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Dawn and photoperiod sensing by phytochrome A

https://doi.org/10.1073/pnas.1803398115
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1016/j.cell.2011.07.023openalex-snapshot
Photoconversion and Nuclear Trafficking Cycles Determine Phytochrome A's Response Profile to Far-Red Light
inferredcites →https://doi.org/10.1016/j.cell.2016.04.038openalex-snapshot
Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape
inferredcites →https://doi.org/10.1016/j.jplph.2007.06.010openalex-snapshot
Expression analysis of anthocyanin regulatory genes in response to different light qualities in Arabidopsis thaliana
inferredcites →https://doi.org/10.1016/j.plantsci.2013.11.013openalex-snapshot
Shedding (far-red) light on phytochrome mechanisms and responses in land plants
inferredcites →https://doi.org/10.1016/j.preteyeres.2004.03.001openalex-snapshot
Dark adaptation and the retinoid cycle of vision
inferredcites →https://doi.org/10.1016/j.tplants.2010.08.003openalex-snapshot
PIFs: pivotal components in a cellular signaling hub
inferredcites →https://doi.org/10.1038/35013076openalex-snapshot
Targeted destabilization of HY5 during light-regulated development of Arabidopsis
inferredcites →https://doi.org/10.1038/msb.2012.6openalex-snapshot
The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops
inferredcites →https://doi.org/10.1038/nature00996openalex-snapshot
Molecular basis of seasonal time measurement in Arabidopsis
inferredcites →https://doi.org/10.1038/nature01696openalex-snapshot
LAF1 ubiquitination by COP1 controls photomorphogenesis and is stimulated by SPA1
inferredcites →https://doi.org/10.1038/nature05946openalex-snapshot
Rhythmic growth explained by coincidence between internal and external cues
inferredcites →https://doi.org/10.1038/nature10182openalex-snapshot
The ELF4–ELF3–LUX complex links the circadian clock to diurnal control of hypocotyl growth
inferredcites →https://doi.org/10.1038/ncb2545openalex-snapshot
Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses
inferredcites →https://doi.org/10.1038/ng767openalex-snapshot
A QTL for flowering time in Arabidopsis reveals a novel allele of CRY2
inferredcites →https://doi.org/10.1038/nrg3976openalex-snapshot
Integrating circadian dynamics with physiological processes in plants
inferredcites →https://doi.org/10.1073/pnas.0437826100openalex-snapshot
Regulation of photoperiodic flowering by Arabidopsis photoreceptors
inferredcites →https://doi.org/10.1073/pnas.0803611105openalex-snapshot
PIF1 directly and indirectly regulates chlorophyll biosynthesis to optimize the greening process in Arabidopsis
inferredcites →https://doi.org/10.1073/pnas.1002352107openalex-snapshot
Fold-change detection and scalar symmetry of sensory input fields
inferredcites →https://doi.org/10.1073/pnas.1302170110openalex-snapshot
LNK genes integrate light and clock signaling networks at the core of the Arabidopsis oscillator
inferredcites →https://doi.org/10.1073/pnas.1412528111openalex-snapshot
Photoreceptor partner FHY1 has an independent role in gene modulation and plant development under far-red light
inferredcites →https://doi.org/10.1073/pnas.1601309113openalex-snapshot
Photoreceptor effects on plant biomass, resource allocation, and metabolic state
inferredcites →https://doi.org/10.1073/pnas.161300998openalex-snapshot
Multiple transcription-factor genes are early targets of phytochrome A signaling
inferredcites →https://doi.org/10.1073/pnas.93.15.8129openalex-snapshot
Action spectra for phytochrome A- and B-specific photoinduction of seed germination in Arabidopsis thaliana.
