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·         Huang X, Yang P, Ouyang X, Chen L, Deng XW.

Photoactivated UVR8-COP1 Module Determines Photomorphogenic UV-B Signaling Output in Arabidopsis.

PLoS Genet 2014. Published online: 2014 Mar 20

 

·         Zhong S, Shi H, Xue C, Wei N, Guo H, Deng XW.

Ethylene-orchestrated circuitry coordinates a seedling's response to soil cover and etiolated growth.

PNAS 2014. Published online: 2014 Mar 5

This contribution is part of the special series of Inaugural Articles by members of the National Academy of Sciences elected in 2013.

 

·         Xu D, Li J, Gangappa SN, Hettiarachchi C, Lin F, Andersson MX, Jiang Y, Deng XW, Holm M.

Convergence of Light and ABA Signaling on the ABI5 Promoter.

PLoS Genet. 2014. Published online: 2014 Feb 27

 

·         Irigoyen ML, Iniesto E, Rodriguez L, Puga MI, Yanagawa Y, Pick E, Strickland E, Paz-Ares J, Wei N, De Jaeger G, Rodriguez PL, Deng XW, Rubio V.

Targeted Degradation of Abscisic Acid Receptors Is Mediated by the Ubiquitin Ligase Substrate Adaptor DDA1 in Arabidopsis.

Plant Cell 2014. Published online: 2014 Feb 21

 

·         Seo KI, Lee JH, Nezames CD, Zhong S, Song E, Byun MO, Deng XW.

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 2014. Published online: 2014 Feb 21



·         Shi H, Zhong S, Mo X, Liu N, Nezames CD, Deng XW.

HFR1 Sequesters PIF1 to Govern the Transcriptional Network Underlying Light-Initiated Seed Germination in Arabidopsis.

Plant Cell 2013 25(10):3770-3784. Published online: 2013 Oct 31

 

·         Huang X, Ouyang X, Yang P, Lau OS, Chen L, He H, Wei N, Deng XW.

Conversion from CUL4-based COP1-SPA E3 apparatus to UVR8-COP1-SPA complexes underlies a distinct biochemical function of COP1 under UV-B.

PNAS. Published online: 2013 Sep 25

 

·         Zhang H, Deng XW, Li L.

Analysis of allele-specific gene expression using a target-oriented tiling microarray assay.

Methods Mol Biol2013 1067:65-76.

 

·         He G, Chen B, Wang X, Li X, Li J, He H, Yang M, Lu L, Qi Y, Wang X, Deng XW.

Conservation and divergence of transcriptomic and epigenomic variation in maize hybrids.

Genome Biol 2013 14:R57. Published online: 2013 Jun 12

 

·         Li J, Yang L, Jin D, Nezames CD, Terzaghi W, Deng XW.

UV-B-induced photomorphogenesis in Arabidopsis.

Protein Cell 2013 4(7):485-92. Published online: 2013 Jun 7

 

·         Chen H, He H, Zhou F, Yu H, Deng XW.

Development of genomics-based genotyping platforms and their applications in rice breeding.

Curr Opin Plant Biol 2013 16:247-254. Published online: 2013 May 21

 

·         Liu C, Guo LQ, Menon S, Jin D, Pick E, Wang XJ, Deng XW, Wei N.

COP9 signalosome subunit Csn8 is involved in maintaining proper duration of the G1 phase.

J Biol Chem Published online: 2013 May 20

 

·         He G, He H, Deng XW.

Epigenetic Variations in Plant Hybrids and Their Potential Roles in Heterosis.

J GENET GENOMICS Published online: 2013 May 20

 

·         Bowler C, Botto J, Deng XW.

Photomorphogenesis, B-Box transcription factors, and the legacy of Magnus Holm.

Plant Cell 2013 25(4):1192-5. Published online: 2013 Apr 26

 

·         Franciosini A, Lombardi B, Iafrate S, Pecce V, Mele G, Lupacchini L, Rinaldi G, Kondou Y, Gusmaroli G, Aki S, Tsuge T, Deng XW, Matsui M, Vittorioso P, Costantino P, Serino G.

The Arabidopsis COP9 SIGNALOSOME INTERACTING F-BOX KELCH 1 Protein Forms an SCF Ubiquitin Ligase and Regulates Hypocotyl Elongation.

Mol Plant 2013 6(5):1616-29. Published online: 2013 Mar 9

 

·         Li B, Duan H, Li J, Deng XW, Yin W, Xia X.

Global identification of miRNAs and targets in Populus euphratica under salt stress.

Plant Mol Biol Published online: 2013 Feb 22

 

·         Wang J, Yu Y, Zhang Z, Quan R, Zhang H, Ma L, Deng XW, Huang R.

Arabidopsis CSN5B Interacts with VTC1 and Modulates Ascorbic Acid Synthesis.

Plant Cell Published online: 2013 Feb 19

 

·         Dai M, Xue Q, McCray T, Margavage K, Chen F, Lee JH, Nezames CD, Guo L, Terzaghi W, Wan J, Deng XW, Wang H.

The PP6 Phosphatase Regulates ABI5 Phosphorylation and Abscisic Acid Signaling in Arabidopsis.

Plant Cell Published online: 2013 Feb 12

 

·         Guo L, Nezames CD, Sheng L, Deng X, Wei N.

Cullin-RING Ubiquitin Ligase Family in Plant Abiotic Stress Pathways.

J Integr Plant Biol Published online: 2013 Jan 30


 

·         Zhou H, Zhao J, Yang Y, Chen C, Liu Y, Jin X, Chen L, Li X, Deng XW, Schumaker KS, Guo Y.

UBIQUITIN-SPECIFIC PROTEASE16 Modulates Salt Tolerance in Arabidopsis by Regulating Na+/H+ Antiport Activity and Serine Hydroxymethyltransferase Stability.

Plant Cell Published online: 2012 Dec 11

 

·         Huang X, Ouyang X, Yang P, Lau OS, Li G, Li J, Chen H, Deng XW.

Arabidopsis FHY3 and HY5 Positively Mediate Induction of COP1 Transcription in Response to Photomorphogenic UV-B Light.

Plant Cell Published online: 2012 Nov 13

 

·         Liu TT, Zhu D, Chen W, Deng W, He H, He G, Bai B, Qi Y, Chen R, Deng XW.

A Global Identification and Analysis of Small Nucleolar RNAs and Possible Intermediate-Sized Non-Coding RNAs in Oryza sativa.

Mol Plant Published online: 2012 Sep 17

 

·         Pick E, Golan A, Zimbler JZ, Guo L, Sharaby Y, Tsuge T, Hofmann K, Wei N.

The minimal deneddylase core of the COP9 signalosome excludes the Csn6 MPN- domain.

PLoS One Published online: 2012 Aug 30

 

·         Zhao J, Huang X, Ouyang X, Chen W, Du A, Zhu L, Wang S, Deng XW, Li S.

OsELF3-1, an Ortholog of Arabidopsis EARLY FLOWERING 3, Regulates Rice Circadian Rhythm and Photoperiodic Flowering.

PLoS One Published online: 2012 Aug 17

 

·         Zhong S, Shi H, Xue C, Wang L, Xi Y, Li J, Quail PH, Deng XW, Guo H.

A Molecular Framework of Light-Controlled Phytohormone Action in Arabidopsis.

Curr Biol Published online: 2012 Jul 20 Comment Comment by F1000

 

·         Chen H, Chen W, Zhou J, He H, Chen L, Chen H, Deng XW.

Basic leucine zipper transcription factor OsbZIP16 positively regulates drought resistance in rice.

Plant Sci Published online: 2012 May 17

 

·         Fan D, Dai Y, Wang X, Wang Z, He H, Yang H, Cao Y, Deng XW, Ma L.

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 Published online: 2012 Jul 5

 

·         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 XW, Wang H.

A PP6-Type Phosphatase Holoenzyme Directly Regulates PIN Phosphorylation and Auxin Efflux in Arabidopsis.

Plant Cell Published online: 2012 Jun 19

 

·         Nezames CD, Deng XW.

The COP9 Signalosome: Its Regulation of Cullin-based E3 Ubiquitin Ligases and Role in Photomorphogenesis.

Plant Physiol Published online: 2012 Jun 19

 

·         Lau OS, Deng XW.

The photomorphogenic repressors COP1 and DET1: 20 years later.

Trends Plant Sci Published online: 2012 Jun 15

 

·         Chen F, Shi X, Chen L, Dai M, Zhou Z, Shen Y, Li J, Li G, Wei N, Deng XW.

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 Published online: 2012 May 11

 

·         Yang DL, Yao J, Mei CS, Tong XH, Zeng LJ, Li Q, Xiao LT, Sun TP, Li J, Deng XW, Lee CM, Thomashow MF, Yang Y, He Z, He SY.

