PHYTOCHROME INTERACTING FACTORs trigger environmentally responsive chromatin dynamics
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PROVIDER: PRJNA579165 | ENA |
REPOSITORIES: ENA
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Project description:The pivotal interplay between light receptors and PHYTOCHROME-INTERACTING FACTORs (PIFs) serves as an essential regulatory hub that perceives and integrates environmental cues into the plant’s transcriptional networks. A critical control component of environmentally-responsive gene networks is the histone variant H2A.Z which provides transcriptional plasticity and prevents undesired gene activation. However, the functional relationship between PIF transcription factors (TFs) and H2A.Z is despite their outstanding importance, only poorly understood. Here, we describe a photo-genomic approach that utilizes the rapid and reversible light-mediated manipulation of PIF7 activity to visualize PIF7 DNA binding and H2A.Z occupancy kinetics on a genome-wide scale. Strikingly, we discovered that PIF shape the H2A.Z landscape in a light quality-dependent manner. We found that DNA binding of PIF7 is not regulated by H2A.Z but most importantly, PIFs initiate H2A.Z eviction and through the direct interaction with EIN6 ENHANCER (EEN), a crucial subunit of INO80 chromatin remodeling complex. Collectively, we describe a PIF-INO80 regulatory module that controls plant growth in response to environmental changes.
2021-04-30 | GSE139296 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE35057: Phytochrome Interacting Factor 4 and 5 regulate different set of genes in high and low red/far-red light GSE35059: ChIP-Seq analysis of Phytochrome Interacting Factor 5 DNA binding in low R/FR condition Refer to individual Series
2012-05-02 | E-GEOD-35062 | biostudies-arrayexpress
Project description:Phytochrome Interacting Factors 4 and 5
| PRJNA150937 | ENA
Project description:Phytochrome Interacting Factor 5 plays an important role in adaptive responses of plants to shaded environment collectively called shade avoidance syndrome. PIF 5 belongs to the bHLH transcription factor family and regulated gene expression in a low R/FR dependent fashion. In this experiment we investigate PIF5-DNA-binding genome wide to generate a candidate list of genes, which are directly regulated by PIF5. ChIP-Seq sample of whole seedlings treated with low R/FR light
2012-05-02 | E-GEOD-35059 | biostudies-arrayexpress
Project description:Phytochrome Interacting Factor 5 plays an important role in adaptive responses of plants to shaded environment collectively called shade avoidance syndrome. PIF 5 belongs to the bHLH transcription factor family and regulated gene expression in a low R/FR dependent fashion. In this experiment we investigate PIF5-DNA-binding genome wide to generate a candidate list of genes, which are directly regulated by PIF5.
2012-05-03 | GSE35059 | GEO
Project description:Arabidopsis seedlings undergo photomorphogenic development even in darkness when the function of De-etiolated 1 (DET1), a repressor of photomorphogenesis, is disrupted. Our results indicate that DET1 directly interacts with a group of transcription factors known as the phytochrome-interacting factors (PIFs). Furthermore, our results suggest that DET1 positively regulates PIF protein levels primarily by stabilizing PIF proteins in the dark. Genomic analysis also revealed that DET1 may control the expression of light-regulated genes to mediate photomorphogenesis partially through PIFs. Total of twelve samples, two treatments and three genotypes, and each have three replicates.
2015-03-19 | E-GEOD-60835 | biostudies-arrayexpress
Project description:Phytochrome B (phyB) is a plant photoreceptor that forms a membraneless organelle called a photobody. However, its constituents are not fully known. Here, we isolated phyB photobodies from Arabidopsis leaves using fluorescence-activated particle sorting and analyzed their components. We found that a photobody comprises ~1,500 phyB dimers along with other proteins that could be classified into two groups: The first includes proteins that directly interact with phyB and localize to the photobody when expressed in protoplasts, while the second includes proteins that interact with the first group proteins and require co-expression of a first-group protein to localize to the photobody. As an example of the second group, TOPLESS (TPL) interacts with PHOTOPERIODIC CONTROL OF HYPOCOTYL 1 (PCH1) and localizes to the photobody when co-expressed with PCH1. Mutations in TPL family members cause shortened hypocotyls under red light, demonstrating that the method identifies photobody components that regulate red light signaling. Together, our results support that phyB photobodies include not only phyB and its primary interacting proteins but also its secondary interacting proteins.
2023-04-03 | PXD040702 | Pride
Project description:Arabidopsis seedlings undergo photomorphogenic development even in darkness when the function of De-etiolated 1 (DET1), a repressor of photomorphogenesis, is disrupted. Our results indicate that DET1 directly interacts with a group of transcription factors known as the phytochrome-interacting factors (PIFs). Furthermore, our results suggest that DET1 positively regulates PIF protein levels primarily by stabilizing PIF proteins in the dark. Genomic analysis also revealed that DET1 may control the expression of light-regulated genes to mediate photomorphogenesis partially through PIFs.
2015-03-19 | GSE60835 | GEO
Project description:Phytochromes are red/far red photosensors regulating numerous developmental programs in plants. Among them phytochrome A (phyA) is essential to enable seedling de-etiolation in continuous far-red (FR) light a condition mimicking the environment under a dense canopy. The ecological relevance of this response is demonstrated by the high mortality rate of phyA mutants germinating in deep vegetational shade. phyA signaling involves a direct interaction of the photoreceptor with members of the bHLH transcription factor family, PIF1 and PIF3 (Phytochrome Interacting Factor). Here we investigated the involvement of PIF4 and PIF5 in phyA signaling and found that they redundantly control de-etiolation in FR light. The pif4pif5 double mutant is hypersensitive to low fluence rates of FR light. This phenotype is dependent on FR light perception by phyA but does not rely on alterations of the phyA level. Our microarrays analysis shows that PIF4 and PIF5 are part of an inhibitory mechanism repressing the expression of some light-responsive genes in the dark and are also needed for full expression of several growth-related genes in the light. Unlike PIF1 and PIF3, PIF4 and PIF5 are not degraded in response to FR light indicating that they are light-regulated by a different mechanism. Our genetic analysis suggests that this is achieved through the sequestration of these PIFs by the closely related bHLH transcription factor HFR1 (long Hypocotyl in FR light).
2009-08-19 | GSE16333 | GEO
Project description:Phytochromes are evolutionarily conserved photoreceptors in bacteria, fungi, and plants. The prototypical phytochrome comprises an N-terminal photosensory module and a C-terminal histidine kinase signaling-output module. However, the plant phytochrome has been postulated to transduce light signals by interacting with a group of nodal Phytochrome-Interacting transcription Factors (PIFs) and triggering their degradation via the N-terminal photosensory module, while its C-terminal output module, including a Histidine Kinase-Related Domain (HKRD), is thought not to participate directly in signaling. Here, we show that the C-terminal module of Arabidopsis phytochrome B (PHYB) is unexpectedly sufficient to mediate the degradation of PIF3 and to induce a distinct set of PIF-regulated photosynthetic genes. These signaling functions require the HKRD and particularly its dimerization. A D1040V mutation, which disrupts the dimerization of HKRD and the interaction between the C-terminal module and PIF3, abrogates the early light signaling functions of PHYB in nuclear accumulation, photobody biogenesis, and PIF3 degradation. In contrast, disruption of the interaction between PIF3 and PHYB’s N-terminal photosensory module has little effect on PIF3 degradation. Together, this study provides novel insight into the central mechanism of early phytochrome signaling that the C-terminal signaling-output module of PHYB interacts with PIF3 in the nucleus to mediate PIF3 degradation by light.
2017-12-31 | GSE90925 | GEO