inferredcites →https://doi.org/10.1093/bioinformatics/btu399openalex-snapshot
TRES predicts transcription control in embryonic stem cells
inferredcites →https://doi.org/10.1093/emboj/19.18.4997openalex-snapshot
HY5 stability and activity in Arabidopsis is regulated by phosphorylation in its COP1 binding domain
inferredcites →https://doi.org/10.1093/jb/mvw031openalex-snapshot
Phytochrome-interacting ankyrin repeat protein 2 modulates phytochrome A-mediated PIF3 phosphorylation in light signal transduction
inferredcites →https://doi.org/10.1093/jxb/ert379openalex-snapshot
Light perception and signalling by phytochrome A
inferredcites →https://doi.org/10.1093/mp/sst060openalex-snapshot
Phytochrome-Interacting Factors (PIFs) as Bridges between Environmental Signals and the Circadian Clock: Diurnal Regulation of Growth and Development
inferredcites →https://doi.org/10.1093/mp/ssu078openalex-snapshot
Phytochrome A Antagonizes PHYTOCHROME INTERACTING FACTOR 1 to Prevent Over-Activation of Photomorphogenesis
inferredcites →https://doi.org/10.1093/mp/ssu087openalex-snapshot
Combinatorial Complexity in a Transcriptionally Centered Signaling Hub in Arabidopsis
inferredcites →https://doi.org/10.1093/nar/gkw377openalex-snapshot
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update
inferredcites →https://doi.org/10.1093/nar/gkx1279openalex-snapshot
TF2Network: predicting transcription factor regulators and gene regulatory networks in Arabidopsis using publicly available binding site information
inferredcites →https://doi.org/10.1093/pcp/pci175openalex-snapshot
Functional Characterization of Phytochrome Interacting Factor 3 for the Arabidopsis thaliana Circadian Clockwork
inferredcites →https://doi.org/10.1093/pcp/pcj087openalex-snapshot
FHY1 and FHL Act Together to Mediate Nuclear Accumulation of the Phytochrome A Photoreceptor
inferredcites →https://doi.org/10.1093/pcp/pcr076openalex-snapshot
PHYTOCHROME-INTERACTING FACTOR 4 and 5 (PIF4 and PIF5) Activate the Homeobox ATHB2 and Auxin-Inducible IAA29 Genes in the Coincidence Mechanism Underlying Photoperiodic Control of Plant Growth of Arabidopsis thaliana
inferredcites →https://doi.org/10.1093/pcp/pcs137openalex-snapshot
Circadian Clock- and PIF4-Controlled Plant Growth: A Coincidence Mechanism Directly Integrates a Hormone Signaling Network into the Photoperiodic Control of Plant Architectures in Arabidopsis thaliana
inferredcites →https://doi.org/10.1093/pcp/pct042openalex-snapshot
Three Transcription Factors, HFR1, LAF1 and HY5, Regulate Largely Independent Signaling Pathways Downstream of Phytochrome A
inferredcites →https://doi.org/10.1101/gad.1247205openalex-snapshot
HFR1 is targeted by COP1 E3 ligase for post-translational proteolysis during phytochrome A signaling
inferredcites →https://doi.org/10.1104/pp.005389openalex-snapshot
Patterns of Expression and Normalized Levels of the Five Arabidopsis Phytochromes
inferredcites →https://doi.org/10.1104/pp.010294openalex-snapshot
Conditional Circadian Regulation of PHYTOCHROME A Gene Expression
inferredcites →https://doi.org/10.1104/pp.010467openalex-snapshot
Circadian Clock-Regulated Expression of Phytochrome and Cryptochrome Genes in Arabidopsis
inferredcites →https://doi.org/10.1104/pp.118.1.27openalex-snapshot
Genetic Interactions between Phytochrome A, Phytochrome B, and Cryptochrome 1 during Arabidopsis Development1
inferredcites →https://doi.org/10.1104/pp.16.01484openalex-snapshot
Photoperiod Affects the Phenotype of Mitochondrial Complex I Mutants
inferredcites →https://doi.org/10.1105/tpc.106.047688openalex-snapshot
Analysis of Transcription Factor HY5 Genomic Binding Sites Revealed Its Hierarchical Role in Light Regulation of Development
inferredcites →https://doi.org/10.1105/tpc.109.070672openalex-snapshot
Definition of Early Transcriptional Circuitry Involved in Light-Induced Reversal of PIF-Imposed Repression of Photomorphogenesis in YoungArabidopsisSeedlings
inferredcites →https://doi.org/10.1105/tpc.112.095711openalex-snapshot
Dynamic Antagonism between Phytochromes and PIF Family Basic Helix-Loop-Helix Factors Induces Selective Reciprocal Responses to Light and Shade in a Rapidly Responsive Transcriptional Network in Arabidopsis
inferredcites →https://doi.org/10.1105/tpc.114.123950openalex-snapshot
Arabidopsis Phytochrome A Directly Targets Numerous Promoters for Individualized Modulation of Genes in a Wide Range of Pathways
inferredcites →https://doi.org/10.1105/tpc.9.10.1727openalex-snapshot
Attenuation of phytochrome A and B signaling pathways by the Arabidopsis circadian clock.