Plant hormone jasmonate prioritizes defense over growth by interfering with gibberellin signaling cascade.

Proc Natl Acad Sci U S A Published online: 2012 Apr 23

 

·         Wu D, Hu Q, Yan Z, Chen W, Yan C, Huang X, Zhang J, Yang P, Deng H, Wang J, Deng XW, Shi Y.

Structural basis of ultraviolet-B perception by UVR8.

Nature Published online: 2012 Feb 29

 

·         Li J, Terzaghi W, Deng XW.

Genomic basis for light control of plant development.

Protein Cell 2012 3:106-116.

 

·         Zhu D, Deng XW.

A non-coding RNA locus mediates environment-conditioned male sterility in rice.

Cell Res Published online: 2012 Mar 20

 

·         Shen H, He H, Li J, Chen W, Wang X, Guo L, Peng Z, He G, Zhong S, Qi Y, Terzaghi W, Deng XW.

Genome-wide analysis of DNA methylation and gene expression changes in two Arabidopsis ecotypes and their reciprocal hybrids.

Plant Cell Published online: 2012 Mar 20. Author Profile Comment


 

·         Li W, Zang B, Liu C, Lu L, Wei N, Cao K, Deng XW, Wang X.

TSA1 interacts with CSN1/CSN and may be functionally involved in Arabidopsis seedling development in darkness.

J Genet Genomics 2011 38:539-546.

 

·         Cui H, Hao Y, Kovtun M, Stolc V, Deng XW, Sakakibara H, Kojima M.

Genome-wide direct target analysis reveals a role for SHORT-ROOT in root vascular patterning through cytokinin homeostasis.

Plant Physiol 2011 157:1221-31.

 

·         Lau OS, Huang X, Charron JB, Lee JH, Li G, Deng XW.

Interaction of Arabidopsis DET1 with CCA1 and LHY in Mediating Transcriptional Repression in the Plant Circadian Clock.

Mol Cell 2011 43: 703-712. Published online: 2011 Sep 1. Preview by C. Robertson McClung Yale News

 

·         Li J, Li G, Wang H, Deng XW.

Phytochrome Signaling Mechanisms.

The Arabidopsis Book 9: e148. Published online: 2011 Aug 22.

 

·         Ouyang X, Li J, Li G, Li B, Chen B, Shen H, Huang X, Mo X, Wan X, Lin R, Li S, Wang H, Deng XW.

Genome-Wide Binding Site Analysis of FAR-RED ELONGATED HYPOCOTYL3 Reveals Its Novel Function in Arabidopsis Development.

Plant Cell 2011 23:2514-2535. Published online: 2011 Jul 29.

 

·         Wang F, Deng XW.

Plant ubiquitin-proteasome pathway and its role in gibberellin signaling.

Cell Res 2011 21:1286-1294. Published online: 2011 Jul 26.

 

·         Li HW, Zang BS, Deng XW, Wang XP.

Overexpression of the trehalose-6-phosphate synthase gene OsTPS1 enhances abiotic stress tolerance in rice.

Planta 2011 234:1007-1018. Published online: 2011 Jun 24.

 

·         Chen H, He H, Zou Y, Chen W, Yu R, Liu X, Yang Y, Gao YM, Xu JL, Fan LM, Li Y, Li ZK, Deng XW.

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 2011 123:869-879. Published online: 2011 Jun 18.

 

·         Tsuge T, Menon S, Tong Y, Wei N.

CSN1 inhibits c-Jun phosphorylation and down-regulates ectopic expression of JNK1.

Protein Cell 2011 2:423-432. Published online: 2011 May 21.

 

·         Zang B, Li H, Li W, Deng XW, Wang X.

Analysis of trehalose-6-phosphate synthase (TPS) gene family suggests the formation of TPS complexes in rice.

Plant Mol Biol. 2011 76:507-522. Published online: 2011 May 20.

 

·         Li G, Siddiqui H, Teng Y, Lin R, Wan XY, Li J, Lau OS, Ouyang X, Dai M, Wan J, Devlin PF, Deng XW, Wang H.

Coordinated transcriptional regulation underlying the circadian clock in Arabidopsis.

Nat Cell Biol 2011 13:616-622. Published online: 2011 Apr 17.

 

·         Lozano-Duran R, Rosas-Diaz T, Gusmaroli G, Luna AP, Taconnat L, Deng XW, Bejarano ER.

Geminiviruses Subvert Ubiquitination by Altering CSN-Mediated Derubylation of SCF E3 Ligase Complexes and Inhibit Jasmonate Signaling in Arabidopsis thaliana.

Plant Cell 2011 23:1014-1032. Published online: 2011 Mar 25.

 

·         He G, Elling AA, Deng XW.

The Epigenome and Plant Development.

Annu Rev Plant Biol 2011 Jun;62:411-35. Published online: 2011 May 18.

 

·         Lee JH, Terzaghi W, Deng XW.

DWA3, an Arabidopsis DWD protein, acts as a negative regulator in ABA signal transduction

Plant Sci 2011 180:352-357. Published online: Oct 21, 2010.

 

·         Zhang H, He H, Wang X, Wang X, Yang X, Li L and Deng XW.

Genome-wide mapping of the HY5-mediated gene networks in Arabidopsis that involve both transcriptional and post-transcriptional regulations

Plant J 2011 65:346-58. Published online: Nov 13, 2010.


 

·         Li J, Li G, Gao S, Martinez C, He G, Zhou Z, Huang X, Lee JH, Zhang H, Shen Y, Wang H and Deng XW.

Arabidopsis Transcription Factor ELONGATED HYPOCOTYL5 Plays a Role in the Feedback Regulation of Phytochrome A Signaling

Plant Cell 2010 22:3634-3649. Published online: Nov 19, 2010.

 

·         Chen F, He G, He H, Chen W, Zhu X, Liang M, Chen L, Deng XW.

Expression Analysis of miRNAs and Highly-expressed Small RNAs in Two Rice Subspecies and their Reciprocal Hybrids

J Integr Plant Biol 2010 52:971-980. Published online: Jul 15, 2010.

 

·         Lau OS and Deng XW.

Plant hormone signaling lightens up: integrators of light and hormones

Curr Opin Plant Biol 2010 13:571-577. Published online: Aug 23, 2010.

 

·         He H, Zhang H, Wang X, Wu N, Yang X, Chen R, Li Y, Deng XW and Li L.

Development of a versatile, target-oriented tiling microarray assay for measuring allele-specific gene expression

Genomics 2010 96:308-315. Published online: Aug 3, 2010.

 

·         Lee JH, Yoon HY, Terzaghi W, Martinez C, Dai M, Li J, Byun MO and Deng XW.

DWA1 and DWA2, Two Arabidopsis DWD Protein Components of CUL4-Based E3 Ligases, Act Together as Negative Regulators in ABA Signal Transduction

Plant Cell 2010 22: 1716-1732. Published online: June 4, 2010.

 

·         Yang Y, Qin Y, Xie C, Zhao F, Zhao J, Liu D, Chen S, Fuglsang AT, Palmgren MG, Schumaker KS, Deng XW and Guo Y.

The Arabidopsis Chaperone J3 Regulates the Plasma Membrane H+-ATPase through Interaction with the PKS5 Kinase

Plant Cell 2010 22:1313-1332. Published online April 23, 2010.

 

·         Bai S, Zhao J, Zhang Y, Huang W, Xu S, Chen H, Fan LM, Chen Y and Deng XW

Rapid and reliable detection of 11 food-borne pathogens using thin-film biosensor chips

Appl Microbiol Biotechnol. 2010 86:983-990. Published online: January 21, 2010.

 

·         He G, Zhu X, Elling AA, Chen L, Wang X, Guo L, Liang M, He H, Zhang H, Chen F, Qi Y, Chen R and Deng XW.

Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids

Plant Cell 2010 22:17-33. Published online: January 19, 2010.

 

·         Chen H, Huang X, Gusmaroli G, Terzaghi W, Lau OS, Yanagawa Y, Zhang Y, Li J, Lee JH, Zhu D and Deng XW.

Arabidopsis CULLIN4-Damaged DNA Binding Protein 1 Interacts with CONSTITUTIVELY PHOTOMORPHOGENIC1-SUPPRESSOR OF PHYA Complexes to Regulate Photomorphogenesis and Flowering Time

Plant Cell 2010 22:108-123. Published online: January 8, 2010.

 

·         Zhou J, Wang X, He K, Charron JB, Elling AA and Deng XW.

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 2010 72:585-595. Published online: January 7, 2010.


 

·         Charron JB, He H, Elling AA and Deng XW.

