Deng, Xing-Wang - Department of Molecular Biophysics and Biochemistry, Yale University

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Deng, Xing-Wang - Department of Molecular Biophysics and Biochemistry, Yale University

Functional characterization of the Arabidopsis ubiquitin-specific protease gene family reveals specific role
Genome-wide analysis of S-Locus F-box-like genes in Arabidopsis thaliana
This article appeared in a journal published by Elsevier. The attached copy is furnished to the author for internal non-commercial research
RESEARCH COMMUNICATION Arabidopsis COP10 is
COP1 from plant photomorphogen-esis to mammalian tumorigenesis
TECHNICAL ADVANCE A simple and reliable assay for detecting specific nucleotide
Brief Communication 711 Evidence for functional conservation of a mammalian homologue
BioMed Central Page 1 of 17
An Arabidopsis promoter microarray and its initial usage in the identification of HY5 binding targets in vitro
[38] Purification of the COP9 Signalosome from Porcine Spleen, Human Cell Lines, and
The RING Finger Motif of Photomorphogenic Repressor COP1 Specifically Interacts with the RING-H2 Motif of a Novel
PHOTOCREDIT:JEREMYBURGESS/PHOTORESEARCHERSINC. PERSPECTIVES
The Plant Cell, Vol. 10, 673683, May 1998, www.plantcell.org 1998 American Society of Plant Physiologists Arabidopsis bZIP Protein HY5 Directly Interacts with
Genome Analysis Organ-Specific Expression of Arabidopsis Genome
Analysis of trehalose-6-phosphate synthase (TPS) gene family suggests the formation of TPS complexes in rice
Biochemical Characterization of Arabidopsis Complexes Containing CONSTITUTIVELY PHOTOMORPHOGENIC1 and
A Rice Glutamate ReceptorLike Gene Is Critical for the Division and Survival of Individual Cells in the Root
Characterization of a Strong Dominant phytochrome A Mutation Unique to Phytochrome A Signal Propagation1
From seed to seed: the role of photoreceptors in Arabidopsis development
Integration of light and abscisic acid signaling during seed germination and early seedling development
A pilot study of transcription unit analysis in rice using oligonucleotide tiling-path microarray
RESEARCH ARTICLES Dynamic Landscapes of Four Histone Modifications during
Analysis of far-red light-regulated genome expression profiles of phytochrome A pathway mutants in Arabidopsis
The Arabidopsis Chaperone J3 Regulates the Plasma Membrane H+-ATPase through Interaction with the
COMMUNICATION The Subunit 1 of the COP9 Signalosome Suppresses
letters to nature 462 NATURE |VOL 405 |25 MAY 2000 |www.nature.com
Genome Analysis Genome-Wide ORFeome Cloning and Analysis
The COP9 signalosome: an alternative lid for the 26S proteasome?
MOLECULAR AND CELLULAR BIOLOGY, July 2007, p. 47084719 Vol. 27, No. 13 0270-7306/07/$08.00 0 doi:10.1128/MCB.02432-06
Arabidopsis FHY1 Protein Stability Is Regulated by Light via Phytochrome A and 26S Proteasome1
Major Vault Protein, in Concert with Constitutively Photomorphogenic 1, Negatively Regulates
Plant Science 180 (2011) 352357 Contents lists available at ScienceDirect
Genome-wide profiling of histone H3 lysine 9 acetylation and dimethylation in Arabidopsis reveals correlation
On the Structural Model of the COP9 Signalosome Ning Wei1,*
Supplementary information -figures SUPPLEMENTARY FIGURES AND LEGENDS
Arabidopsis CULLIN4 Forms an E3 Ubiquitin Ligase with RBX1 and the CDD Complex in Mediating
Genome Biology 2005, 6:R52 commentreviewsreportsdepositedresearchrefereedresearchinteractionsinformation
Genome Biology 2007, 8:R28 commentreviewsreportsdepositedresearchrefereedresearchinteractionsinformation
MOLECULAR AND CELLULAR BIOLOGY, Oct. 2003, p. 67906797 Vol. 23, No. 19 0270-7306/03/$08.00 0 DOI: 10.1128/MCB.23.19.67906797.2003
80 Rice is life: scientific perspectives for the 21st century system, random overexpression of the Arabidopsis full-length
Plant Signaling & Behavior 4:10, 956-958; October 2009; 2009 Landes Bioscience articLe addendum
Genome Analysis Genome Analysis and Functional Characterization of
Gibberellins modulate light signaling pathways to prevent Arabidopsis seedling de-etiolation in darkness
F-Box Protein DOR Functions As a Novel Inhibitory Factor for Abscisic Acid-Induced Stomatal Closure
Genome Analysis Evolutionary Expansion, Gene Structure, and Expression
Update on Photomorphogenesis The Cell Biology of the COP/DET/FUS