inferredcites →https://doi.org/10.1111/j.1365-313x.2006.02914.xopenalex-snapshot
phyA dominates in transduction of red‐light signals to rapidly responding genes at the initiation of Arabidopsis seedling de‐etiolation
inferredcites →https://doi.org/10.1111/j.1365-313x.2009.03971.xopenalex-snapshot
Phytochrome interacting factors 4 and 5 redundantly limit seedling de‐etiolation in continuous far‐red light
inferredcites →https://doi.org/10.1111/j.1365-313x.2012.05033.xopenalex-snapshot
Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling
inferredcites →https://doi.org/10.1111/j.1365-313x.2012.05114.xopenalex-snapshot
Phytochrome B inhibits binding of phytochrome‐interacting factors to their target promoters
inferredcites →https://doi.org/10.1111/pce.12754openalex-snapshot
Photoperiod‐dependent changes in the phase of core clock transcripts and global transcriptional outputs at dawn and dusk in Arabidopsis
inferredcites →https://doi.org/10.1111/tpj.13022openalex-snapshot
Phosphorylation of CONSTANS and its COP 1‐dependent degradation during photoperiodic flowering of Arabidopsis
inferredcites →https://doi.org/10.1126/science.282.5393.1488openalex-snapshot
Phytochromes and Cryptochromes in the Entrainment of the Arabidopsis Circadian Clock
inferredcites →https://doi.org/10.1177/074873001129002213openalex-snapshot
Resetting of the Circadian Clock by Phytochromes and Cryptochromes in Arabidopsis
inferredcites →https://doi.org/10.1371/journal.pbio.0060225openalex-snapshot
A Morning-Specific Phytohormone Gene Expression Program underlying Rhythmic Plant Growth
inferredcites →https://doi.org/10.1371/journal.pgen.1003244openalex-snapshot
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
inferredcites →https://doi.org/10.15252/msb.20145766openalex-snapshot
Linked circadian outputs control elongation growth and flowering in response to photoperiod and temperature
inferredcites →https://doi.org/10.4161/psb.6.11.17613openalex-snapshot
Influence of abiotic stress signals on secondary metabolites in plants
inferredcites →https://doi.org/10.7554/elife.02009openalex-snapshot
Transport of soluble proteins through the Golgi occurs by diffusion via continuities across cisternae
inferredcites →https://doi.org/10.7554/elife.03031openalex-snapshot
Cell elongation is regulated through a central circuit of interacting transcription factors in the Arabidopsis hypocotyl

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.2139/ssrn.4058205openalex-extracted
Light and Carbohydrate Signaling Genes Co-Regulate Carotenoid Accumulation in the Endocarp of Cucumber Fruit Under Photoperiodic Treatment as Revealed by Transcriptomic Analysis
inferred← citeshttps://doi.org/10.1002/csc2.21062openalex-snapshot
Spring wheat canopy effects on light dynamics and yield of intercropped fine fescues
inferred← citeshttps://doi.org/10.1007/s11103-024-01455-8openalex-snapshot
Petunia PHYTOCHROME INTERACTING FACTOR 4/5 transcriptionally activates key regulators of floral scent
inferred← citeshttps://doi.org/10.1007/s11756-021-00976-7openalex-snapshot
Expression analyses of soluble starch synthase and starch branching enzyme isoforms in stem and leaf tissues under different photoperiods in lentil (Lens culinaris Medik.)