Dynamic Landscapes of Four Histone Modifications during Deetiolation in Arabidopsis

Plant Cell 2009 21:3732-3748. Published online: December 11, 2009. Commentary and Author Profile

 

·         Xie CG, Lin H, Deng XW and Guo Y.

Roles of SCaBP8 in salt stress response

Plant Signal Behav 2009 4(10):956-8. Epub 2009 Oct 17.

 

·         Elling AA and Deng XW.

Next-generation sequencing reveals complex relationships between the epigenome and transcriptome in maize

Plant Signal Behav 2009 4(8):760-2. Epub 2009 Aug 3

 

·         Wang F, Zhu D, Huang X, Li S, Gong Y, Yao Q, Fu X, Fan LM and Deng XW.

Biochemical Insights on Degradation of Arabidopsis DELLA Proteins Gained From a Cell-Free Assay System

Plant Cell 2009 21: 2378-2390. Published online: August 28, 2009.

 

·         He K, Li X, Zhou J, Deng XW, Zhao H and Luo J.

NTAP: for NimbleGen tiling array ChIP-chip data analysis

Bioinformatics 2009 25:1838-40. Epub 2009 May 25.

 

·         Wang X, Elling AA, Li X, Li N, Peng Z, He G, Sun H, Qi Y, Liu XS, and Deng XW.

Genome-Wide and Organ-Specific Landscapes of Epigenetic Modifications and Their Relationships to mRNA and Small RNA Transcriptomes in Maize

Plant Cell 2009 21:1053-69. [Epub ahead of print] Commentary and Author Profile

 

·         Wang X, Yu Z, Yang X, Deng XW and Li L.

Transcriptionally active gene fragments derived from potentially fast-evolving donor genes in the rice genome.

Bioinformatics 2009 Mar 16. [Epub ahead of print]

 

·         Shen Y, Zhou Z, Feng S, Li J, Tan-Wilson A, Qu LJ, Wang H and Deng XW.

Phytochrome A Mediates Rapid Red Light-Induced Phosphorylation of Arabidopsis FAR-RED ELONGATED HYPOCOTYL1 in a Low Fluence Response

Plant Cell 2009 Feb 10. [Epub ahead of print]

 

·         Wang X, Li W, Piqueras R, Cao K, Deng XW and Wei N.

Regulation of COP1 nuclear localization by the COP9 Signalosome via direct interaction with CSN1.

Plant J. 2009 Jan 28. [Epub ahead of print]

 

·         Wei N.

On the Structural Model of the COP9 Signalosome.

Structure. 2009 Jan;17(1):1-2.

 

·         Jiao Y, Lori Tausta S, Gandotra N, Sun N, Liu T, Clay NK, Ceserani T, Chen M, Ma L, Holford M, Zhang HY, Zhao H, Deng XW and Nelson T.

A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies.

Nat Genet. 2009 Jan 4. [Epub ahead of print].


 

·         Yu JW, Rubio V, Lee NY, Bai S, Lee SY, Kim SS, Liu L, Zhang Y, Irigoyen ML, Sullivan JA, Zhang Y, Lee I, Xie Q, Paek NC and Deng XW.

COP1 and ELF3 Control Circadian Function and Photoperiodic Flowering by Regulating GI Stability.

Mol Cell 2008 32:617-630, 5 December 2008.

 

·         Lau OS and Deng XW.

Effect of Arabidopsis COP10 ubiquitin E2 enhancement activity across E2 families and functional conservation among its canonical homologs.

Biochem J 2008 Dec 5. [Epub ahead of print].

 

·         Peng ZY, Zhang H, Liu T, Dzikiewicz KM, Li S, Wang X, Hu G, Zhu Z, Wei X, Zhu QH, Sun Z, Ge S, Ma L, Li L and Deng XW.

Characterization of the genome expression trends in the heading-stage panicle of six rice lineages.

Genomics 2008 Nov 24. [Epub ahead of print]

 

·         Wei N, Serino G and Deng XW.

The COP9 signalosome: more than a protease.

Trends Biochem Sci. 2008 Oct 14. [Epub ahead of print]

 

·         Zhang Y, Xu W, Li Z, Deng XW, Wu W and Xue Y.

F-box Protein DOR Functions as a Novel Inhibitory Factor for ABA-induced Stomatal Closure under Drought Stress in Arabidopsis thaliana.

Plant Physiol. 2008 Oct 3. [Epub ahead of print]

 

·         Zhu D, Maier A, Lee JH, Laubinger S, Saijo Y, Wang H, Qu LJ, Hoecker and Deng XW.

Biochemical Characterization of Arabidopsis Complexes Containing CONSTITUTIVELY PHOTOMORPHOGENIC1 and SUPPRESSOR OF PHYA Proteins in Light Control of Plant Development.

Plant Cell 2008 Sep 23. [Epub ahead of print]

 

·         Yin BL, Guo L, Zhang DF, Terzaghi W, Wang XF, Liu TT, He H, Cheng ZK and Deng XW.

Integration of Cytological Features with Molecular and Epigenetic Properties of Rice Chromosome 4.

Mol Plant 2008 1: 816-829; doi:10.1093/mp/ssn037. Advance Access published on August 8, 2008.

 

·         Zhang HY, He H, Chen LB, Li L, Liang MZ, Wang XF, Liu XG, He GM, Chen RS, Ma LG, and Deng XW.

A Genome-Wide Transcription Analysis Reveals a Close Correlation of Promoter INDEL Polymorphism and Heterotic Gene Expression in Rice Hybrids.

Mol Plant 2008 1: 720-731; doi:10.1093/mp/ssn022. Advance Access published on August 5, 2008.

 

·         Zhang Q, Li J, Xue Y, Han B and Deng XW.

Rice 2020: A Call For An International Coordinated Effort In Rice Functional Genomics.

Mol Plant 2008 1: 715-719; doi:10.1093/mp/ssn043. Advance Access published on August 13, 2008.

 

·         Saijo Y, Zhu D, Li J, Rubio V, Zhou Z, Shen Y, Hoecker U, Wang H, and Deng XW.

Arabidopsis COP1/SPA1 Complex and FHY1/FHY3 Associate with Distinct Phosphorylated Forms of Phytochrome A in Balancing Light Signaling.

Mol. Cell 2008 Aug 22;31:607-613.

 

·         Zhang Y, Feng S, Chen F, Chen H, Wang J, McCall C, Xiong Y, Deng XW.

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. 2008 Jun 13. [Epub ahead of print]

 

·         Guo L, Zhou J, Elling AA, Charron JB, Deng XW.

Histone Modifications and Expression of Light Regulated Genes in Arabidopsis Are Cooperatively Influenced by Changing Light Conditions.

Plant Physiol. 2008 Jun 11. [Epub ahead of print]

 

·         Liu Y, Wang F, Zhang H, He H, Ma L, Deng XW.

Functional Characterization of Arabidopsis Ubiquitin-Specific Protease Gene Family Reveals Specific Role and Redundancy of Individual Members in Development.

Plant J. 2008 May 14. [Epub ahead of print]

 

·         Jang S, Marchal V, Panigrahi KC, Wenkel S, Soppe W, Deng XW, Valverde F, Coupland G.

Arabidopsis COP1 shapes the temporal pattern of CO accumulation conferring a photoperiodic flowering response.

EMBO J. 2008 Apr 23;27(8):1277-88. Epub 2008 Apr 3.

 

·         Li L, He H, Zhang J, Wang X, Bai S, Stolc V, Tongprasit W, Young ND, Yu O, Deng XW.

Transcriptional analysis of highly syntenic regions between Medicago truncatula and Glycine max using tiling microarrays.

Genome Biol. 2008 Mar 19;9(3):R57. [Epub ahead of print]

 

·         Chen H, Zhang J, Neff MM, Hong SW, Zhang H, Deng XW, Xiong L.

Integration of light and abscisic acid signaling during seed germination and early seedling development.

Proc Natl Acad Sci U S A 2008 Mar 18;105(11):4495-500. Epub 2008 Mar 10.

 

·         Li X, Wang X, He K, Ma Y, Su N, He H, Stolc V, Tongprasit W, Jin W, Jiang J, Terzaghi W, Li S & Deng XW

High-Resolution Mapping of Epigenetic Modifications of the Rice Genome Uncovers Interplay between DNA Methylation, Histone Methylation, and Gene Expression.

Plant Cell 2008; Epub Feb 8. 2008. Suppl. Dataset 1, 2.

 

·         Lee JH, Terzaghi W, Gusmaroli G, Charron JB, Yoon HJ, Chen H, He YJ, Xiong Y & Deng XW

Characterization of Arabidopsis and rice DWD proteins and their roles as substrate receptors for CUL4-RING E3 ubiquitin ligases.

Plant Cell 2008; Jan;20:152-67. Epub 2008 Jan 25. Suppl. Dataset 1a, 1b, 2.

