue, Y. (2004). Genome-wide analysis of S-Locus F-box-like genes in Arabidopsis thaliana. Plant Mol Biol 56, 929-945.
120 Gusmaroli, G., Feng, S., and Deng, X.W. (2004). The Arabidopsis CSN5A and CSN5B subunits are present in distinct COP9 signalosome complexes, and mutations in their JAMM domains exhibit differential dominant negative effects on development. Plant Cell 16, 2984-3001.
119 Gong, W., Shen, Y.P., Ma, L.G., Pan, Y., Du, Y.L., Wang, D.H., Yang, J.Y., Hu, L.D., Liu, X.F., Dong, C.X., Ma, L., Chen, Y.H., Yang, X.Y., Gao, Y., Zhu, D., Tan, X., Mu, J.Y., Zhang, D.B., Liu, Y.L., Dinesh-Kumar, S.P., Li, Y., Wang, X.P., Gu, H.Y., Qu, L.J., Bai, S.N., Lu, Y.T., Li, J.Y., Zhao, J.D., Zuo, J., Huang, H., Deng, X.W., and Zhu, Y.X. (2004). Genome-wide ORFeome cloning and analysis of Arabidopsis transcription factor genes. Plant Physiol 135, 773-782.
118 Gao, Y., Li, J., Strickland, E., Hua, S., Zhao, H., Chen, Z., Qu, L., and Deng, X.W. (2004). An arabidopsis promoter microarray and its initial usage in the identification of HY5 binding targets in vitro. Plant Mol Biol 54, 683-699.
117 Feng, S., Shen, Y., Sullivan, J.A., Rubio, V., Xiong, Y., Sun, T.P., and Deng, X.W. (2004). Arabidopsis CAND1, an unmodified CUL1-interacting protein, is involved in multiple developmental pathways controlled by ubiquitin/proteasome-mediated protein Degradation. Plant Cell 16, 1870-1882.
116 Boccalandro, H.E., Rossi, M.C., Saijo, Y., Deng, X.W., and Casal, J.J. (2004). Promotion of photomorphogenesis by COP1. Plant Mol Biol 56, 905-915.
115 Wu, P., Ma, L., Hou, X., Wang, M., Wu, Y., Liu, F., and Deng, X.W. (2003). Phosphate starvation triggers distinct alterations of genome expression in Arabidopsis roots and leaves. Plant Physiol 132, 1260-1271.
114 Wei, N., and Deng, X.W. (2003). The COP9 signalosome. Annu Rev Cell Dev Biol 19, 261-286.
113 Wang, X., Feng, S., Nakayama, N., Crosby, W.L., Irish, V., Deng, X.W., and Wei, N. (2003). The COP9 signalosome interacts with SCF UFO and participates in Arabidopsis flower development. Plant Cell 15, 1071-1082.
112 Wang, H., and Deng, X.W. (2003). Dissecting the phytochrome A-dependent signaling network in higher plants. Trends Plant Sci 8, 172-178.
111 Sun, N., Ma, L., Pan, D., Zhao, H., and Deng, X.W. (2003). Evaluation of light regulatory potential of Calvin cycle steps based on large-scale gene expression profiling data. Plant Mol Biol 53, 467-478.
110 Sullivan, J.A., Shirasu, K., and Deng, X.W. (2003). The diverse roles of ubiquitin and the 26S proteasome in the life of plants. Nat Rev Genet 4, 948-958.
109 Sullivan, J.A., and Deng, X.W. (2003). From seed to seed: the role of photoreceptors in Arabidopsis development. Dev Biol 260, 289-297.
108 Serino, G., Su, H., Peng, Z., Tsuge, T., Wei, N., Gu, H., and Deng, X.W. (2003). Characterization of the last subunit of the Arabidopsis COP9 signalosome: implications for the overall structure and origin of the complex. Plant Cell 15, 719-731.
