Next Generation Sequencing Facilitates Quantitative Analysis of WT and cry1 cry2 in blue light or WT, cry2 and prr5 at ZT11 in 12/12 white light condition Transcriptomes
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE253941 | GEO | 2025/12/31
REPOSITORIES: GEO
Similar Datasets
Project description:Next Generation Sequencing Facilitates Quantitative Analysis of WT and cry1 cry2 in blue light or WT, cry2 and prr5 at ZT11 in 12/12 white light condition Transcriptomes
| PRJNA1067718 | ENA
Project description:Analysis of differential differential gene expression regulated by Blue light.
2025-01-06 | GSE232026 | GEO
Project description:Blue light receptors in Arabidopsis include two types of proteins, cryptochromes and phototropins. Previous studies have suggested that the cryptochromes cry1 and cry2 function mainly in photomorphogenic responses and that the phototropins phot1 and phot2 mainly regulate photo-induced movements. Receptors in the same family have redundant functions, although their responses to the fluence rate of blue light differ. To uncover functions of blue light receptors that may be concealed by their functional redundancy, we conducted analyses of combinatorial multiple mutants of blue light receptors. Comparison of the responses of the quadruple mutant cry1 cry2 phot1 phot2 to blue light with those of related triple mutants revealed that cryptochromes function in blue light-dependent, random hypocotyl-bending and that phototropins function in one photomorphogenic response, cotyledon expansion. Microarray analysis suggested that cry1 and cry2 independently function as key regulators of early blue light-induced genes, whereas phot1 and phot2 play subsidiary roles in transcriptional regulation by blue light.
| S-EPMC356932 | biostudies-literature
Project description:Light is a crucial exogenous signal sensed by cryptochrome (CRY) blue light receptors to modulate growth and the circadian clock in plants and animals. However, how CRYs interpret light quantity to regulate growth in plants remains poorly understood. Furthermore, CRY2 protein levels and activity are tightly regulated in light to fine-tune hypocotyl growth; however, details of the mechanisms that explain precise control of CRY2 levels are not fully understood. We show that in Arabidopsis, UBP12 and UBP13 deubiquitinases physically interact with CRY2 in light. UBP12/13 negatively regulates CRY2 by promoting its ubiquitination and turnover to modulate hypocotyl growth. Growth and development were explicitly affected in blue light when UBP12/13 were disrupted or overexpressed, indicating their role alongside CRY2. UBP12/13 also interacted with and stabilized COP1, which is partially required for CRY2 turnover. Our combined genetic and molecular data support a mechanistic model in which UBP12/13 interact with CRY2 and COP1, leading to the stabilization of COP1. Stabilized COP1 then promotes the ubiquitination and degradation of CRY2 under blue light. Despite decades of studies on deubiquitinases, the knowledge of how their activity is regulated is limited. Our study provides insight into how exogenous signals and ligands, along with their receptors, regulate deubiquitinase activity by protein-protein interaction. Collectively, our results provide a framework of cryptochromes and deubiquitinases to detect and interpret light signals to control plant growth at the most appropriate time.
2022-06-13 | GSE201685 | GEO
Project description:Sun-loving plants have the ability to detect and avoid shading through sensing of both blue and red light wavelengths. Higher plant cryptochromes (CRYs) control how plants modulate growth in response to changes in blue light. For growth under a canopy, where blue light is diminished, CRY1 and CRY2 perceive this change and respond by directly contacting two bHLH transcription factors, PIF4 and PIF5. These factors are also known to be controlled by phytochromes, the red/far-red photoreceptors; however, transcriptome analyses indicate that the gene regulatory programs induced by the different light wavelengths are distinct. Our results indicate that CRYs signal by modulating PIF activity genome-wide, and that these factors integrate binding of different plant photoreceptors to facilitate growth changes under different light conditions.
2015-12-31 | GSE68193 | GEO
Project description:Sun-loving plants have the ability to detect and avoid shading through sensing of both blue and red light wavelengths. Higher plant cryptochromes (CRYs) control how plants modulate growth in response to changes in blue light. For growth under a canopy, where blue light is diminished, CRY1 and CRY2 perceive this change and respond by directly contacting two bHLH transcription factors, PIF4 and PIF5. These factors are also known to be controlled by phytochromes, the red/far-red photoreceptors; however, transcriptome analyses indicate that the gene regulatory programs induced by the different light wavelengths are distinct. Our results indicate that CRYs signal by modulating PIF activity genome-wide, and that these factors integrate binding of different plant photoreceptors to facilitate growth changes under different light conditions.