 

·         Menon S, Tsuge T, Dohmae N, Takio K, Wei N.

Association of SAP130/SF3b-3 with Cullin-RING ubiquitin ligase complexes and its regulation by the COP9 signalosome.

BMC Biochem 2008 Jan 3;9:1.

 

·         Feng S, Martinez C, Gusmaroli G, Wang Y, Zhou J, Wang F, Chen L, Yu L, Iglesias-Pedraz JM, Kircher S, Schafer E, Fu X, Fan LM & Deng XW.

Coordinated regulation of Arabidopsis thaliana development by light and gibberellins.

Nature 2008 Jan 24; 451(475-479).

 

·         Alabadi D, Gallego-Bartolome J, Orlando L, Garcia-Carcel L, Rubio V, Martinez C, Frigerio M, Iglesias-Pedraz JM, Espinosa A, Deng XW, Blazquez MA.

Gibberellins modulate light signaling pathways to prevent Arabidopsis seedling de-etiolation in darkness.

Plant J 2008 Jan;53(2):324-35. Epub 2007 Dec 5.


 

·         Gong W, He K, Covington M, Dinesh-Kumar SP., Snyder M, Harmer SL, Zhu YX & Deng XW.

The Development of Protein Microarrays and Their Applications in DNA-Protein and Protein-Protein Interaction Analyses of Arabidopsis Transcription Factors

Molecular Plant 2007 Oct23; [Epub ahead of print].

 

·         Rubio V and Deng XW.

Standing on the Shoulders of GIGANTEA

Science 2007 Oct 12; 318(5848): 206 - 207.

 

·         Menon S, Chi H, Zhang H, Deng XW, Flavell RA, Wei N.

COP9 signalosome subunit 8 is essential for peripheral T cell homeostasis and antigen receptorA?Cinduced entry into the cell cycle from quiescence

Nat Immunol. 2007 Nov; 8(11):1236-45. Epub 2007 Sep 30.

Supplementary information

 

·         Han B, Xue Y, Li J, Deng XW, Zhang Q.

Rice functional genomics research in China.

Philos Trans R Soc Lond B Biol Sci. 2007 Jun 29;362(1482):1009-21.

 

·         Pick E, Lau OS, Tsuge T, Menon S, Tong Y, Dohmae N, Plafker SM, Deng XW, Wei N.

Mammalian DET1 regulates Cul4A activity and forms stable complexes with E2 ubiquitin-conjugating enzymes.

Mol Cell Biol. 2007 Jul;27(13):4708-19. Epub 2007 Apr 23.

 

·         Qin G, Gu H, Ma L, Peng Y, Deng XW, Chen Z, Qu LJ.

Disruption of phytoene desaturase gene results in albino and dwarf phenotypes in Arabidopsis by impairing chlorophyll, carotenoid, and gibberellin biosynthesis

Cell Res. 2007 (17): 471-482. Epub 2007 May 8.

 

·         Li L, Wang X, Sasidharan R., Stolc V, Deng W, He H, Korbel J, Chen X, Tongprasit W, Ronald P, Chen R, Gerstein M, Deng XW.

Global Identification and Characterization of Transcriptionally Active Regions in the Rice Genome

PLoS ONE. 2007; 2(3): e294.

 

·         Jiao Y, Deng XW.

A genome-wide transcriptional activity survey of rice transposable element-related genes

Genome Biology. 2007 8(2):R28. Epub 2007 Feb 27.

 

·         Lee J, He K, Stolc V, Lee H, Figueroa P, Gao Y, Tongprasit W, Zhao H, Lee I, Deng XW.

Analysis of Transcription Factor HY5 Genomic Binding Sites Revealed Its Hierarchical Role in Light Regulation of Development.

Plant Cell. 2007 Mar; 19: 731-749. Epub 2007 Mar 2.

Editorial Comment

 

·         Jiao Y, Lau OS, Deng XW.

Light-regulated transcriptional networks in higher plants.

Nat Rev Genet. 2007 Mar;8(3):217-30.

 

·         Gusmaroli G, Figueroa P, Serino G, Deng XW.

Role of the MPN Subunits in COP9 Signalosome Assembly and Activity, and Their Regulatory Interaction with Arabidopsis Cullin3-Based E3 Ligases.

Plant Cell. 19(2):564-81. Epub 2007 Feb 16.

 

·         Zhou J, Wang X, Jiao Y, Qin Y, Liu X, He K, Chen C, Ma L, Wang J, Xiong L, Zhang Q, Fan L, Deng XW.

Global genome expression analysis of rice in response to drought and high-salinity stresses in shoot, flag leaf, and panicle

Plant Mol Biol. 2007 Mar;63(5):591-608. Epub 2007 Jan 16.

 

·         Zhang, Y, Wen, P, Lau, OS, Deng XW.

Characterization of the Ubiquitin E2 Enzyme Variant Gene Family in Arabidopsis

JIPB 2007 Jan;49(1):120-126.

 

·         Bai S, Zhong X, Ma L, Zheng W, Fan LM, Wei N, Deng XW.

A simple and reliable assay for detecting specific nucleotide sequences in plants using optical thin-film biosensor chips

Plant J. 2007 Jan; 49 (2): 354-366. Epub 2006 Dec 6.


 

·         Chen H, Karplus VJ, Ma H, Deng XW.

Plant Biology Research Comes of Age in China.

Plant Cell. 2006 Nov;18(11):2855-64.

 

·         Su N, He K, Jiao Y, Chen C, Zhou J, Li L, Bai S, Li X, Deng XW.

Distinct reorganization of the genome transcription associates with organogenesis of somatic embryo, shoots, and roots in rice.

Plant Mol Biol. 2006 Oct 28; [Epub ahead of print]

 

·         Wang X, He H, Li L, Chen R, Deng XW, Li S

NMPP: a user-customized NimbleGen microarray data processing pipeline.

Bioinformatics. 2006 Dec; 22(23): 2955-7. Epub 2006 Oct 12.

 

·         Lee JH, Deng XW, Kim WT

Possible role of light in the maintenance of EIN3/EIL1 stability in Arabidopsis seedlings.

Biochem Biophys Res Commun. 2006 Nov; 350(2): 484-491. Epub 2006 Sep 25.

 

·         Chen, H, Shen Y, Tang X, Yu L, Wang J, Guo L, Zhang Y, Zhang H, Feng S, Strickland E, Zheng N, and Deng XW

Arabidopsis CULLIN4 Forms an E3 Ubiquitin Ligase with RBX1 and the CDD Complex in Mediating Light Control of Development

Plant Cell 2006;18(8):1991-2004. Epub 2006 July 14.

 

·         Guo L, Yin B, Zhou J, Li X, Deng XW

Development of rabbit monoclonal and polyclonal antibodies for detection of site-specific histone modifications and their application in analyzing overall modification levels.

Cell Research. 2006 May; 16(5): 519-27. Epub 2006 May 15

 

·         Dong L, Wang L, Zhang Y, Zhang Y, Deng X, Xue Y.

An auxin-inducible F-box protein CEGENDUO negatively regulates auxin-mediated lateral root formation in Arabidopsis.

Plant Mol Biol. 2006 Mar; 60(4): 599-615.

 

·         Yi C, Li S, Wang J, Wei N, Deng XW.

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. 2006; 38(7): 1076-83. Epub 2006 Feb 8.

 

·         Li J, Zhu S, Song X, Shen Y, Chen H, Yu J, Yi K, Liu Y, Karplus VJ, Wu P, Deng XW.

A Rice Glutamate Receptor-Like Gene Is Critical for the Division and Survival of Individual Cells in the Root Apical Meristem.

Plant Cell. 2006 Feb; 18(2):340-9. Epub 2005 Dec 23.

 

·         Li L, Wang X, Stolc V, Li X, Zhang D, Su N, Tongprasit W, Li S, Cheng Z, Wang J, Deng XW.

Genome-wide transcription analyses in rice using tiling microarrays.

Nature Genetics. 2006 Jan; 38: 124 – 129. Epub Dec 20.  

 

·         Datta S, Hettiarachchi GH, Deng XW, Holm M. 

Arabidopsis CONSTANS-LIKE3 Is a Positive Regulator of Red Light Signaling and Root Growth.

Plant Cell. 2006 Jan;18(1):70-84. Epub 2005 Dec 9.

 


 

 

·         Jiao Y, Ma L, Strickland E, Deng XW.

Conservation and Divergence of Light-Regulated Genome Expression Patterns during Seedling Development in Rice and Arabidopsis.

Plant Cell. 2005 Dec; 17(12):3239-56. Epub 2005 Nov 11.

 

·         Kraft E, Stone SL, Ma L, Su N, Gao Y, Lau OS, Deng XW, Callis J.