107 Serino, G., and Deng, X.W. (2003). The COP9 signalosome: regulating plant development through the control of proteolysis. Annu Rev Plant Biol 54, 165-182.
106 Saijo, Y., Sullivan, J.A., Wang, H., Yang, J., Shen, Y., Rubio, V., Ma, L., Hoecker, U., and Deng, X.W. (2003). The COP1-SPA1 interaction defines a critical step in phytochrome A-mediated regulation of HY5 activity. Genes Dev 17, 2642-2647.
105 Peng, Z., Shen, Y., Feng, S., Wang, X., Chitteti, B.N., Vierstra, R.D., and Deng, X.W. (2003). Evidence for a physical association of the COP9 signalosome, the proteasome, and specific SCF E3 ligases in vivo. Curr Biol 13, R504-505.
104 Pan, D., Sun, N., Cheung, K.H., Guan, Z., Ma, L., Holford, M., Deng, X.W., and Zhao, H. (2003). PathMAPA: a tool for displaying gene expression and performing statistical tests on metabolic pathways at multiple levels for Arabidopsis. BMC bioinformatics 4, 56.
103 Ma, L., Zhao, H., and Deng, X.W. (2003). Analysis of the mutational effects of the COP/DET/FUS loci on genome expression profiles reveals their overlapping yet not identical roles in regulating Arabidopsis seedling development. Development 130, 969-981.
102 Lykke-Andersen, K., Schaefer, L., Menon, S., Deng, X.W., Miller, J.B., and Wei, N. (2003). Disruption of the COP9 signalosome Csn2 subunit in mice causes deficient cell proliferation, accumulation of p53 and cyclin E, and early embryonic death. Mol Cell Biol 23, 6790-6797.
101 Li, L., and Deng, X.W. (2003). The COP9 signalosome: an alternative lid for the 26S proteasome? Trends Cell Biol 13, 507-509.
100 Jiao, Y., Yang, H., Ma, L., Sun, N., Yu, H., Liu, T., Gao, Y., Gu, H., Chen, Z., Wada, M., Gerstein, M., Zhao, H., Qu, L.J., and Deng, X.W. (2003). A genome-wide analysis of blue-light regulation of Arabidopsis transcription factor gene expression during seedling development. Plant Physiol 133, 1480-1493.
99 Feng, S., Ma, L., Wang, X., Xie, D., Dinesh-Kumar, S.P., Wei, N., and Deng, X.W. (2003). The COP9 signalosome interacts physically with SCF COI1 and modulates jasmonate responses. Plant Cell 15, 1083-1094.
98 Yi, C., Wang, H., Wei, N., and Deng, X.W. (2002). An initial biochemical and cell biological characterization of the mammalian homologue of a central plant developmental switch, COP1. BMC Cell Biol 3, 30.
97 Yadav, V., Kundu, S., Chattopadhyay, D., Negi, P., Wei, N., Deng, X.W., and Chattopadhyay, S. (2002). Light regulated modulation of Z-box containing promoters by photoreceptors and downstream regulatory components, COP1 and HY5, in Arabidopsis. Plant J 31, 741-753.
96 Wang, H., Ma, L., Habashi, J., Li, J., Zhao, H., and Deng, X.W. (2002). Analysis of far-red light-regulated genome expression profiles of phytochrome A pathway mutants in Arabidopsis. Plant J 32, 723-733.
95 Wang, H., and Deng, X.W. (2002). Arabidopsis FHY3 defines a key phytochrome A signaling component directly interacting with its homologous partner FAR1. EMBO J 21, 1339-1349.
94 Suzuki, G., Yanagawa, Y., Kwok, S.F., Matsui, M., and Deng, X.W. (2002). Arabidopsis COP10 is a ubiquitin-conjugating enzyme variant that acts together with COP1 and the COP9 signalosome in repressing photomorphogenesis. Genes Dev 16, 554-559.
93 Schwechheimer, C., Serino, G., and Deng, X.W. (2002). Multiple ubiquitin ligase-mediated processes require COP9 signalosome and AXR1 function. Plant Cell 14, 2553-2563.