(15 425 predicted complete coding regions) was estimated by counting the number of matching Expressed Sequence Tags
Annu. Rev. Cell Dev. Biol. 2003. 19:26186 doi: 10.1146/annurev.cellbio.19.111301.112449
alteration. However, the evidence strongly suggests issue of Cell, Ryu et al. (2005) show that PAPP5, a type 5 protein phosphatase, acts on a biologicallythat a critical biosynthetic threshold is required for
Regulation of COP1 nuclear localization by the COP9 signalosome via direct interaction with CSN1
The Plant Cell, Vol. 14, 23832398, October 2002, www.plantcell.org 2002 American Society of Plant Biologists Genomic Evidence for COP1 as a Repressor of Light-Regulated
RESEARCH ARTICLE CSN1 inhibits c-Jun phosphorylation and
Development of a versatile, target-oriented tiling microarray assay for measuring allele-specific gene expression
DWA1 and DWA2, Two Arabidopsis DWD Protein Components of CUL4-Based E3 Ligases, Act Together as Negative
RESEARCH ARTICLES Global Epigenetic and Transcriptional Trends among Two Rice
Arabidopsis CULLIN4-Damaged DNA Binding Protein 1 Interacts with CONSTITUTIVELY
[Plant Signaling & Behavior 4:8, 760-762; August 2009]; 2009 Landes Bioscience Epigenetic modifications and small RNAs play an important
Biochemical Insights on Degradation of Arabidopsis DELLA Proteins Gained From a Cell-Free Assay System W
BIOINFORMATICS APPLICATIONS NOTE Vol. 25 no. 14 2009, pages 18381840
RESEARCH ARTICLES Genome-Wide and Organ-Specific Landscapes of Epigenetic
IN THIS ISSUE Deep Sequencing Maps the Maize Epigenomic Landscape
Phytochrome A Mediates Rapid Red LightInduced Phosphorylation of Arabidopsis FAR-RED ELONGATED
A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies
Molecular Cell COP1 and ELF3 Control Circadian Function and
Characterization of the genome expression trends in the heading-stage panicle of six rice lineages
Molecular Plant Volume 1 Number 5 Pages 816829 September 2008 RESEARCH ARTICLE Integration of Cytological Features with
Molecular Plant Volume 1 Number 5 Pages 720731 September 2008 RESEARCH ARTICLE A Genome-Wide Transcription Analysis Reveals
Molecular Plant Volume 1 Number 5 Pages 715719 September 2008 Perspective
Molecular Cell Short Article
RESEARCH ARTICLES Arabidopsis DDB1-CUL4 ASSOCIATED FACTOR1 Forms a
Genome Biology 2008, 9:R57 Open Access2008Liet al.Volume 9, Issue 3, Article R57Research
High-Resolution Mapping of Epigenetic Modifications of the Rice Genome Uncovers Interplay between DNA Methylation,
Characterization of Arabidopsis and Rice DWD Proteins and Their Roles as Substrate Receptors for CUL4-RING
Home About Scientific Press Room Contact Us ScienceWatch Home
Molecular Plant Pages 115, 2007 The Development of Protein Microarrays
Genji Qin et al. www.cell-research.com | Cell Research
Light is one of the most important environmental factors for plants, as it provides the source of energy for plant
Role of the MPN Subunits in COP9 Signalosome Assembly and Activity, and Their Regulatory Interaction with
Journal of Integrative Plant Biology 2007, 49 (1): 120-126 Received 22 Sept. 2006 Accepted 1 Oct. 2006
An auxin-inducible F-box protein CEGENDUO negatively regulates auxin-mediated lateral root formation in Arabidopsis
Arabidopsis CONSTANS-LIKE3 Is a Positive Regulator of Red Light Signaling and Root Growth W
Conservation and Divergence of Light-Regulated Genome Expression Patterns during Seedling Development in Rice
An annotation update via cDNA sequence analysis and comprehensive profiling of developmental, hormonal or environmental responsiveness
A microarray analysis of the rice transcriptome and its comparison to Arabidopsis
It runs in the family: regulation of brassinosteroid signaling by the BZR1BES1 class of transcription
N-Terminal DomainMediated Homodimerization Is Required for Photoreceptor Activity of Arabidopsis
Arabidopsis Has Two Redundant Cullin3 Proteins That Are Essential for Embryo Development and That Interact with
TECHNICAL ADVANCE An alternative tandem affinity purification strategy applied to
The Arabidopsis CSN5A and CSN5B Subunits Are Present in Distinct COP9 Signalosome Complexes, and Mutations
Gene structure and embryonic expression of mouse COP9 signalosome subunit 8 (Csn8)
RESEARCH COMMUNICATION The COP1SPA1 interaction
Plant Molecular Biology 53: 467478, 2003. 2003 Kluwer Academic Publishers. Printed in the Netherlands.