inferred← citeshttps://doi.org/10.1007/s12298-022-01186-4openalex-snapshot
Comparative transcriptome analysis provides insight into the molecular mechanisms of long-day photoperiod in Moringa oleifera
inferred← citeshttps://doi.org/10.1007/s13562-026-01062-2openalex-snapshot
Functional characterization of photo-thermo-insensitive traits in chickpea through integrated morpho-physiological and gene expression analyses
inferred← citeshttps://doi.org/10.1016/j.aquaculture.2023.739253openalex-snapshot
Efficient methods of seedling culture and cultivation of the economic macroalga Scytosiphon lomentaria (Phaeophyta): A systematic review
inferred← citeshttps://doi.org/10.1016/j.envexpbot.2026.106328openalex-snapshot
Circadian clock regulation of low R/FR light signaling and photosynthetic cross-talk in crop development
inferred← citeshttps://doi.org/10.1016/j.molp.2020.02.006openalex-snapshot
Light Perception: A Matter of Time
inferred← citeshttps://doi.org/10.1016/j.molp.2021.03.019openalex-snapshot
An early-morning gene network controlled by phytochromes and cryptochromes regulates photomorphogenesis pathways in Arabidopsis
inferred← citeshttps://doi.org/10.1016/j.ncrops.2024.100028openalex-snapshot
The hormonal, metabolic, and environmental regulation of plant shoot branching
inferred← citeshttps://doi.org/10.1016/j.plantsci.2024.112050openalex-snapshot
Plant-specific environmental and developmental signals regulate the mismatch repair protein MSH6 in Arabidopsis thaliana
inferred← citeshttps://doi.org/10.1016/j.plaphy.2022.10.020openalex-snapshot
Summer dormancy of Myricaria laxiflora to escape flooding stress: Changes in phytohormones and enzymes induced by environmental factors
inferred← citeshttps://doi.org/10.1016/j.scienta.2024.113337openalex-snapshot
Effect of different photoperiods on the period of maturity of hot peppers (Capsicum annuum L.) and their changes in color
inferred← citeshttps://doi.org/10.1016/j.scienta.2025.114463openalex-snapshot
Photoperiod and temperature treatments affect vegetative and reproductive growth of an everbearing blueberry genotype
inferred← citeshttps://doi.org/10.1016/j.xplc.2021.100265openalex-snapshot
WRKY2 and WRKY10 regulate the circadian expression of PIF4 during the day through interactions with CCA1/LHY and phyB
inferred← citeshttps://doi.org/10.1017/qpb.2021.8openalex-snapshot
What is quantitative plant biology?
inferred← citeshttps://doi.org/10.1038/s41467-019-13045-0openalex-snapshot
Molecular mechanisms underlying phytochrome-controlled morphogenesis in plants
inferred← citeshttps://doi.org/10.1038/s41467-025-65242-9openalex-snapshot
A circadian morning complex modulates far-red light signaling in Arabidopsis
inferred← citeshttps://doi.org/10.1038/s41598-025-00430-7openalex-snapshot
Transcriptomic analysis of CDL-gated photoperiodic flowering mechanisms in cannabis and their responsiveness to R: FR ratios in controlled environment agriculture
inferred← citeshttps://doi.org/10.1073/pnas.2512201123openalex-snapshot
Arabidopsis thaliana phytochrome A sensory properties in canopy shade
inferred← citeshttps://doi.org/10.1093/insilicoplants/diab022openalex-snapshot
Testing the inferred transcription rates of a dynamic, gene network model in absolute units
inferred← citeshttps://doi.org/10.1093/plcell/koac138openalex-snapshot
TIME FOR COFFEE regulates phytochrome A-mediated hypocotyl growth through dawn-phased signaling
inferred← citeshttps://doi.org/10.1093/plphys/kiad028openalex-snapshot
Phytochrome F mediates red light responsiveness additively with phytochromes B1 and B2 in tomato
inferred← citeshttps://doi.org/10.1093/plphys/kiad081openalex-snapshot
SCARECROW-like GRAS protein PES positively regulates petunia floral scent production
inferred← citeshttps://doi.org/10.1101/2021.03.11.434971openalex-snapshot
Effects of long-term high-temperature stress on reproductive growth and seed development in development in Brassica napus
inferred← citeshttps://doi.org/10.1101/2021.06.20.449137openalex-snapshot
Phytochrome gene expression studies: PHYE is required for FR-induced expression of PHYA and PHYD suppresses expression of PHYA
inferred← citeshttps://doi.org/10.1101/2022.10.05.510993openalex-snapshot
Diverse photoperiodic gene expression patterns are likely mediated by distinct transcriptional systems in Arabidopsis
inferred← citeshttps://doi.org/10.1101/2025.05.14.654025openalex-snapshot
Arabidopsis thaliana Phytochrome A Sensory Properties in Canopy Shade
inferred← citeshttps://doi.org/10.1101/2025.10.07.680213openalex-snapshot
PHYTOCHROME INTERACTING FACTOR 7 moderates the activity of phytochrome A in canopy shade conditions
inferred← citeshttps://doi.org/10.1111/pce.14367openalex-snapshot
Fillable and unfillable gaps in plant transcriptome under field and controlled environments
inferred← citeshttps://doi.org/10.1111/ppl.13092openalex-snapshot
PHYTOCHROME ‐ INTERACTING FACTORS at the interface of light and temperature signalling
inferred← citeshttps://doi.org/10.1111/tpj.15036openalex-snapshot
What is going on with the hormonal control of flowering in plants?