92 Ma, L., Gao, Y., Qu, L., Chen, Z., Li, J., Zhao, H., and Deng, X.W. (2002). Genomic evidence for COP1 as a repressor of light-regulated gene expression and development in Arabidopsis. Plant Cell 14, 2383-2398.
91 Liu, Y., Schiff, M., Serino, G., Deng, X.W., and Dinesh-Kumar, S.P. (2002). Role of SCF ubiquitin-ligase and the COP9 signalosome in the N gene-mediated resistance response to Tobacco mosaic virus. Plant Cell 14, 1483-1496.
90 Holm, M., Ma, L.G., Qu, L.J., and Deng, X.W. (2002). Two interacting bZIP proteins are direct targets of COP1-mediated control of light-dependent gene expression in Arabidopsis. Genes Dev 16, 1247-1259.
89 Hardtke, C.S., Okamoto, H., Stoop-Myer, C., and Deng, X.W. (2002). Biochemical evidence for ubiquitin ligase activity of the Arabidopsis COP1 interacting protein 8 (CIP8). Plant J 30, 385-394.
88 Fry, R.C., Habashi, J., Okamoto, H., and Deng, X.W. (2002). Characterization of a strong dominant phytochrome A mutation unique to phytochrome A signal propagation. Plant Physiol 130, 457-465.
87 Yamamoto, Y.Y., Deng, X.W., and Matsui, M. (2001). Cip4, a new COP1 target, is a nucleus-localized positive regulator of Arabidopsis photomorphogenesis. Plant Cell 13, 399-411.
86 Wang, H., Ma, L.G., Li, J.M., Zhao, H.Y., and Deng, X.W. (2001). Direct interaction of Arabidopsis cryptochromes with COP1 in light control development. Science 294, 154-158.
85 Schwechheimer, C., Serino, G., Callis, J., Crosby, W.L., Lyapina, S., Deshaies, R.J., Gray, W.M., Estelle, M., and Deng, X.W. (2001). Interactions of the COP9 signalosome with the E3 ubiquitin ligase SCFTIRI in mediating auxin response. Science 292, 1379-1382.
84 Schwechheimer, C., and Deng, X.W. (2001). COP9 signalosome revisited: a novel mediator of protein degradation. Trends Cell Biol 11, 420-426.
83 Peng, Z., Staub, J.M., Serino, G., Kwok, S.F., Kurepa, J., Bruce, B.D., Vierstra, R.D., Wei, N., and Deng, X.W. (2001). The cellular level of PR500, a protein complex related to the 19S regulatory particle of the proteasome, is regulated in response to stresses in plants. Mol Biol Cell 12, 383-392.
82 Peng, Z., Serino, G., and Deng, X.W. (2001). Molecular characterization of subunit 6 of the COP9 signalosome and its role in multifaceted developmental processes in Arabidopsis. Plant Cell 13, 2393-2407.
81 Peng, Z., Serino, G., and Deng, X.W. (2001). A role of Arabidopsis COP9 signalosome in multifaceted developmental processes revealed by the characterization of its subunit 3. Development 128, 4277-4288.
80 Okamoto, H., Qu, L., and Deng, X.W. (2001). Does EID1 aid the fine-tuning of phytochrome A signal transduction in Arabidopsis? Plant Cell 13, 1983-1986.
79 Okamoto, H., Matsui, M., and Deng, X.W. (2001). Overexpression of the heterotrimeric G-protein alpha-subunit enhances phytochrome-mediated inhibition of hypocotyl elongation in Arabidopsis. Plant Cell 13, 1639-1652.
78 Ma, L., Li, J., Qu, L., Hager, J., Chen, Z., Zhao, H., and Deng, X.W. (2001). Light control of Arabidopsis development entails coordinated regulation of genome expression and cellular pathways. Plant Cell 13, 2589-2607.