Genome Analysis and Functional Characterization of the E2 and RING-Type E3 Ligase Ubiquitination Enzymes of Arabidopsis.

Plant Physiol. 2005 Dec; 139(4):1597-611.

 

·         Feng JX, Liu D, Pan Y, Gong W, Ma LG, Luo JC, Deng XW, Zhu YX.

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. 2005 Dec; 59(6):853-68.

 

·         Wang X, Li L, Chen C, Wang J, Li S, and Deng XW

Analysis of oligo hybridization properties by high-resolution tiling arrays in rice.

Proceeding report, 5th International Rice Genetics Symposium, 2005: 65-76. 19-23 November, 2005; Manila, Philippines.

 

·         Shen Y, Feng S, Ma L, Lin R, Qu LJ, Chen Z, Wang H, Deng XW.

Arabidopsis FHY1 Protein Stability Is Regulated by Light via Phytochrome A and 26S Proteasome.

Plant Physiol. 2005 Nov; 139: 1234–1243.

 

·         Zhang S, Chen C, Li L, Meng L, Singh J, Jiang N, Deng XW, He ZH, Lemaux PG.

Evolutionary expansion, gene structure, and expression of the rice wall-associated kinase gene family.

Plant Physiol. 2005 139(3):1107-24.

 

·         Stolc V, Li L,  Wang X, Li X, Su N, Tongprasit W, Han B, Xue Y, Li J, Snyder1 M, Gerstein M, Wang J, Deng XW.

A pilot study of transcription unit analysis in rice using oligonucleotide tiling-path microarray.

Plant Molecular Biology. 2005 Sep; 59(1):137–149.

 

·         Yi C, Deng XW.

COP1 - from plant photomorphogenesis to mammalian tumorigenesis.

Trends Cell Biol. 2005 Nov; 15 (11): 618-625.

 

·         Ma L, Chen C, Liu XJiao 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 GKS, Wang J, Deng XW, Wang J.
A microarray analysis of the rice transcriptome and its comparison to Arabidopsis.

Genome Research. 2005 September; 15(9):1274-1283.

 

·         Yi C, Li S, Chen X, Wiemer EAC, Wang J, Wei N, Deng XW.

Major Vault Protein, in Concert with Constitutively Photomorphogenic 1, Negatively Regulates c-Jun–Mediated Activator Protein 1 Transcription in Mammalian Cells.

Cancer Res. 2005 July; 65(13): 5835 – 5840.

 

·         Menon S, Rubio V, Wang X, Deng XW, Wei N.

Purification of the COP9 Signalosome from Porcine Spleen, Human Cell Lines, and Arabidopsis thaliana Plants

Methods Enzymol 2005; 398:468-481.

 

·         Li L, Deng XW.
It runs in the family: regulation of brassinosteroid signaling by the BZR1-BES1 class of transcription factors.
Trends Plant Sci. 2005 Jun; 10(6): 266-8.

 

·         Li L, Wang X, Xia M, Stolc V, Su N, Peng Z, Li S, Wang J, Wang X, Deng XW.
Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture.
Genome Biol. 2005 Jun ;6(6):R52. Epub 2005 May 27.

·         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, Deng XW.
A Tiling Microarray Expression Analysis of Rice Chromosome 4 Suggests a Chromosome-Level Regulation of Transcription.
Plant Cell. 2005 June; 17(6):1641-57. Epub 2005 Apr 29.

·         Ma L, Sun N, Liu X, Jiao Y, Zhao H, Deng XW.
Organ-Specific Expression of Arabidopsis Genome during Development.
Plant Physiol. 2005 May;138(1):80-91.

·         Sang Y, Li QH, Rubio V, Zhang YC, Mao J, Deng XW, Yang HQ.
N-Terminal Domain-Mediated Homodimerization Is Required for Photoreceptor Activity of Arabidopsis CRYPTOCHROME 1.
Plant Cell. 2005 May;17(5):1569-84. Epub 2005 Apr 1.

·         Figueroa P, Gusmaroli G, Serino G, Habashi J, Ma L, Shen Y, Feng S, Bostick M, Callis J, Hellmann H, Deng XW.
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. 2005 Apr;17(4):1180-95. Epub 2005 Mar 16.

·         Yang J, Lin R, Sullivan J, Hoecker U, Liu B, Xu L, Deng XW, Wang H.
Light Regulates COP1-Mediated Degradation of HFR1, a Transcription Factor Essential for Light Signaling in Arabidopsis.
Plant Cell. 2005 Mar;17(3):804-21. Epub 2005 Feb 10.

·         Su N, Sullivan J, Deng XW
Modulation of F1 hybrid stature without altering parent plants through trans-activated expression of a mutated rice GAI homologue
Plant Biotechnology Journal. 2005 March,3(2):157.

·         Rubio V, Shen Y, Saijo Y, Liu Y, Gusmaroli G, Dinesh-Kumar SP, Deng XW.
An alternative tandem affinity purification strategy applied to Arabidopsis protein complex isolation
The Plant Journal. 2005 March;41(5):767.

·         Rubio V, Deng XW
Phytunes: phosphorylation status and phytochrome-mediated signaling.
Cell. 2005 Feb 11;120(3):290-2.

·         Li L, Wang X, Li X, Su N, Stolc V, Han B, Li J, Xue Y, Wang J, Deng XW.

Toward genome-wide transcriptional analysis in rice using MAS oligonucelotide tiling-path microarrays.

In Rice Is Life: Scientific Perspectives For The 21st Century, eds. K. Toriyama, KL Heong and B Hardy, 2005: 80-83. Proceedings of the World Rice Research Conference held in Tokyo and Tsukuba, Japan, November, 2004.


·         Wang L, Dong L, Zhang Y, Zhang Y, Wu W, Deng XW, Xue Y.
Genome-wide analysis of S-Locus F-box-like genes in Arabidopsis thaliana
Plant Mol Biol. 2004 Dec; 56(6):929-945.

·         Boccalandro HE, Rossi MC, Saijo Y, Deng XW, Casal JJ.
Promotion of photomorphogenesis by COP1.
Plant Mol Biol. 2004 Dec;56(6):905-15. Epub 2005 Apr 7.

·         Gusmaroli G, Feng S, Deng XW
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. 2004 Nov;16(11):2984-3001. Epub 2004 Oct 14.

·         Yanagawa Y, Sullivan JA, Komatsu S, Gusmaroli G, Suzuki G, Yin J, Ishibashi T, Saijo Y, Rubio V, Kimura S, Wang J, Deng XW.
Arabidopsis COP10 forms a complex with DDB1 and DET1 in vivo and enhances the activity of ubiquitin conjugating enzymes
Genes Dev. 2004 Sep;18: 2172-2181.

·         Feng S, Shen Y, Sullivan JA, Rubio V, Xiong Y, Sun TP, Deng XW.
Arabidopsis CAND1, an unmodified CUL1-interacting protein, is involved in multiple developmental pathways controlled by ubiquitin/proteasome-mediated protein Degradation.
Plant Cell. 2004 Jul;16(7):1870-82. Epub 2004 Jun 18.

·         Gong W, Shen YP, Ma LG, Pan Y, Du YL, Wang DH, Yang JY, Hu LD, Liu XF, Dong CX, Ma L, Chen YH, Yang XY, Gao Y, Zhu D, Tan X, Mu JY, Zhang DB, Liu YL, Dinesh-Kumar SP, Li Y, Wang XP, Gu HY, Qu LJ, Bai SN, Lu YT, Li JY, Zhao JD, Zuo J, Huang H, Deng XW, Zhu YX.
Genome-Wide ORFeome Cloning and Analysis of Arabidopsis Transcription Factor Genes.
Plant Physiol. 2004 Jun;135(2):773-82.

·         Gao Y, Li J, Strickland E, Hua S, Zhao H, Chen Z, Qu L, Deng XW
An arabidopsis promoter microarray and its initial usage in the identification of HY5 binding targets in vitro.
Plant Mol Biol. 2004 Mar;54(5):683-99.


·         Sullivan JA, Shirasu K, Deng XW.
The diverse roles of ubiquitin and the 26S proteasome in the life of plants.
Nat Rev Genet. 2003 Dec;4(12):948-58.

·         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 LJ, Deng XW.
A genome wide analysis of blue light regulation of Arabidopsis transcription factor gene expression during seedling development.
Plant Physiol. 2003 Dec;133(4):1480-1493.

·         Lykke-Andersen K, Wei N
Gene structure and embryonic expression of mouse CDP9 signalosome subunit 8 (Csn8)
Gen.e 2003 Dec 4;321:65-72.

·         Saijo Y, Sullivan JA, Wang H, Yang J, Shen Y, Rubio V, Ma L, Hoecker U, Deng XW.
The COP1-SPA1 interaction defines a critical step in phytochrome A-mediated regulation of HY5 activity.
Genes Dev. 2003 Nov 1;17(21):2642-7.