2015-12-31 | GSE59699 | GEO
Project description:Sun-loving plants have the ability to detect and avoid shading through sensing of both blue and red light wavelengths. Higher plant cryptochromes (CRYs) control how plants modulate growth in response to changes in blue light. For growth under a canopy, where blue light is diminished, CRY1 and CRY2 perceive this change and respond by directly contacting two bHLH transcription factors, PIF4 and PIF5. These factors are also known to be controlled by phytochromes, the red/far-red photoreceptors; however, transcriptome analyses indicate that the gene regulatory programs induced by the different light wavelengths are distinct. Our results indicate that CRYs signal by modulating PIF activity genome-wide, and that these factors integrate binding of different plant photoreceptors to facilitate growth changes under different light conditions. We performed whole-genome chromatin immunoprecipitation with sequencing (ChIP-Seq) analysis on 5 day old Flash-CRY2, PIF4-Flash and PIF5-Flash treated in low blue-light for 16h.
2015-12-31 | E-GEOD-68193 | biostudies-arrayexpress
Project description:Plants use sunlight as a source of energy for photosynthesis but also as an important environmental cue to regulate growth, development and light acclimation. Wavelengths in the UV-B (280-315 nm) and UV-A/blue (315-500 nm) regions of the spectrum are perceived by UV RESISTANCE LOCUS 8 (UVR8) and cryptochromes (CRY1 and CRY2), respectively. Despite recent advances in our understanding of how these photoreceptors promote photomorphogenesis, very little is known about the molecular mechanisms regulated by UVR8 and CRYs in sunlight exposed plants. Here, a factorial experiment was designed to assess the roles of UVR8 and CRYs in regulating transcriptome wide changes, hormone accumulation, and growth competence of Arabidopsis thaliana plants exposed to solar UV-B, UV-A, and blue radiation.
2019-05-29 | GSE117199 | GEO
Project description:Sun-loving plants have the ability to detect and avoid shading through sensing of both blue and red light wavelengths. Higher plant cryptochromes (CRYs) control how plants modulate growth in response to changes in blue light. For growth under a canopy, where blue light is diminished, CRY1 and CRY2 perceive this change and respond by directly contacting two bHLH transcription factors, PIF4 and PIF5. These factors are also known to be controlled by phytochromes, the red/far-red photoreceptors; however, transcriptome analyses indicate that the gene regulatory programs induced by the different light wavelengths are distinct. Our results indicate that CRYs signal by modulating PIF activity genome-wide, and that these factors integrate binding of different plant photoreceptors to facilitate growth changes under different light conditions. We performed whole-genome transcriptome (mRNA-seq) analysis on 5-day-old Arabidopsis thaliana Columbia wild-type (WT) and pif4pif5 seedlings exposed to low blue-light (LBL) or mock-treated for 1, 6 and 24 hours. In addition we performed mRNA-seq on WT, 35S::PIF4-9xMyc-6x-His-3xFlag(Flash) and 35S::PIF5-9xMyc-6x-His-3xFlag (Flash) seedlings treated with LBL or mock-treated for 16 hours.
2015-12-31 | E-GEOD-59699 | biostudies-arrayexpress
Project description:Temperature increases as light intensity rises, but whether light signals can be directly linked to high temperature response in plants is unclear. Here, we find that light pre-treatment enables plants to survive better under high temperature, designated as light-induced thermotolerance (LIT). With short-term light treatment, plants induce light-signaling pathway genes and heat shock genes. Blue light photoreceptor cryptochrome 1 (CRY1) is required for LIT. We also find that CRY1 physically interacts with the heat shock transcription factor A1d (HsfA1d) and that HsfA1d is involved in thermotolerance under light treatment. Furthermore, CRY1 promotes HsfA1d nuclear localization through importin alpha 1 (IMPα1). Consistent with this, CRY1 shares more than half of the chromatin binding sites with HsfA1d. Mutation of CRY1 (cry1-304) diminishes a large number of HsfA1d binding sites that are shared with CRY1. We present a model where, by coupling light sensing to high-temperature stress, CRY1 confers thermotolerance in plants via HsfA1d.
| S-EPMC10591714 | biostudies-literature