77 Jiang, C.J., Shoji, K., Matsuki, R., Baba, A., Inagaki, N., Ban, H., Iwasaki, T., Imamoto, N., Yoneda, Y., Deng, X.W., and Yamamoto, N. (2001). Molecular cloning of a novel importin alpha homologue from rice, by which constitutive photomorphogenic 1 (COP1) nuclear localization signal (NLS)-protein is preferentially nuclear imported. J Biol Chem 276, 9322-9329.
76 Holm, M., Hardtke, C.S., Gaudet, R., and Deng, X.W. (2001). Identification of a structural motif that confers specific interaction with the WD40 repeat domain of Arabidopsis COP1. EMBO J 20, 118-127.
75 Yamamoto, Y.Y., Puente, P., and Deng, X.W. (2000). An Arabidopsis cotyledon-specific albino locus: a possible role in 16S rRNA maturation. Plant Cell Physiol 41, 68-76.
74 Schwechheimer, C., and Deng, X.W. (2000). The COP/DET/FUS proteins-regulators of eukaryotic growth and development. Semin Cell Dev Biol 11, 495-503.
73 Osterlund, M.T., Wei, N., and Deng, X.W. (2000). The roles of photoreceptor systems and the COP1-targeted destabilization of HY5 in light control of Arabidopsis seedling development. Plant Physiol 124, 1520-1524.
72 Osterlund, M.T., Hardtke, C.S., Wei, N., and Deng, X.W. (2000). Targeted destabilization of HY5 during light-regulated development of Arabidopsis. Nature 405, 462-466.
71 Leyser, O., and Deng, X.W. (2000). Cell signalling and gene regulation: New directions in plant signalling: Editorial Overview. Curr Opin Plant Biol 3, 351-352.
70 Kang, D., Wang, X., Cao, K., Sun, C., Deng, X.W., and Wei, N. (2000). A gain-of-function phenotype conferred by over-expression of functional subunits of the COP9 signalosome in Arabidopsis. Plant J 23, 597-608.
69 Hsieh, H.L., Okamoto, H., Wang, M., Ang, L.H., Matsui, M., Goodman, H., and Deng, X.W. (2000). FIN219, an auxin-regulated gene, defines a link between phytochrome A and the downstream regulator COP1 in light control of Arabidopsis development. Genes Dev 14, 1958-1970.
68 Hardtke, C.S., Gohda, K., Osterlund, M.T., Oyama, T., Okada, K., and Deng, X.W. (2000). HY5 stability and activity in arabidopsis is regulated by phosphorylation in its COP1 binding domain. EMBO J 19, 4997-5006.
67 Hardtke, C.S., and Deng, X.W. (2000). The cell biology of the COP/DET/FUS proteins. Regulating proteolysis in photomorphogenesis and beyond? Plant Physiol 124, 1548-1557.
66 Deng, X.W., Dubiel, W., Wei, N., Hofmann, K., Mundt, K., Colicelli, J., Kato, J., Naumann, M., Segal, D., Seeger, M., Carr, A., Glickman, M., and Chamovitz, D.A. (2000). Unified nomenclature for the COP9 signalosome and its subunits: an essential regulator of development. Trends Genet 16, 202-203.
65 Abel, S., Blazquez, M., Dangl, J., Deng, X.W., Graham, I., Harada, J., Jones, J., and Nilsson, O. (2000). Arabidopsis Research 2000. Plant Cell 12, 2302-2308.
64 Yamamoto, N., and Deng, X.W. (1999). Protein nucleocytoplasmic transport and its light regulation in plants. Genes Cells 4, 489-500.
63 Wei, N., and Deng, X.W. (1999). Making sense of the COP9 signalosome. A regulatory protein complex conserved from Arabidopsis to human. Trends Genet 15, 98-103.
62 Wang, H., Kang, D., Deng, X.W., and Wei, N. (1999). Evidence for functional conservation of a mammalian homologue of the light-responsive plant protein COP1. Curr Biol 9, 711-714.