·         Sun N, Ma L, Pan D, Zhao H, Deng XW.
A Evaluation of light regulatory potential of Calvin cycle steps based on large-scale gene expression profiling data.
Plant Mol Biol. 2003 Nov;53(4):467-78.

·         Pan D, Sun N, Cheung KH, Guan Z, Ma L, Holford M, Deng XW, Zhao H.
PathMAPA: a tool for displaying gene expression and performing statistical tests on metabolic pathways at multiple levels for Arabidopsis.
BMC Bioinformatics. 2003 Nov 7

·         Li L, Deng X.W.
The COP9 signalosome: an alternative lid for the 26S proteasome?
Trends Cell Biol. 2003 Oct;13(10):507-9.

·         Lykke-Andersen K, Schaefer L, Menon S, Deng XW, Miller JB, Wei N
Disruption of the COP9 signalosome Csn2 subunit in mice causes deficient cell proliferation, accumulation of p53 and cyclin E, and early embryonic deat
Mol. Cell. Biol. 2003 Oct;23(19):6790-7.

·         Sullivan JA, Deng XW
From seed to seed: the role of photoreceptors in Arabidopsis development
Dev Biol. 2003 Aug 15;260(2):289-97

·         Wu P, Ma L, Hou X, Wang M, Wu Y, Liu F, Deng XW
Phosphate starvation triggers distinct alterations of genome expression in Arabidopsis roots and leaves
Plant Physiol. 2003 Jul;132(3):1260-71.

·         Peng Z, Shen Y, Feng S, Wang X, Chitteti BN, Vierstra RD, Deng XW
Evidence for a physical association of the COP9 signalosome, the proteasome, and specific SCF E3 ligases in vivo.
Curr Biol. 2003 Jul 1;13(13):R504-5. supplementary data

·         Feng S, Ma L, Wang X, Xie D, Dinesh-Kumar SP, Wei N, Deng XW.
The COP9 Signalosome Interacts Physically with SCFCOI1 and Modulates Jasmonate Responses
Plant Cell. 2003May;15(5):1083-94.

·         Wang X, Feng S, Nakayama N, Crosby WL, Irish V, Deng XW, Wei N.
The COP9 Signalosome Interacts with SCFUFO and Participates in Arabidopsis Flower Development
Plant Cell. 2003 May;15(5):1071-82.

·         Wang H, Deng XW.
Dissecting the phytochrome A-dependent signaling network in higher plants
Trends in Plant Sciences (2003),Apr;8(4):172-8.

·         Ma, L.G., Zhao, H.Y., and Deng, X.W.
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. 2003; 130: 969-981.

·         Serino, G., Su, H.W., Peng, Z.H., Tsuge, T., Wei, N., Gu, H.Y., and Deng, X.W.
Characterization of the last subunit of Arabidopsis COP9 signalosome: implications for the overall structure and origin of the complex
Plant Cell . 2003; 15:719-731.

HIGHLIGHT: Characterization of the last Subunit of the Arabidopsis COP9 Signalosome
Plant Cell. 2003; 15:580.

·         Wei N, Deng X.W.
The COP9 signalosome
Ann. Rev. Cell Dev Biol. 2003; 19:261-286.

·         Serino G, Deng XW.
The COP9 Signalosome: Regulating Plant Development Through the Control of Proteolysis
Annu. Rev. Plant Biol. 2003; 10


·         Chunling Yi, Haiyang Wang, Ning Wei, and Xing-Wang Deng
An initial biochemical and cell biological characterization of mammalian homologue of a central plant developmental switch, COP1
BMC Cell Biology. 2002;
3:30.

·         Claus Schwechheimer, Giovanna Serino, and Xing-Wang Deng
Multiple Ubiquitin Ligase-Mediated Processes Require COP9 Signalosome and AXR1 Function
Plant Cell 2002;14:2553-2563.

·         Wang H, Ma L.G, Habashi, J., Li J.M, Zhao H.Y, Deng X.W.
Analysis of far-red light regulated genome expression profiles of phytochrome A pathway mutants in Arabidopsis.
Plant J. 2002 Dec;32(5):723-733.

·         Ligeng Ma, Ying Gao, Lijia Qu, Zhangliang Chen, Jinming Li, Hongyu Zhao, and Xing Wang Deng
Genomic evidence for COP1 as repressor of light regulated gene expression and development in Arabidopsis.
Plant Cell 2002;14:2383-2398.

·         Yadav V, Kundu S, Chattopadhyay D, Negi P, Wei N, Deng XW, Chattopadhyay S.
Light regulated modulation of Z-box containing promoters by photoreceptors and downstream regulatory components, COP1 and HY5, in Arabidopsis.
Plant J. 2002 Sep;31(6):741-53.

·         Fry RC, Habashi J, Okamoto H, Deng XW.
Characterization of a Strong Dominant phytochrome A Mutation Unique to Phytochrome A Signal Propagation.
Plant Physiol. 2002 Sep;130(1):457-65.

·         Liu Y, Schiff M, Serino G, Deng XW, Dinesh-Kumar SP.
Role of SCF Ubiquitin-Ligase and the COP9 Signalosome in the N Gene-Mediated Resistance Response to Tobacco mosaic virus.
Plant Cell. 2002 Jul;14(7):1483-96.

·         Claus Schwechheimer and Xing-Wang Deng
FPLC Gel Filtration
(2002) pp. 226-228, In Weigel, D., and Glazebrook, J. ed "Arabidopsis-A Laboratory Manual".
Cold Spring Harbor Laboratory Press, Cold Spring Harbor.

·         Jessica Habashi and Xing-Wang Deng
Nondenaturing Gel Electrophoresis of Proteins
(2002) pp. 228-233, In Weigel, D., and Glazebrook, J. ed "Arabidopsis-A Laboratory Manual".
Cold Spring Harbor Laboratory Press, Cold Spring Harbor.

·         Giovanno Serino and Xing Wang Deng
Protein Coimmunoprecipitation
(2002) pp. 233-237. In Weigel, D., and Glazebrook, J. ed "Arabidopsis-A Laboratory Manual".
Cold Spring Harbor Laboratory Press, Cold Spring Harbor.

·         Haiyang Wang and Xing Wang Deng
Phytochrome signaling.
(2002). In The Arabidopsis Book, eds. C.R. Somerville and E.M. Meyerowitz, American Society of Plant Biologists, Rockville, MD, DOI 10.1199-tab.0074 http://www.aspb.org/publications/arabidopsis/

·         Schwechheimer, C., and Deng, X. W.
Studying protein-protein interactions with the yeast two-hybid system.
Chapter 9 in "Molecular Plant Biology: A practical Approach", volume II, pages 173-198.
Editors: Philip M. Gilmartin and Chris Bowler.
(2002),
Oxford University Press.

·         Christian S. Hardtke, Haruko Okamoto, Chatanika Stoop-Myer and Xing-Wang Deng
Biochemical evidence for ubiquitin ligase activity of the Arabidopsis COP1 interacting protein 8 (CIP8).
Plant J. 2002 May;30(4):385-94.

·         Magnus Holm, Li-Geng Ma, Li-Jia Qu and Xing-Wang Deng
Two interacting bZIP proteins are direct targets of COP1-mediated control of light-dependent gene expression in Arabidopsis.
Genes Dev. 2002 May 15;16(10):1247-1259.

·         Wang H, Deng XW.
Arabidopsis FHY3 defines a key phytochrome A signaling component directly interacting with its homologous partner FAR1.
EMBO J. 2002 Mar 15;21(6):1339-49.

·         Xiaoming Yang,Suchithra Menon, Karin Lykke-Andersen, Tomohiko Tsuge, Di Xiao, Xiping Wang, Roberto J. Rodriguez-Suarez, Hui Zhang and Ning Wei.
The COP9 Signalosome Inhibits p27 kip1 Degradation and Impedes G1-S Phase Progression via Deneddylation of SCF Cul1.
Current Biology. 2002. 12:667-672.

·         Suzuki G, Yanagawa Y, Kwok SF, Matsui M, Deng XW.
Arabidopsis COP10 is a ubiquitin-conjugating enzyme variant that acts together with COP1 and the COP9 signalosome in repressing photomorphogenesis.
Genes Dev. 2002 Mar 1;16(5):554-9.

·         Wang X, Kang D, Feng S, Serino G, Schwechheimer C, Wei N.
CSN1 N-Terminal-dependent Activity Is Required for Arabidopsis Development But Not for Rub1/Nedd8 Deconjugation of Cullins: A Structure-Function Study of CSN1 Subunit of COP9 Signalosome.
Mol Biol Cell 2002 Feb;13(2):646-55.


