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ChIP-Seq analysis of Phytochrome Interacting Factor 5 DNA binding in low R/FR condition

ABSTRACT: 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.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE35059 | GEO | 2012/05/03

SECONDARY ACCESSION(S): PRJNA156179

REPOSITORIES: GEO

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ChIP-Seq analysis of Phytochrome Interacting Factor 5 DNA binding in low R/FR condition

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

Phytochrome Interacting Factor 4 and 5 regulate different set of genes in high and low red/far-red light

Project description:As sessile organisms plants developed a veriety of adaptive responses to the ever changing environment. One of these responses is the shade avoidance syndrome which is composed of different responses like elongation growth, hyponastic leafs or early flowering to shade (low R/FR). Phytochrcome Interacting Factor 4 and 5 are bHLH transcription factors reported to activate gene expression upon perception of low R/FR. Using this miroarray experiment we identified new genes regulated by PIF4 and PIF5 in response to shade and investigated their genome wide role. Here pif4pif5 double mutant, pif5 single mutant and PIF5 overexpressing line were compared to Col-0 wild type A. thaliana plants when grown under 12:12 DL circles for 14 days in high R/FR and either kept in high R/FR or transferred to low R/FR for additional 2 hours

2012-05-02 | E-GEOD-35057 | biostudies-arrayexpress

phytochrome A-mediated shade avoidance responses

Project description:Arabidopsis is a shade avioding plant. Under simulated shade light with reduced red-to-far red (R:FR) ratio around 0.7, hypocotyls of Arabidopsis seedlings elongate, which is one of the typical shade avoidance responses.We discovered that when the R:FR ratio further decreases to around 0.1 (strong shade), the shade-induced elongation of hypocotyl is abolished and phytochrome A (phyA) mediates this response.In this study, we aim to examine the difference between shade and strong shade treatment and uncover the role of phyA in regulating the shade avoidance responses.

2019-12-21 | GSE55899 | GEO

Phytochrome Interacting Factor 4 and 5 regulate different set of genes in high and low red/far-red light

2012-05-03 | GSE35057 | GEO

Phytochrome Interacting Factors 4 and 5 redundantly limit seedling de-etiolation in continuous far-red light.

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

Transcription profiling of Arabidopsis thaliana phytochrome interacting factors 4 and 5 redundantly limit seedling de-etiolation in continuous far-red light.

2009-09-17 | E-GEOD-16333 | biostudies-arrayexpress

Central clock components modulate plant shade avoidance by directly repressing transcriptional activation activity of PHYTOCHROME-INTERACTING FACTORS

Project description:Light-environment signals, sensed by plant phytochrome (phy) photoreceptors, are transduced to target genes through direct regulation of PHYTOCHROME-INTERACTING FACTOR (PIF) transcription factor abundance and activity. Previous genome-wide DNA-binding and expression analysis has identified a set of genes that are direct targets of PIF transcriptional regulation. However, quantitative analysis of promoter occupancy versus expression level has suggested that unknown “trans factors” modulate the intrinsic transcriptional activation activity of DNA-bound PIF proteins. Here, using computational analysis of published data, we have identified PSEUDO-RESPONSE REGULATORS (PRR5 and PRR7) as displaying a high frequency of co-localization with the PIF proteins at their binding sites in the promoters of PIF Direct Target Genes (DTGs). We show that the PRRs function to suppress PIF-stimulated growth in the light and vegetative shade, and that they repress the rapid PIF-induced expression of PIF-DTGs triggered by exposure to shade. The repressive action of the PRRs on both growth and DTG expression requires the PIFs, indicating direct action on PIF activity, rather than a parallel antagonistic pathway. Protein interaction assays indicate that the PRRs exert their repressive activity by binding directly to the PIF proteins in the nucleus. These findings support the conclusion that the PRRs function as direct outputs from the core circadian oscillator, to regulate the expression of PIF-DTGs, through modulation of PIF transcriptional activation activity, thus expanding the roles of the multifunctional PIF signaling hub.

2020-09-01 | GSE136843 | GEO

PHYTOCHROME-INTERACTING FACTOR 7 and RELATIVE OF EARLY FLOWERING 6 act in shade avoidance memory in Arabidopsis

Project description:Shade avoidance helps plants maximize their access to light for growth under crowding. It is unknown, however, whether a priming shade avoidance mechanism exists that allows plants to respond more effectively to successive shade conditions. Here, we show that the shade-intolerant plant Arabidopsis can remember a first experienced shade event and respond more efficiently to the next event on hypocotyl elongation. The transcriptional regulator PHYTOCHROME-INTERACTING FACTOR 7 (PIF7) and the histone H3K27-demethylase RELATIVE OF EARLY FLOWERING 6 (REF6) were identified as being required for this shade avoidance memory. RNA-sequencing analysis revealed that shade induction of shade memory-related genes was impaired in the pif7 and ref6 mutants. Based on the enrichments of H3K27me3, REF6 and PIF7, we found that priming shade treatment induced PIF7 accumulation, which further recruited REF6 to demethylate H3K27me3 on the chromatin of certain memory-related genes, leading to a state poised for their transcription. Upon the second shade treatment, enhanced shade-mediated induction of these genes resulted in stronger hypocotyl growth responses. We conclude that the transcriptional memory mediated by epigenetic modification plays a key role in the ability of primed plants to remember previously experienced shade and acquire enhanced responses to recurring shade conditions.

2024-07-29 | GSE268785 | GEO

Expression data from low R:FR - SA crosstalk in Arabidopsis

Project description:Low R:FR signaling through phytochromes induces shade avoidance responses, including petiole elongation. Salicylic acid-mediated defense against pathogens is inhibited under these conditions. Using microarrays we studied the crosstalk between low R:FR and SA at the global gene expression level in Arabidopsis thaliana.

2013-04-03 | GSE45728 | GEO

Expression data from low R:FR - JA crosstalk in Arabidopsis

Project description:Low reduced red:far-red ratio [R:FR] signaling through phytochromes induces shade avoidance responses, including petiole elongation. Jasmonic acid-mediated defense against herbivores and pathogens is inhibited under these conditions. Using microarrays we studied the crosstalk between low R:FR and JA at the global gene expression level in Arabidopsis thaliana.

2012-05-01 | GSE35700 | GEO

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