61 Torii, K.U., Stoop-Myer, C.D., Okamoto, H., Coleman, J.E., Matsui, M., and Deng, X.W. (1999). The RING finger motif of photomorphogenic repressor COP1 specifically interacts with the RING-H2 motif of a novel Arabidopsis protein. J Biol Chem 274, 27674-27681.
60 Stoop-Myer, C., Torii, K.U., McNellis, T.W., Coleman, J.E., and Deng, X.W. (1999). Short communication: the N-terminal fragment of Arabidopsis photomorphogenic repressor COP1 maintains partial function and acts in a concentration-dependent manner. Plant J 20, 713-717.
59 Serino, G., Tsuge, T., Kwok, S., Matsui, M., Wei, N., and Deng, X.W. (1999). Arabidopsis cop8 and fus4 mutations define the same gene that encodes subunit 4 of the COP9 signalosome. Plant Cell 11, 1967-1980.
58 Osterlund, M.T., Ang, L.H., and Deng, X.W. (1999). The role of COP1 in repression of Arabidopsis photomorphogenic development. Trends Cell Biol 9, 113-118.
57 Kwok, S.F., Staub, J.M., and Deng, X.W. (1999). Characterization of two subunits of Arabidopsis 19S proteasome regulatory complex and its possible interaction with the COP9 complex. J Mol Biol 285, 85-95.
56 Holm, M., and Deng, X.W. (1999). Structural organization and interactions of COP1, a light-regulated developmental switch. Plant Mol Biol 41, 151-158.
55 Deng, X.W., and Quail, P.H. (1999). Signalling in light-controlled development. Semin Cell Dev Biol 10, 121-129.
54 Yamamoto, Y.Y., Matsui, M., and Deng, X.W. (1998). Positive feedback in plant signaling pathways. Trends Plant Sci 3, 374-375.
53 Yamamoto, Y.Y., Matsui, M., Ang, L.H., and Deng, X.W. (1998). Role of a COP1 interactive protein in mediating light-regulated gene expression in arabidopsis. Plant Cell 10, 1083-1094.
52 Yamamoto, Y.Y., and Deng, X.W. (1998). A New Vector Set for GAL4-Dependent Transactivation Assay in Plants. Plant Biotechnol 15, 217-220.
51 Wei, N., Tsuge, T., Serino, G., Dohmae, N., Takio, K., Matsui, M., and Deng, X.W. (1998). The COP9 complex is conserved between plants and mammals and is related to the 26S proteasome regulatory complex. Curr Biol 8, 919-922.
50 Wei, N., and Deng, X.W. (1998). Characterization and purification of the mammalian COP9 complex, a conserved nuclear regulator initially identified as a repressor of photomorphogenesis in higher plants. Photochem Photobiol 68, 237-241.
49 von Arnim, A.G., Deng, X.W., and Stacey, M.G. (1998). Cloning vectors for the expression of green fluorescent protein fusion proteins in transgenic plants. Gene 221, 35-43.
48 Torii, K.U., McNellis, T.W., and Deng, X.W. (1998). Functional dissection of Arabidopsis COP1 reveals specific roles of its three structural modules in light control of seedling development. EMBO J 17, 5577-5587.
47 Osterlund, M.T., and Deng, X.W. (1998). Multiple photoreceptors mediate the light-induced reduction of GUS-COP1 from Arabidopsis hypocotyl nuclei. Plant J 16, 201-208.
46 Kwok, S.F., Solano, R., Tsuge, T., Chamovitz, D.A., Ecker, J.R., Matsui, M., and Deng, X.W. (1998). Arabidopsis homologs of a c-Jun coactivator are present both in monomeric form and in the COP9 complex, and their abundance is differentially affected by the pleiotropic cop/det/fus mutations. Plant Cell 10, 1779-1790.