·         Ma L, Li J, Qu L, Hager J, Chen Z, Zhao H, Deng XW.
Light control of Arabidopsis development entails coordinated regulation of genome expression and cellular pathways.
Plant Cell 2001 Dec;13(12):2589-607.

·         Zhaohua Peng, Giovanna Serino, and Xing-Wang Deng.
Molecular characterization of subunit 6 of the COP9 signalosome and its role in multifaceted developmental processes in Arabidopsis.
Plant Cell 2001 Nov;13(11):2393-407.

·         Zhaohua Peng, Giovanna Serino, and Xing-Wang Deng.
A role of Arabidopsis COP9 signalosome in multifaceted developmental processes revealed by the characterization of its subunit 3.
Development 2001 Nov;128(21):4277-88.

·         Wang H, Ma LG, Li JM, Zhao HY, Deng XW.
Direct Interaction of Arabidopsis Cryptochromes with COP1 in Mediation of Photomorphogenic Development.
Science 2001 Oct 5;294(5540):154-8.

·         Schwechheimer C, Deng XW.
COP9 signalosome revisited: a novel mediator of protein degradation
Trends Cell Biol. 2001 Oct; 11(10):420-426.

·         Okamoto H, Qu L, Deng XW.
Does EID1 Aid the Fine-Tuning of Phytochrome A Signal Transduction in Arabidopsis?
Plant Cell. 2001 Sep;13(9):1983-1986.

·         Okamoto H, Matsui M, Deng XW.
Overexpression of the heterotrimeric G-protein alpha-subunit enhances phytochrome-mediated inhibition of hypocotyl elongation in Arabidopsis.
Plant Cell. 2001 Jul;13(7):1639-52.

·         Schwechheimer C, Serino G, Callis J, Crosby WL, Lyapina S, Deshaies RJ, Gray WM, Estelle M, Deng XW.
Interactions of the COP9 Signalosome with the E3 Ubiquitin Ligase SCFTIR1 Mediating Auxin Response.
Science. 2001 May 18; 292:1379-1382.
RESEARCH HOT PAPERS--Comments about this paper from The Scientist. Fabruary 16 2004; 28-29

·         Lyapina S, Cope G, Shevchenko A, Serino G, Tsuge T, Zhou C, Wolf DA, Wei N, Shevchenko A, Deshaies RJ.
Promotion of NEDD-CUL1 conjugate cleavage by COP9 signalosome.
Science. 2001 May 18;292(5520):1382-5.

·         Jiang CJ, Shoji K, Matsuki R, Baba A, Inagaki N, Ban H, Iwasaki T, Imamoto N, Yoneda Y, Deng XW, Yamamoto N.
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. 2001 Mar 23;276(12):9322-9.

·         Yamamoto YY, Deng XW, Matsui M.
Cip4, a new cop1 target, is a nucleus-localized positive regulator of arabidopsis photomorphogenesis.
Plant Cell. 2001 Feb;13(2):399-411.

·         Holm M, Hardtke CS, Gaudet R, Deng XW.
Identification of a structural motif that confers specific interaction with the WD40 repeat domain of Arabidopsis COP1.
EMBO J. 2001 Jan 15;20(1 & 2):118-127.

·         Peng Z, Staub JM, Serino G, Kwok SF, Kurepa J, Bruce BD, Vierstra RD, Wei N, Deng XW.
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. 2001 Feb;12(2):383-392.

·         Tsuge T, Matsui M, Wei N
The subunit 1 of the COP9 signalosome suppresses gene expression through its N-terminal domain and incorporates into the complex through the PCI domain.
J Mol Biol. 2001 Jan 5;305(1):1-9.


·         Abel S, Blazquez M, Dangl J, Deng XW, Graham I, Harada J, Jones J, Nilsson O.
Arabidopsis Research 2000.
Plant Cell. 2000 Dec;12(12):2302-2308.

·         Schwechheimer C, Deng XW.
The COP/DET/FUS proteins-regulators of eukaryotic growth and development.
Semin Cell Dev Biol. 2000 Dec;11(6):495-503.

·         Hardtke CS, Deng XW.
The cell biology of the COP/DET/FUS proteins. Regulating proteolysis in photomorphogenesis and beyond?
Plant Physiol. 2000 Dec;124(4):1548-57.

·         Osterlund MT, Wei N, Deng XW.
The roles of photoreceptor systems and the COP1-targeted destabilization of HY5 in light control of arabidopsis seedling development
Plant Physiol. 2000 Dec;124(4):1520-4.

·         Kang D, Wang X, Cao K, Sun C, Deng XW, Wei N.
A gain-of-function phenotype conferred by over-expression of functional subunits of the COP9 signalosome in Arabidopsis.
Plant J. 2000 Sep;23(5):597-608.

·         Hardtke CS, Gohda K, Osterlund MT, Oyama T, Okada K, Deng XW.
HY5 stability and activity in Arabidopsis is regulated by phosphorylation in its COP1 binding domain.
EMBO J. 2000 Sep 15;19(18):4997-5006.

·         Hsieh HL, Okamoto H, Wang M, Ang LH, Matsui M, Goodman H, Deng XW.
FIN219, an auxin-regulated gene, defines a link between phytochrome A and the downstream regulator COP1 in light control of arabidopsis development.
Genes Dev. 2000 Aug 1;14(15):1958-70.

·         Deng XW, Dubiel W, Wei N, Hofmann K, Mundt K.
Unified nomenclature for the COP9 signalosome and its subunits: an essential regulator of development.
Trends Genet. 2000 Jul;16(7):289.

·         Osterlund MT, Hardtke CS, Wei N, Deng XW.
Targeted destabilization of HY5 during light-regulated development of Arabidopsis
Nature 2000 May;405:462-466.

·         Deng XW, Dubiel W, Wei N, Hofmann K, Mundt K, Colicelli J, Kato Jy, Naumann M, Segal D, Seeger M, Glickman M, Chamovitz DA, Carr A.
Unified nomenclature for the COP9 signalosome and its subunits: an essential regulator of development.
Trends Genet. 2000 May;16(5):202-3.

·         Yamamoto YY, Puente P, Deng XW.
An Arabidopsis cotyledon-specific albino locus: a possible role in 16S rRNA maturation.
Plant Cell Physiol 2000; 41(1): 68-76.


·         Stoop-Myer C, Torii KU, McNellis TW, Coleman JE, Deng XW.
Short Communication: The N-terminal fragment of Arabidopsis photomorphogenic repressor COP1 maintains partial function and acts in a concentration-dependent manner.
Plant J 1999 Dec;20(6):713-717.

·         Holm M, Deng XW.
Structural organization and interactions of COP1, a light-regulated developmental switch.
Plant Mol Biol 1999 Sep;41(2):151-8.

·         Yamamoto N, Deng XW.
Protein nucleocytoplasmic transport and its light regulation in plants.
Genes Cells. 1999 Sep;4(9):489-500.

·         Serino G, Tsuge T, Kwok S, Matsui M, Wei N, Deng XW.
Arabidopsis cop8 and fus4 mutations define the same gene that encodes subunit 4 of the COP9 signalosome.
Plant Cell 1999 Oct;11(10):1967-80.

·         Torii KU, Stoop-Myer CD, Okamoto H, Coleman JE, Matsui M, Deng XW.
The RING finger motif of photomorphogenic repressor COP1 specifically interacts with the RING-H2 motif of a novel Arabidopsis protein.
J Biol Chem. 1999 Sep 24;274(39):27674-81.

·         Wang H, Kang D, Deng XW, Wei N.
Evidence for functional conservation of a mammalian homologue of the light-responsive plant protein COP1.
Curr Biol. 1999 Jul 1;9(13):711-4.

·         Deng XW, Quail PH.
Signalling in light-controlled development.
Semin Cell Dev Biol. 1999 Apr;10(2):121-9.

·         Wei N, Deng XW.
Making sense of the COP9 signalosome, a conserved regulatory protein complex from Arabidopsis to human
Trends Genet. 1999 Mar;15(3):98-103.

·         Osterlund MT, Ang LH, Deng XW.
The molecular and cellular basis of COP1 as a repressor of photomorphogenetic development in Arabidopsis
Trends Cell Biol. 1999 Mar;9(3):113-8.

·         Kwok SF, Staub JM, Deng XW.
Characterization of two subunits of Arabidopsis 19S proteasome regulatory complex and its possible interaction with the COP9 complex.
J Mol Biol. 1999 Jan 8;285(1):85-95.


·         Yamamoto YY, Deng XW.
A new vector set for GAL4-dependent transactivation assay in plants
Plant Biotech.1998;15(4):217-220.

·         Yamamoto YY, Matsui M, Deng XW.
Positive feedback in plant signaling pathways
Trends Plant Sci. 1998;(3): 374-375.