Phosphate Starvation Triggers Distinct Alterations of Genome Expression in Arabidopsis Roots and Leaves1[w]
Correspondence Evidence for a
The Plant Cell, Vol. 15, 10831094, May 2003, www.plantcell.org 2003 American Society of Plant Biologists The COP9 Signalosome Interacts Physically with SCFCOI1 and
The Plant Cell, Vol. 15, 10711082, May 2003, www.plantcell.org 2003 American Society of Plant Biologists The COP9 Signalosome Interacts with SCFUFO and Participates in
Dissecting the phytochrome A-dependent signaling network in
Light regulated modulation of Z-box containing promoters by photoreceptors and downstream regulatory
The Plant Cell, Vol. 14, 14831496, July 2002, www.plantcell.org 2002 American Society of Plant Biologists Role of SCF Ubiquitin-Ligase and the COP9 Signalosome in
Biochemical evidence for ubiquitin ligase activity of the Arabidopsis COP1 interacting protein 8 (CIP8)
Two interacting bZIP proteins are direct targets of COP1-mediated control
Molecular Biology of the Cell Vol. 13, 646655, February 2002
The Plant Cell, Vol. 13, 25892607, December 2001, www.plantcell.org 2001 American Society of Plant Biologists Light Control of Arabidopsis Development Entails Coordinated
INTRODUCTION The COP9 signalosome was originally identified as a repressor
The Plant Cell, Vol. 13, 19831986, September 2001, www.plantcell.org 2001 American Society of Plant Biologists The field of plant photobiology has
The Plant Cell, Vol. 13, 16391651, July 2001, www.plantcell.org 2001 American Society of Plant Biologists Overexpression of the Heterotrimeric G-Protein -Subunit
18. H. M. O. Leyser, F. B. Pickett, S. Dharmasiri, M. Estelle, Plant J. 10, 403 (1996).
Molecular Cloning of a Novel Importin Homologue from Rice, by Which Constitutive Photomorphogenic 1 (COP1) Nuclear
The Plant Cell, Vol. 13, 399411, February 2001, www.plantcell.org 2001 American Society of Plant Physiologists CIP4, a New COP1 Target, Is a Nucleus-Localized Positive
Molecular Biology of the Cell Vol. 12, 383392, February 2001
Scientific Correspondence The Roles of Photoreceptor Systems and the COP1-
A gain-of-function phenotype conferred by over-expression of functional subunits of the COP9 signalosome in
FIN219, an auxin-regulated gene, defines a link between phytochrome A and the
Xing-Wang Deng xingwang.deng@
SHORT COMMUNICATION The N-terminal fragment of Arabidopsis photomorphogenic
Protein nucleocytoplasmic transport and its light regulation in plants
Characterization of Two Subunits of Arabidopsis 19S Proteasome Regulatory Complex and its Possible
The EMBO Journal Vol.17 No.19 pp.55775587, 1998 Functional dissection of Arabidopsis COP1 reveals
Brief Communication 919 The COP9 complex is conserved between plants and mammals
Molecular Cell, Vol. 1, 213222, January, 1998, Copyright 1998 by Cell Press Molecular Interaction between COP1 and HY5
The Plant Cell, Vol. 13, 23932407, November 2001, www.plantcell.org 2001 American Society of Plant Biologists RESEARCH ARTICLE
Dynamic Histone Modifications in Light-Regulated Gene Expression
Abstract Most plant cells retain the capacity to dif-ferentiate into all the other cell and organ types that
INTRODUCTION Arabidopsis seedlings follow two distinct development
The Plant Cell, Vol. 10, 10831094, July 1998, www.plantcell.org 1998 American Society of Plant Physiologists RESEARCH ARTICLE
This article appeared in a journal published by Elsevier. The attached copy is furnished to the author for internal non-commercial research
The International Journal of Biochemistry & Cell Biology xxx (2006) xxxxxx Short communication
Genome-wide mapping of the HY5-mediated gene networks in Arabidopsis that involve both transcriptional
948 | DECEMBER 2003 | VOLUME 4 www.nature.com/reviews/genetics R E V I E W S
Arabidopsis COP10 forms a complex with DDB1 and DET1 in vivo
Rice functional genomics research in China Bin Han1,7,*, Yongbiao Xue2