45 Karniol, B., Yahalom, A., Kwok, S., Tsuge, T., Matsui, M., Deng, X.W., and Chamovitz, D.A. (1998). The Arabidopsis homologue of an eIF3 complex subunit associates with the COP9 complex. FEBS Lett 439, 173-179.
44 Deng, X.W. (1998). Light control of Arabidopsis developmental pattern. Symp Soc Exp Biol 51, 93-96.
43 Chattopadhyay, S., Puente, P., Deng, X.W., and Wei, N. (1998). Combinatorial interaction of light-responsive elements plays a critical role in determining the response characteristics of light-regulated promoters in Arabidopsis. Plant J 15, 69-77.
42 Chattopadhyay, S., Ang, L.H., Puente, P., Deng, X.W., and Wei, N. (1998). Arabidopsis bZIP protein HY5 directly interacts with light-responsive promoters in mediating light control of gene expression. Plant Cell 10, 673-683.
41 Ang, L.H., Chattopadhyay, S., Wei, N., Oyama, T., Okada, K., Batschauer, A., and Deng, X.W. (1998). Molecular interaction between COP1 and HY5 defines a regulatory switch for light control of Arabidopsis development. Mol Cell 1, 213-222.
40 von Arnim, A.G., Osterlund, M.T., Kwok, S.F., and Deng, X.W. (1997). Genetic and developmental control of nuclear accumulation of COP1, a repressor of photomorphogenesis in Arabidopsis. Plant Physiol 114, 779-788.
39 Torii, K.U., and Deng, X.W. (1997). The role of COP1 in light control of Arabidopsis seedling development. Plant Cell Environ 20, 728-733.
38 Deng, X.W., and Mei, Z. (1997). The higher plant thylakoid pigment-protein complexes migration and the reduction of light energy distribution between two photosystems. Scientia Sinica (series B) 4, 377-386.
37 Chamovitz, D.A., and Deng, X.W. (1997). The COP9 complex: a link between photomorphogenesis and general developmental regulation? Plant Cell Environ 20, 734-739.
36 Wei, N., and Deng, X.W. (1996). The role of the COP/DET/FUS genes in light control of arabidopsis seedling development. Plant Physiol 112, 871-878.
35 von Arnim, A., and Deng, X.W. (1996). A role for transcriptional repression during light control of plant development. Bioessays 18, 905-910.
34 Von Arnim, A., and Deng, X.W. (1996). Light control of seedling development. Annu Rev Plant Physiol Plant Mol Biol 47, 215-243.
33 Staub, J.M., Wei, N., and Deng, X.W. (1996). Evidence for FUS6 as a component of the nuclear-localized COP9 complex in Arabidopsis. Plant Cell 8, 2047-2056.
32 Staub, J.M., and Deng, X.W. (1996). Light signal transduction in plants. Photochem Photobiol 64, 897-905.
31 Puente, P., Wei, N., and Deng, X.W. (1996). Combinatorial interplay of promoter elements constitutes the minimal determinants for light and developmental control of gene expression in Arabidopsis. EMBO J 15, 3732-3743.
30 McNellis, T.W., Torii, K.U., and Deng, X.W. (1996). Expression of an N-terminal fragment of COP1 confers a dominant-negative effect on light-regulated seedling development in Arabidopsis. Plant Cell 8, 1491-1503.
29 Kwok, S.F., Piekos, B., Misera, S., and Deng, X.W. (1996). A complement of ten essential and pleiotropic arabidopsis COP/DET/FUS genes is necessary for repression of photomorphogenesis in darkness. Plant Physiol 110, 731-742.
28 Deng, X.W., and Melis, A. (1996). Phosphorylation of the light-harvesting complex II in higher plant chloroplasts: effect on photosystem II and photosystem I absorption cross section. Photochem Photobiol 13, 41-52.
27 Chamovitz, D.A., Wei, N., Osterlund, M.T., von Arnim, A.G., Staub, J.M., Matsui, M., and Deng, X.W. (1996). The COP9 complex, a novel multisubunit nuclear regulator involved in light control of a plant developmental switch. Cell 86, 115-121.
