Cryptochromes Interact Directly with PIFs to Control Plant Growth in Limiting Blue Light

[1]  Harry Smith,et al.  Light Quality, Photoperception, and Plant Strategy , 1982 .

[2]  AC Tose.  Cell , 1993, Cell.

[3]  Mutations in the gene for the red/far-red light receptor phytochrome B alter cell elongation and physiological responses throughout Arabidopsis development. , 1993, The Plant cell.

[4]  Derekt . A. Lamport,et al.  Extensin: repetitive motifs, functional sites, post-translational codes, and phylogeny. , 1994, The Plant journal : for cell and molecular biology.

[5]  S. Clough,et al.  Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. , 1998, The Plant journal : for cell and molecular biology.

[6]  T. Mockler,et al.  Enhancement of blue-light sensitivity of Arabidopsis seedlings by a blue light receptor cryptochrome 2. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[7]  Thomas K. Darlington,et al.  Light-dependent sequestration of TIMELESS by CRYPTOCHROME. , 1999, Science.

[8]  T. Mockler,et al.  Antagonistic actions of Arabidopsis cryptochromes and phytochrome B in the regulation of floral induction. , 1999, Development.

[9]  C. Ballaré,et al.  Keeping up with the neighbours: phytochrome sensing and other signalling mechanisms. , 1999, Trends in plant science.

[10]  E. Huq,et al.  Direct targeting of light signals to a promoter element-bound transcription factor. , 2000, Science.

[11]  S. Kay,et al.  Functional interaction of phytochrome B and cryptochrome 2 , 2000, Nature.

[12]  A Hall,et al.  Circadian clock-regulated expression of phytochrome and cryptochrome genes in Arabidopsis. , 2001, Plant physiology.

[13]  J. Casal,et al.  Interactive signalling by phytochromes and cryptochromes generates de‐etiolation homeostasis in Arabidopsis thaliana , 2001 .

[14]  Richard C. Moore,et al.  The growing world of expansins. , 2002, Plant & cell physiology.

[15]  Hongwei Guo,et al.  Plant Responses to Ethylene Gas Are Mediated by SCFEBF1/EBF2-Dependent Proteolysis of EIN3 Transcription Factor , 2003, Cell.

[16]  Klaus Harter,et al.  Visualization of protein interactions in living plant cells using bimolecular fluorescence complementation. , 2004, The Plant journal : for cell and molecular biology.

[17]  E. Huq,et al.  A Novel Molecular Recognition Motif Necessary for Targeting Photoactivated Phytochrome Signaling to Specific Basic Helix-Loop-Helix Transcription Factorsw⃞ , 2004, The Plant Cell Online.

[18]  N. Mochizuki,et al.  Phytochrome B in the Mesophyll Delays Flowering by Suppressing FLOWERING LOCUS T Expression in Arabidopsis Vascular Bundles , 2005, The Plant Cell Online.

[19]  J. Becker,et al.  A dynamic balance between gene activation and repression regulates the shade avoidance response in Arabidopsis. , 2005, Genes & development.

[20]  S. Berger,et al.  In vivo dual cross-linking for identification of indirect DNA-associated proteins by chromatin immunoprecipitation. , 2006, BioTechniques.

[21]  Trudie Allen,et al.  Phytochrome-mediated inhibition of shade avoidance involves degradation of growth-promoting bHLH transcription factors , 2007 .

[22]  Ullas V. Pedmale,et al.  Regulation of Phototropic Signaling in Arabidopsis via Phosphorylation State Changes in the Phototropin 1-interacting Protein NPH3* , 2007, Journal of Biological Chemistry.

[23]  Xuanming Liu,et al.  Arabidopsis Cryptochrome 2 Completes Its Posttranslational Life Cycle in the Nucleus[W] , 2007, The Plant Cell Online.

[24]  N. Mochizuki,et al.  CRYPTOCHROME2 in Vascular Bundles Regulates Flowering in Arabidopsis , 2007, The Plant Cell Online.

[25]  Filip Vandenbussche,et al.  Cryptochrome Blue Light Photoreceptors Are Activated through Interconversion of Flavin Redox States* , 2007, Journal of Biological Chemistry.

[26]  S. Rusconi,et al.  Interaction of circadian clock proteins PER2 and CRY with BMAL1 and CLOCK , 2008, BMC Molecular Biology.