The Plant Cell, Vol. 10, 17791790, November 1998, www.plantcell.org 1998 American Society of Plant Physiologists RESEARCH ARTICLE
BMC Bioinformatics This Provisional PDF corresponds to the article as it appeared upon acceptance. The fully-formatted
Histone Modifications and Expression of Light-Regulated Genes in Arabidopsis Are Cooperatively Influenced
Cell, Vol. 86, 115121, July 12, 1996, Copyright 1996 by Cell Press The COP9 Complex,
COP9 signalosome subunit 8 is essential for peripheral T cell homeostasis and antigen receptorinduced entry
The Plant Cell, Vol. 11, 19671979, October 1999, www.plantcell.org 1999 American Society of Plant Physiologists Arabidopsis cop8 and fus4 Mutations Define the Same Gene
Arabidopsis Transcription Factor ELONGATED HYPOCOTYL5 Plays a Role in the Feedback Regulation of
Global genome expression analysis of rice in response to drought and high-salinity stresses in shoot, flag leaf, and panicle
Biochem. J. (2009) 418, 683690 (Printed in Great Britain) doi:10.1042/BJ20081943 683 Effect of Arabidopsis COP10 ubiquitin E2 enhancement activity across E2
1040-2519/96/0601-0215$08.00 215 Annu. Rev. Plant Physiol. Plant Mol. Biol. 1996. 47:21543
PP62CH21-Deng ARI 13 March 2011 0:50 The Epigenome and
RESEARCH ARTICLES Analysis of Transcription Factor HY5 Genomic Binding Sites
RESEARCH ARTICLES A Tiling Microarray Expression Analysis of Rice Chromosome
Arabidopsis CAND1, an Unmodified CUL1-Interacting Protein, Is Involved in Multiple Developmental Pathways Controlled
Gene 221 (1998) 3543 Cloning vectors for the expression of green fluorescent protein fusion
www.cell-research.com | Cell Research Lan Guo et al.
A Genome-Wide Analysis of Blue-Light Regulation of Arabidopsis Transcription Factor Gene Expression during
Plant Biotechnology Journal (2005) 3, pp. 157164 doi: 10.1111/j.1467-7652.2004.00107.x 2005 Blackwell Publishing Ltd 157
Analysis of oligo hybridization properties by high-resolution tiling microarrays in rice Analysisofoligohybridization
Rapid and reliable detection of 11 food-borne pathogens using thin-film biosensor chips
Journal of Integrative Plant Biology 2010, 52 (11): 971980 Research Article
Geminiviruses Subvert Ubiquitination by Altering CSN-Mediated Derubylation of SCF E3 Ligase Complexes
Coordinated regulation of Arabidopsis thaliana development by light and gibberellins
L E T T E R S Coordinated transcriptional regulation underlying the
The Plant Cell, Vol. 12, 2299, December 2000, www.plantcell.org 2000 American Society of Plant Physiologists IN THIS ISSUE
Global Identification and Characterization of Transcriptionally Active Regions in the Rice Genome
Arabidopsis COP1 shapes the temporal pattern of CO accumulation conferring a photoperiodic
Possible role of light in the maintenance of EIN3/EIL1 stability in Arabidopsis seedlings
Light Regulates COP1-Mediated Degradation of HFR1, a Transcription Factor Essential for Light Signaling
BioMed Central Page 1 of 10
Vol. 22 no. 23 2006, pages 29552957 doi:10.1093/bioinformatics/btl525BIOINFORMATICS APPLICATIONS NOTE
Plant Biology Research Comes of Age in China Haodong Chen,a,b,c Valerie J. Karplus,b Hong Ma,d and Xing Wang Denga,b,c
Promotion of photomorphogenesis by COP1 Herna n E. Boccalandro1
change in the past. However, historical cli-mate changes were generally much slower
DOI 10.1007/s00425-011-1458-0 ORIGINAL ARTICLE
Plant ubiquitin-proteasome pathway and its role in gibberellin signaling
Molecular Cell The Photomorphogenic Protein, DE-ETIOLATED 1,
BioOne sees sustainable scholarly publishing as an inherently collaborative enterprise connecting authors, nonprofit publishers, academic institutions, research libraries, and research funders in the common goal of maximizing access to critical research.
Genome-Wide Binding Site Analysis of FAR-RED ELONGATED HYPOCOTYL3 Reveals Its Novel
ORIGINAL PAPER Development and application of a set of breeder-friendly SNP
Molecular Cell Interaction of Arabidopsis DET1 with CCA1