26 Chamovitz, D.A., Deng, X.W., and Lam, E. (1996). Light signaling in plants. Crit Rev Plant Sci 15, 455-478.
25 Torii, K.U., and Deng, X.W. (1995). Regulation of plant form: Identification of a molecule controlling cell expansion. Bioessays 17, 383-386.
24 McNellis, T.W., and Deng, X.W. (1995). Light control of seedling morphogenetic pattern. Plant Cell 7, 1749-1761.
23 Matsui, M., Stoop, C.D., von Arnim, A.G., Wei, N., and Deng, X.W. (1995). Arabidopsis COP1 protein specifically interacts in vitro with a cytoskeleton-associated protein, CIP1. Proc Natl Acad Sci U S A 92, 4239-4243.
22 Chamovitz, D.A., and Deng, X.W. (1995). The novel components of the Arabidopsis light signaling pathway may define a group of general developmental regulators shared by both animal and plant kingdoms. Cell 82, 353-354.
21 Wei, N., Kwok, S.F., von Arnim, A.G., Lee, A., McNellis, T.W., Piekos, B., and Deng, X.W. (1994). Arabidopsis COP8, COP10, and COP11 genes are involved in repression of photomorphogenic development in darkness. Plant Cell 6, 629-643.
20 Wei, N., Chamovitz, D.A., and Deng, X.W. (1994). Arabidopsis COP9 is a component of a novel signaling complex mediating light control of development. Cell 78, 117-124.
19 von Arnim, A.G., and Deng, X.W. (1994). Light inactivation of Arabidopsis photomorphogenic repressor COP1 involves a cell-specific regulation of its nucleocytoplasmic partitioning. Cell 79, 1035-1045.
18 McNellis, T.W., von Arnim, A.G., and Deng, X.W. (1994). Overexpression of Arabidopsis COP1 results in partial suppression of light-mediated development: evidence for a light-inactivable repressor of photomorphogenesis. Plant Cell 6, 1391-1400.
17 McNellis, T.W., von Arnim, A.G., Araki, T., Komeda, Y., Misera, S., and Deng, X.W. (1994). Genetic and molecular analysis of an allelic series of cop1 mutants suggests functional roles for the multiple protein domains. Plant Cell 6, 487-500.
16 Deng, X.W. (1994). Fresh view of light signal transduction in plants. Cell 76, 423-426.
15 Ang, L.H., and Deng, X.W. (1994). Regulatory hierarchy of photomorphogenic loci: allele-specific and light-dependent interaction between the HY5 and COP1 loci. Plant Cell 6, 613-628.
14 von Arnim, A.G., and Deng, X.W. (1993). Ring finger motif of Arabidopsis thaliana COP1 defines a new class of zinc-binding domain. J Biol Chem 268, 19626-19631.
13 Hou, Y., Von Arnim, A.G., and Deng, X.W. (1993). A New Class of Arabidopsis Constitutive Photomorphogenic Genes Involved in Regulating Cotyledon Development. Plant Cell 5, 329-339.
12 Wei, N., and Deng, X.W. (1992). COP9: a new genetic locus involved in light-regulated development and gene expression in arabidopsis. Plant Cell 4, 1507-1518.
11 Tonkyn, J.C., Deng, X.W., and Gruissem, W. (1992). Regulation of Plastid Gene Expression during Photooxidative Stress. Plant Physiol 99, 1406-1415.
10 Deng, X.W., and Quail, P.H. (1992). Genetic and phenotypic characterization of cop1 mutants of Arabidopsis thaliana. Plant J 2, 83-95.
9 Deng, X.W., Matsui, M., Wei, N., Wagner, D., Chu, A.M., Feldmann, K.A., and Quail, P.H. (1992). COP1, an Arabidopsis regulatory gene, encodes a protein with both a zinc-binding motif and a G beta homologous domain. Cell 71