inferred← citeshttps://doi.org/10.1111/tpj.16279openalex-snapshot
CsMYBL2 homologs modulate the light and temperature stress‐regulated anthocyanin and catechins biosynthesis in tea plants (Camellia sinensis)
inferred← citeshttps://doi.org/10.1186/s12864-019-6247-3openalex-snapshot
Hybrid de novo transcriptome assembly of poinsettia (Euphorbia pulcherrima Willd. Ex Klotsch) bracts
inferred← citeshttps://doi.org/10.1371/journal.pbio.3002283openalex-snapshot
Systematic characterization of photoperiodic gene expression patterns reveals diverse seasonal transcriptional systems in Arabidopsis
inferred← citeshttps://doi.org/10.1371/journal.pgen.1012229openalex-snapshot
Photoperiodic patterns in miRNA-mRNA pairs and tRNA fragments revealed by time-course co-sequencing in Arabidopsis
inferred← citeshttps://doi.org/10.15252/embr.202256105openalex-snapshot
Shade‐induced lncRNA PUAR promotes shade response by repressing PHYA expression
inferred← citeshttps://doi.org/10.1590/2447-536x.v27i3.2338openalex-snapshot
Control of growth and flowering of chrysanthemum (Dendranthema x grandiflorum Kitam.) using day length extension and Red Light Night Break
inferred← citeshttps://doi.org/10.20868/upm.thesis.70305openalex-snapshot
Caracterización funcional de la subunidad EAF6 del complejo NuA4 en la regulación del tiempo de floración en Arabidopsis thaliana
inferred← citeshttps://doi.org/10.3389/fpls.2021.706316openalex-snapshot
Protein Kinase Activity of Phytochrome A Positively Correlates With Photoresponses in Arabidopsis
inferred← citeshttps://doi.org/10.3389/fpls.2021.769194openalex-snapshot
EARLY FLOWERING 3 and Photoperiod Sensing in Brachypodium distachyon
inferred← citeshttps://doi.org/10.3389/fpls.2022.844292openalex-snapshot
Long-Term High-Temperature Stress Impacts on Embryo and Seed Development in Brassica napus
inferred← citeshttps://doi.org/10.3389/fpls.2024.1340260openalex-snapshot
Functional dissection of phytochrome A in plants
inferred← citeshttps://doi.org/10.3389/fsufs.2022.856162openalex-snapshot
A Perspective Emphasizing Circadian Rhythm Entrainment to Ensure Sustainable Crop Production in Controlled Environment Agriculture: Dynamic Use of LED Cues
inferred← citeshttps://doi.org/10.3390/ijms20246165openalex-snapshot
Regulation of Photomorphogenic Development by Plant Phytochromes
inferred← citeshttps://doi.org/10.3390/ijms24032110openalex-snapshot
Regulation of Plant Photoresponses by Protein Kinase Activity of Phytochrome A
inferred← citeshttps://doi.org/10.3390/ijms25179357openalex-snapshot
CLAVATA3 Signaling Buffers Arabidopsis Shoot Apical Meristem Activity in Response to Photoperiod
inferred← citeshttps://doi.org/10.3390/plants14101533openalex-snapshot
Complex Signaling Networks Underlying Blue-Light-Mediated Floral Transition in Plants
inferred← citeshttps://doi.org/10.64898/2026.04.28.721246openalex-snapshot
Structural and coding variation in PHYTOCHROMES A and C underlies differences in flowering time and shade avoidance in wheat
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