[27]  Stacey L. Harmer,et al.  Rhythmic growth explained by coincidence between internal and external cues , 2007, Nature.

[28]  S. Conway,et al.  Mutations within Helix I of Twist1 Result in Distinct Limb Defects and Variation of DNA Binding Affinities* , 2007, Journal of Biological Chemistry.

[29]  Joanne Chory,et al.  Rapid Synthesis of Auxin via a New Tryptophan-Dependent Pathway Is Required for Shade Avoidance in Plants , 2008, Cell.

[30]  Clifford A. Meyer,et al.  Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.

[31]  K. Ljung,et al.  Requirement of B2-Type Cyclin-Dependent Kinases for Meristem Integrity in Arabidopsis thaliana[W][OA] , 2008, The Plant Cell Online.

[32]  Chentao Lin,et al.  Photoexcited CRY2 Interacts with CIB1 to Regulate Transcription and Floral Initiation in Arabidopsis , 2008, Science.

[33]  C. Fankhauser,et al.  Phytochrome-mediated inhibition of shade avoidance involves degradation of growth-promoting bHLH transcription factors. , 2007, The Plant journal : for cell and molecular biology.

[34]  R. Pierik,et al.  Auxin and Ethylene Regulate Elongation Responses to Neighbor Proximity Signals Independent of Gibberellin and DELLA Proteins in Arabidopsis1[C][W][OA] , 2009, Plant Physiology.

[35]  Z. Avramova,et al.  Wall-modifying genes regulated by the Arabidopsis homolog of trithorax, ATX1: repression of the XTH33 gene as a test case. , 2009, The Plant journal : for cell and molecular biology.

[36]  Olivier Michielin,et al.  Inhibition of the shade avoidance response by formation of non‐DNA binding bHLH heterodimers , 2009, The EMBO journal.

[37]  N. Harberd,et al.  High Temperature-Mediated Adaptations in Plant Architecture Require the bHLH Transcription Factor PIF4 , 2009, Current Biology.

[38]  Renaud Gaujoux,et al.  A flexible R package for nonnegative matrix factorization , 2010, BMC Bioinformatics.

[39]  Mikael Bodén,et al.  MEME Suite: tools for motif discovery and searching , 2009, Nucleic Acids Res..

[40]  David S. Lapointe,et al.  ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data , 2010, BMC Bioinformatics.

[41]  T. Mizuno,et al.  PHYTOCHROME-INTERACTING FACTORS PIF4 and PIF5 Are Implicated in the Regulation of Hypocotyl Elongation in Response to Blue Light in Arabidopsis thaliana , 2010, Bioscience, biotechnology, and biochemistry.

[42]  R. Pierik,et al.  Auxin transport through PIN-FORMED 3 (PIN3) controls shade avoidance and fitness during competition , 2010, Proceedings of the National Academy of Sciences.

[43]  J. Chory.  Light signal transduction: an infinite spectrum of possibilities. , 2010, The Plant journal : for cell and molecular biology.

[44]  R. Pierik,et al.  Physiological regulation and functional significance of shade avoidance responses to neighbors , 2010, Plant signaling & behavior.

[45]  Aaron R. Quinlan,et al.  Bioinformatics Applications Note Genome Analysis Bedtools: a Flexible Suite of Utilities for Comparing Genomic Features , 2022 .

[46]  J. Casal,et al.  Cryptochrome as a Sensor of the Blue/Green Ratio of Natural Radiation in Arabidopsis1[C][W][OA] , 2010, Plant Physiology.

[47]  Zhou Du,et al.  agriGO: a GO analysis toolkit for the agricultural community , 2010, Nucleic Acids Res..

[48]  J. Botto,et al.  AtBBX21 and COP1 genetically interact in the regulation of shade avoidance. , 2010, The Plant journal : for cell and molecular biology.

[49]  Mark D. Robinson,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[50]  L. Farinelli,et al.  Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP) , 2010, Nature Protocols.

[51]  Steve A. Kay,et al.  The ELF4-ELF3-LUX Complex Links the Circadian Clock to Diurnal Control of Hypocotyl Growth , 2011, Nature.

[52]  R. Pierik,et al.  Blue-light-mediated shade avoidance requires combined auxin and brassinosteroid action in Arabidopsis seedlings. , 2011, The Plant journal : for cell and molecular biology.

