Project description:RNA-Seq of Arabidopsis thaliana Col-0 and 35S::FLAG-GR-KAN1 plants grown in ambient light or shade. 8 samples (Col-0 wildtype, 35S::FLAG-GR-KAN1 each in shade or ambient light, each with mock or Dexamethasone treatment) with two technical replicates were sequenced.
Project description:In Arabidopsis thaliana, cytokinin responsive B-type ARR transcription factors and HD-ZIP III transcription factors such as REVOLUTA (REV), act cooperatively as master regulators of shoot regeneration. To identify the downstream targets of ARR-HD-ZIP III transcriptional complex, we used an inducible line of REV, 35S::FLAG-GR-rREV, in which FLAG-tagged miR165/6-non-targetable form of REV (rREV)-GR fusion protein was expressed from 35S promoter. DEX treatment induced activation of REV by translocation of FLAG-GR-rREV fusion protein from cytoplasm to the nucleus. We treated 35S::FLAG-GR-rREV seedlings with 6-benzylaminopurine (6-BA, a cytokinin), dexamethasone (DEX), or 6-BA+DEX for 2 hours. Total RNAs were extracted and subjected to Agilent Arabidopsis Gene Expression Microarray analyses. The differentially expressed genes (>1.5-fold, p<0.05) were identified.
Project description:To investigate how the sucrose-TOR signaling pathway regulates phyA, we conducted LC-MS/MS analysis to identify phosphorylation sites on phyA. In vivo, the phyA protein was immunoprecipitated from 35S::PHYA-YFP/phyA-211 seedlings treated with shade and 30 mM sucrose for 6 hours. In vitro, we used recombinant phyA protein purified from insect cells as the substrate and endogenous TOR complex immunoprecipitated from the 35S::LST8-1-FLAG transgenic line as the kinase source. Phosphopeptide enrichment and LC–MS/MS analysis of the in vitro reaction were performed.
Project description:Shade can trigger the shade avoidance syndrome (SAS) in shade-intolerant species,which cause exaggerated growth and affect crop yield.We report that Arabidopsis transcription factors bZIP59 negatively regulate SAS. To investigate the function of bZIP59 during SAS, we performed RNA-Seq of wild type Col-0 and a T-DNA insertion line bzip59 (SALK_024459) in while light and shade.
Project description:A high-depth strand-specific RNA sequencing (ssRNA-seq) using 5-day-old white-light grown Col-0 and pif7-1 seedlings with additional 1 hr shade or white light treatment.
Project description:In Arabidopsis thaliana, cytokinin responsive B-type ARR transcription factors and HD-ZIP III transcription factors such as REVOLUTA (REV), act cooperatively as master regulators of shoot regeneration. To identify the downstream targets of ARR-HD-ZIP III transcriptional complex, we used an inducible line of REV, 35S::FLAG-GR-rREV, in which FLAG-tagged miR165/6-non-targetable form of REV (rREV)-GR fusion protein was expressed from 35S promoter. DEX treatment induced activation of REV by translocation of FLAG-GR-rREV fusion protein from cytoplasm to the nucleus. We treated 35S::FLAG-GR-rREV seedlings with 6-benzylaminopurine (6-BA, a cytokinin), dexamethasone (DEX), or 6-BA+DEX for 2 hours. Total RNAs were extracted and subjected to Agilent Arabidopsis Gene Expression Microarray analyses. The differentially expressed genes (>1.5-fold, p<0.05) were identified. 10-day-old 35S::FLAG-GR-rREV plants were treated with 6-benzylaminopurine (6-BA), dexamethasone (DEX), or 6-BA+DEX for 2 hours. DEX treatment induced activation of REV by translocation of FLAG-GR-rREV fusion protein from cytoplasm to the nucleus. Total RNA was extracted with RNeasy Mini Kit and hybridized to Agilent Arabidopsis Gene Expression Microarray. Differentially expressed genes were defined by a 1.5-fold expression difference with a P value<0.05. Biological replicates were performed.
Project description:For shade-intolerant species, shade light indicates the close proximity of neighboring plants and triggers the shade avoidance syndrome (SAS), which causes exaggerated growth and reduced crop yield. We report that nonsecreted ROT FOUR LIKE (RTFL)/DEVIL (DVL) peptides negatively regulate the SAS by repressing the activities of BRASSINOSTEROID SIGNALING KINASEs (BSKs) and PHYTOCHROME INTERACTING FACTOR 4 (PIF4) in Arabidopsis. To identify RTFL function during SAS, we performed RNA-seq to search for differentially expressed genes (DEGs) by comparing transcript levels between Col-0 and dvl1-1D, bsk36, or pif47 seedlings during white light and shade conditions.
Project description:Shade can trigger shade avoidance responses with increasing the elongation of stem-like organs at the expense of leaf development. We report that exogenous sucrose alleviates shade-induced inhibition of leaf development through a mechanism dependent on both the TOR complex and phyA. To investigate the function of sucrose and phyA, we performed RNA-Seq of wild type Col-0 and phyA-211 with sucrose treatment under shade.
Project description:For shade-intolerant plants, changes in light quality indicative of competition from neighboring plants trigger shade avoidance syndrome (SAS). PYHTOCHROME-INTERACTING FACTOR 7 is the major transcriptional regulator of SAS in Arabidopsis. However, the epigenetic reprogramming under shade is poorly understood. To identify the histone chaperone ASF1 and HIRA function during SAS, we performed transcriptome deep sequencing (RNA-seq) to search for differentially expressed genes (DEGs) by comparing transcript levels between Col-0 and pif7-1, asf1ab, or hira-1 seedlings during white light and shade conditions. Our data shown that histone chaperone ASF1, through interacting with PIF7 and helping of HIRA, positively regulates shade-induced genes expression.
Project description:The Arabidopsis thaliana transcription factor LATERAL ORGAN BOUNDARIES (LOB) is expressed in the boundary between the shoot apical meristem and initiating lateral organs. To identify genes regulated by LOB activity, we used an inducible 35S:LOB-GR line. This analysis identified genes that are differentially expressed in response to ectopic LOB activity. 35S:LOB-GR and Col wild-type seedlings were treated with dexamethasone (DEX) or mock-treated. Three biological replicates were conducted for each treatment.