The JA-pathway MYC transcription factors regulate photomorphogenic responses by modulating the expression of HY5 and PIF targets
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PROVIDER: PRJNA471885 | ENA |
REPOSITORIES: ENA
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Project description:Jasmonates are key regulators of the balance between defence and growth in plants. However, the molecular mechanisms by which activation of defences reduces growth are not yet understood. Here, we analyze the role of MYC transcription factors (TFs) and JA in photomorphogenic growth. We found that multiple myc mutants share light-related phenotypes with mutants of the phytochrome B photoreceptor, regarding seed germination and hypocotyl growth. Over-expression of MYC2 in a phyB background partially suppressed its long hypocotyl phenotype. We show that the activity of MYC TFs is partially independent of COI1 and that JA inhibition of hypocotyl growth acts through alteration of auxin homeostasis and is partially independent of the classical JA signalling pathway. Transcriptomic analysis of multiple myc mutants confirmed that MYCs are required for full expression of R-light regulated genes, including the master regulator HY5. ChIP-Seq analyses revealed that MYC2 and MYC3 directly bind to the promoter of HY5 and that HY5 gene expression and protein levels are compromised in multiple myc mutants. Moreover, MYC2 and MYC3 share a high amount of direct targets with PIFs, and have an opposite effect on gene expression of these targets. Altogether, our results pinpoint MYCs as photomorphogenic TFs that regulate phytochrome responses by regulating PIFs targets and activating HY5 expression. This has important implication to understand the trade-off between growth and defence, since the same TFs that activate defence responses are photomorphogenic growth regulators.
2019-07-31 | GSE114590 | GEO
Project description:DE-ETIOLATED1 (DET1) is a negative regulator of plant photomorphogenesis acting as a component of the C3D complex, which can further associate to CULLIN4 to form a CRL4C3D E3 ubiquitin ligase. CRL4C3D is thought to act together with CRL4COP1SPA ubiquitin ligase, to promote the ubiquitin-mediated degradation of the master regulatory transcription factor ELONGATED HYPOCOTYL5 (HY5), thereby controlling photomorphogenic gene regulatory networks. Yet, functional links between COP1 and DET1 have long remained elusive. Here, upon mass spectrometry identification of DET1 and COP1-associated proteins, we provide in vivo evidence that DET1 associates with COP1 to promote its destabilization, a process necessary to dampen HY5 protein abundance. By regulating HY5 over-accumulation, DET1 is critical to avoid its association to second-site loci, including many PIF3 target genes. Accordingly, excessive HY5 levels result in an increased HY5 repressive activity and are sufficient to trigger fusca-like phenotypes otherwise observed typically in COP1 and COP9 signalosome mutant seedlings. This study therefore identifies that DET1-mediated regulation of COP1 stability tunes down HY5 cistrome and avoids hyper-photomorphogenic responses that might compromise plant viability.
2021-09-09 | GSE155147 | GEO
Project description:We show that longer-term inhibition of shade avoidance in Arabidopsis is sustained by ELONGATED HYPOCOTYL 5 (HY5) and HY5 HOMOLOG (HYH) which, together, regulate transcriptional reprogramming of genes involved in hormone signalling and cell wall modification.
2023-06-07 | GSE192469 | GEO
Project description:Transcription regulation requires many protein interactions on chromatin, and only a subset of transcription factors have well-defined activation or repression domains. The Arabidopsis transcription factor HY5 controls critical growth-related gene expression programs during plant development, but it’s primary activity in regulating transcription remains unclear. To address this question, we generated constitutive repressor and activator HY5 fusion proteins to direct the expression of HY5 target genes. We used RNA-seq, ChIP-seq, and multiple phenotypes to demonstrate that HY5 depends on accessory factors to promote transcription and identify high confidence direct targets of HY5. We suggest that this strategy can be used broadly to define the transcription regulation activity and direct targets of transcription factors. Interestingly, this approach also revealed a mechanism by which HY5 promotes the accumulation of its own negative regulators. We show that HY5 directly regulates components of the COP1 E3-ubiquitin ligase complex, and by uncoupling this feedback loop we can induce partial de-etiolation in the dark. This provides a system by which plants can quickly repress growth upon light exposure. Lastly, we show that modulating this system can generate significant phenotypic diversity and provide proof of concept that these fusion proteins can modulate growth in tomato, opening a novel path toward selecting desirable traits in crop species.