[53]  Philip Machanick,et al.  MEME-ChIP: motif analysis of large DNA datasets , 2011, Bioinform..

[54]  C. Ballaré,et al.  Cryptochrome 1 and phytochrome B control shade-avoidance responses in Arabidopsis via partially independent hormonal cascades , 2011, The Plant journal : for cell and molecular biology.

[55]  J. Chory,et al.  Tyrosine phosphorylation controls brassinosteroid receptor activation by triggering membrane release of its kinase inhibitor. , 2011, Genes & development.

[56]  Christian S. Hardtke,et al.  Hormone Signalling Crosstalk in Plant Growth Regulation , 2011, Current Biology.

[57]  Jaak Vilo,et al.  g:Profiler—a web server for functional interpretation of gene lists (2011 update) , 2011, Nucleic Acids Res..

[58]  S. Kay,et al.  Automated analysis of hypocotyl growth dynamics during shade avoidance in Arabidopsis. , 2011, The Plant journal : for cell and molecular biology.

[59]  A. Nagatani,et al.  Tissue-Autonomous Promotion of Palisade Cell Development by Phototropin 2 in Arabidopsis[W] , 2011, Plant Cell.

[60]  Jorge J Casal,et al.  Shade Avoidance , 2012, The arabidopsis book.

[61]  Robert J. Schmitz,et al.  Linking photoreceptor excitation to changes in plant architecture. , 2012, Genes & development.

[62]  M. Thomashow,et al.  Photoperiodic regulation of the C-repeat binding factor (CBF) cold acclimation pathway and freezing tolerance in Arabidopsis thaliana , 2012, Proceedings of the National Academy of Sciences.

[63]  Cole Trapnell,et al.  TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.

[64]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[65]  Jeongmoo Park,et al.  Phytochrome B inhibits binding of phytochrome-interacting factors to their target promoters. , 2012, The Plant journal : for cell and molecular biology.

[66]  I. Xenarios,et al.  Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling. , 2012, The Plant journal : for cell and molecular biology.

[67]  C. Schwechheimer,et al.  D6PK AGCVIII Kinases Are Required for Auxin Transport and Phototropic Hypocotyl Bending in Arabidopsis[C][W] , 2013, Plant Cell.

[68]  T. Speed,et al.  A Quartet of PIF bHLH Factors Provides a Transcriptionally Centered Signaling Hub That Regulates Seedling Morphogenesis through Differential Expression-Patterning of Shared Target Genes in Arabidopsis , 2013, PLoS genetics.

[69]  Caleb Webber,et al.  GAT: a simulation framework for testing the association of genomic intervals , 2013, Bioinform..

[70]  J. Yates,et al.  Tyrosine phosphorylation regulates the activity of phytochrome photoreceptors. , 2013, Cell reports.

[71]  P. Leivar,et al.  PIFs: Systems Integrators in Plant Development[W] , 2014, Plant Cell.

[72]  M. Hersch,et al.  Light intensity modulates the regulatory network of the shade avoidance response in Arabidopsis , 2014, Proceedings of the National Academy of Sciences.

[73]  Fidel Ramírez,et al.  deepTools: a flexible platform for exploring deep-sequencing data , 2014, Nucleic Acids Res..

[74]  Eunkyoo Oh,et al.  Cell elongation is regulated through a central circuit of interacting transcription factors in the Arabidopsis hypocotyl , 2014, eLife.

[75]  F. Harmon,et al.  The time of day effects of warm temperature on flowering time involve PIF4 and PIF5 , 2014, Journal of experimental botany.

[76]  A. Burlingame,et al.  A mutually assured destruction mechanism attenuates light signaling in Arabidopsis , 2014, Science.

[77]  K. Vissenberg,et al.  The Arabidopsis thaliana hypocotyl, a model to identify and study control mechanisms of cellular expansion , 2014, Plant Cell Reports.

[78]  X. Deng,et al.  Arabidopsis Phytochrome A Directly Targets Numerous Promoters for Individualized Modulation of Genes in a Wide Range of Pathways[W] , 2014, Plant Cell.

[79]  S. Hazen,et al.  PIL1 participates in a negative feedback loop that regulates its own gene expression in response to shade. , 2014, Molecular plant.

[80]  Paul Theodor Pyl,et al.  HTSeq—a Python framework to work with high-throughput sequencing data , 2014, bioRxiv.