·         von Arnim AG, Deng XW, Stacey MG.
Cloning vectors for the expression of green fluorescent protein fusion proteins in transgenic plants.
Gene. 1998 Oct 9;221(1):35-43.

·         Karniol B, Yahalom A, Kwok S, Tsuge T, Matsui M, Deng XW, Chamovitz DA.
The Arabidopsis homologue of an eIF3 complex subunit associates with the COP9 complex.
FEBS Lett. 1998 Nov 13;439(1-2):173-9.

·         Osterlund MT, Deng XW.
Multiple photoreceptors mediate the light-induced reduction of GUS-COP1 from Arabidopsis hypocotyl nuclei.
Plant J. 1998 Oct;16(2):201-8.

·         Chamovitz DA, Deng XW.
Molecular approaches to biochemical purification: the COP9 complex paradigm
NATO ASI series, vol. H104, 83-91 (1998)

·         Kwok SF, Solano R, Tsuge T, Chamovitz DA, Ecker JR, Matsui M, Deng XW.
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 1998 Nov;10(11):1779-90.

·         Torii KU, McNellis TW, Deng XW.
Functional dissection of Arabidopsis COP1 reveals specific roles of its three structural modules in light control of seedling development.
EMBO J. 1998 Oct 1;17(19):5577-87.

·         Chattopadhyay S, Puente P, Deng XW, Wei N.
Combinatorial interaction of light-responsive elements plays a critical role in determining the response characteristics of light-regulated promoters in Arabidopsis.
Plant J. 1998 Jul;15(1):69-77.

·         Wei N, Deng XW.
Characterization and purification of the mammalian COP9 complex, a conserved nuclear regulator initially identified as a repressor of photomorphogenesis in higher plants.
Photochem Photobiol. 1998 Aug;68(2):237-41.

·         Wei N, Tsuge T, Serino G, Dohmae N, Takio K, Matsui M, Deng XW.
The COP9 complex is conserved between plants and mammals and is related to the 26S proteasome regulatory complex.
Curr Biol. 1998;8(16):919-22.

·         Yamamoto YY, Matsui M, Ang LH, Deng XW.
Role of a COP1 interactive protein in mediating light-regulated gene expression in arabidopsis.
Plant Cell 1998 Jul;10(7):1083-94.

·         Deng XW.
Light control of Arabidopsis developmental pattern.
SEB symposium 51 (1998): Control of Plant Development-Genes and signals p.93-96

·         Ang LH, Chattopadhyay S, Wei N, Oyama T, Okada K, Batschauer A, Deng XW.
Molecular interaction between COP1 and HY5 defines a regulatory switch for light control of Arabidopsis development.
Mol Cell 1998 Jan;1(2):213-22.

·         Chattopadhyay S, Ang LH, Puente P, Deng XW, Wei N.
Arabidopsis bZIP protein HY5 directly interacts with light-responsive promoters in mediating light control of gene expression.
Plant Cell 1998 May;10(5):673-83.


·         von Arnim AG, Osterlund MT, Kwok SF, Deng XW.
Genetic and developmental control of nuclear accumulation of COP1, a repressor of photomorphogenesis in Arabidopsis.
Plant Physiol. 1997 Jul;114(3):779-88.

·         Torii KU, Deng XW.
The role of COP1 in light control of Arabidopsis seedling development
Plant, Cell Environment 1997 (20):728-33.

·         Chamovitz DA, Deng XW.
The COP9 complex: a link between photomorphogenesis and general developmental regulation?
Plant, Cell Environment 1997 (20):734-9.


·         Chamovitz DA, Deng XW.
Light signaling in plants. Critical reviews
Plant Sci.1996(15): 455-478

·         Kwok SF, Deng XW.
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](1996) vol. 17 pg.134-143

·         von Arnim A, Deng XW.
Light control of seedling development
Annu. Rev. Plant Physiol. Plant Mol. Biol. 1996;47::215-43.

·         Staub JM, Deng XW.
Light signal transduction in plants.
Photochem Photobiol 1996 Dec;64(6):897-905.

·         Staub JM, Wei N, Deng XW.
Evidence for FUS6 as a component of the nuclear-localized COP9 complex in Arabidopsis.
Plant Cell 1996 Nov;8(11):2047-56.

·         von Arnim A, Deng XW.
A role for transcriptional repression during light control of plant development.
Bioessays 1996 Nov;18(11):905-10.

·         Wei N, Deng XW.
The role of the COP/DET/FUS genes in light control of arabidopsis seedling development.
Plant Physiol. 1996 Nov;112(3):871-8.

·         McNellis TW, Torii KU, Deng XW.
Expression of an N-terminal fragment of COP1 confers a dominant-negative effect on light-regulated seedling development in Arabidopsis.
Plant Cell 1996 Sep;8(9):1491-503.

·         Puente P, Wei N, Deng XW.
Combinatorial interplay of promoter elements constitutes the minimal determinants for light and developmental control of gene expression in Arabidopsis.
EMBO J. 1996 Jul 15;15(14):3732-43.

·         Chamovitz DA, Wei N, Osterlund MT, von Arnim AG, Staub JM, Matsui M, Deng XW.
The COP9 complex, a novel multisubunit nuclear regulator involved in light control of a plant developmental switch.
Cell 1996 Jul 12;86(1):115-21.

·         Kwok SF, Piekos B, Misera S, Deng XW.
A complement of ten essential and pleiotropic arabidopsis COP/DET/FUS genes is necessary for repression of photomorphogenesis in darkness.
Plant Physiol 1996 Mar;110(3):731-42.


·         McNellis TW, Deng XW.
Light control of seedling morphogenetic pattern.
Plant Cell 1995 Nov;7(11):1749-61.

·         Chamovitz DA, Deng XW.
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 1995 Aug 11;82(3):353-4.

·         Matsui M, Stoop CD, von Arnim AG, Wei N, Deng XW.
Arabidopsis COP1 protein specifically interacts in vitro with a cytoskeleton-associated protein, CIP1.
Proc Natl Acad Sci
USA 1995 May 9;92(10):4239-43.


·         von Arnim AG, Deng XW.
Light inactivation of Arabidopsis photomorphogenic repressor COP1 involves a cell-specific regulation of its nucleocytoplasmic partitioning.
Cell 1994 Dec 16;79(6):1035-45.

·         McNellis TW, von Arnim AG, Deng XW.
Overexpression of Arabidopsis COP1 results in partial suppression of light-mediated development: evidence for a light-inactivable repressor of photomorphogenesis.
Plant Cell 1994 Oct;6(10):1391-400.

·         Wei N, Chamovitz DA, Deng XW.
Arabidopsis COP9 is a component of a novel signaling complex mediating light control of development.
Cell 1994 Jul 15;78(1):117-24.
Published erratum appears in Cell 1994 Oct 7;79(1):following 179

·         Wei N, Kwok SF, von Arnim AG, Lee A, McNellis TW, Piekos B, Deng XW.
Arabidopsis COP8, COP10, and COP11 genes are involved in repression of photomorphogenic development in darkness.
Plant Cell 1994 May;6(5):629-43.

·         Ang LH, Deng XW.
Regulatory hierarchy of photomorphogenic loci: allele-specific and light-dependent interaction between the HY5 and COP1 loci.
Plant Cell 1994 May;6(5):613-28

·         McNellis TW, von Arnim AG, Araki T, Komeda Y, Misera S, Deng XW.
Genetic and molecular analysis of an allelic series of cop1 mutants suggests functional roles for the multiple protein domains.
Plant Cell 1994 Apr;6(4):487-500.

·         Deng XW
Fresh view of light signal transduction in plants.
Cell 1994 Feb 11;76(3):423-6.


·         von Arnim AG, Deng XW.
Ring finger motif of Arabidopsis thaliana COP1 defines a new class of zinc-binding domain.
J Biol Chem. 1993 Sep 15;268(26):19626-31


·         Wei N, Deng XW.
COP9: a new genetic locus involved in light-regulated development and gene expression in arabidopsis.
Plant Cell 1992 Dec;4(12):1507-18.

·         Deng XW, Matsui M, Wei N, Wagner D, Chu AM, Feldmann KA, Quail PH.
COP1, an Arabidopsis regulatory gene, encodes a protein with both a zinc-binding motif and a G beta homologous domain.
Cell 1992 Nov 27;71(5):791-801.


·         Bruce WB, Deng XW, Quail PH.
A negatively acting DNA sequence element mediates phytochrome-directed repression of phyA gene transcription.
EMBO J. 1991 Oct;10(10):3015-24.

·         Deng XW, Caspar T, Quail PH.
cop1: a regulatory locus involved in light-controlled development and gene expression in Arabidopsis.
Genes Dev. 1991 Jul;5(7):1172-82.