2020-04-20 | GSE132860 | GEO
Project description:Transcription regulation requires many protein interactions on chromatin, and only a subset of transcription factors have well-defined activation or repression domains. The Arabidopsis transcription factor HY5 controls critical growth-related gene expression programs during plant development, but it’s primary activity in regulating transcription remains unclear. To address this question, we generated constitutive repressor and activator HY5 fusion proteins to direct the expression of HY5 target genes. We used RNA-seq, ChIP-seq, and multiple phenotypes to demonstrate that HY5 depends on accessory factors to promote transcription and identify high confidence direct targets of HY5. We suggest that this strategy can be used broadly to define the transcription regulation activity and direct targets of transcription factors. Interestingly, this approach also revealed a mechanism by which HY5 promotes the accumulation of its own negative regulators. We show that HY5 directly regulates components of the COP1 E3-ubiquitin ligase complex, and by uncoupling this feedback loop we can induce partial de-etiolation in the dark. This provides a system by which plants can quickly repress growth upon light exposure. Lastly, we show that modulating this system can generate significant phenotypic diversity and provide proof of concept that these fusion proteins can modulate growth in tomato, opening a novel path toward selecting desirable traits in crop species.
2020-04-20 | GSE132859 | GEO
Project description:Gene expression profiles between wild type (WT) and hy5 were compared to know HY5-targets.
2015-01-06 | GSE62119 | GEO
Project description:In this study, we found that a light signaling factor, Long Hypocotyl 5 (HY5) is closely involved in the regulation of GSLs contents in light condition. In addition, HY5 was shown to physically interact with a histone deacetylase HDA9 and bind to proximal promoter region of MYB29 and IMD1 to suppress aliphatic GSL biosynthetic process. These results demonstrate that HY5 acts to suppress GSL accumulation at daytime, thus properly modulating the GSL contents on a daily basis of Arabidopsis plant.
2024-06-12 | GSE250418 | GEO
Project description:The transcription factor HY5 acts downstream of multiple families of the photoreceptors and promotes photomorphogenesis. Although it is well accepted that HY5 acts to regulate target gene expression, in vivo binding of HY5 to any of its target gene promoters has yet to be demonstrated. Here we used a chromatin immunoprecipitation procedure to verify suspected in vivo HY5 binding sites. We demonstrated that in vivo association of HY5 with promoter targets is not altered under distinct light qualities or during light-to-dark transition. Coupled with DNA chip hybridization using high density 60-nucleotide oligomer microarray that contains one probe for every 500 nucleotides over the entire Arabidopsis genome, we mapped genome wide in vivo HY5 binding sites. This analysis showed that HY5 binds preferentially to promoter regions in vivo and revealed over 3 thousand chromosomal sites as putative HY5 binding targets. HY5 binding targets tend to be enriched in the early light responsive genes and transcription factor genes. Our data thus supports a model in which HY5 is a high hierarchical regulator of the transcriptional cascades for photomorphogenesis. Keywords: ChIP-chip
2007-03-01 | GSE6510 | GEO
Project description:Gene expression profiles between wild type (WT) and hy5 were compared to know HY5-targets. Gene expression profiles between wild type (WT) and hy5 were compared to known HY5-targets.
2015-01-06 | E-GEOD-62119 | biostudies-arrayexpress
Project description:Jasmonic acid (JA) is a fatty-acid derived signaling molecule that regulates a wide variety of plant developmental and stress-related responses. We identified a jasmonate-insensitive1 (jai1) mutant of tomato that is defective in the LeCOI1 gene, which plays an essential role in induced resistance of tomato to a broad spectrum of pests, and is also required for maternal control of seed and fruit development. The present study is aimed at identifying genes involved in two JA-signaled processes that have not been studied in other plants. The first specific aim is to identify the set of JA/COI1-regulated genes in tomato reproductive tissues, with emphasis on genes expressed in maternal tissues. We hypothesize that JA/COI1 signaling regulates maternal processes that nurture the developing embryo and seed. The second aim of the study is to identify JA/COI1-regulated genes that are specifically expressed in tomato roots. Although it has been shown that JA promotes root defenses against various pests, virtually nothing is known about the JA-regulated transcriptome in roots. Tomato (Solanum lycopersicum) cv Micro-Tom wild-type and jai1 seed were grown in peat pots and maintained in growth chambers. To identify COI1-regulated genes in reproductive tissues, flower buds, open flowers and immature fruit at 7 and 17 days post-pollination were collected from 8 to 10 week old plants. To identify COI1-regulated genes in roots, 3 week old plants were exposed to exogenous JA by a single soil drench with 0.1mM JA, and roots were collected after 1, 6, 12 and 24 hours. Plants treated with water were used for the 0hr time point. All tissue was snap-frozen in liquid nitrogen, and RNA was extracted and analyzed as described in the TIGR Potato Microarray protocol (phenol method). Three biological replicates were collected for this study. Keywords: Direct comparison
2007-09-01 | GSE8284 | GEO