Project description:Plant Topless-related 1 (TPR1), belonging to a family of transcriptional corepressors found across eukaryotes, contributes to immunity signaling in Arabidopsis thaliana and wild tobacco. We used chromatin immunoprecipitation and sequencing (ChIP-seq) of Arabidopsis TPR1-GFP expressing transgenic lines to characterize genome-wide TPR1-chromatin associations.
Project description:In eukaryotes, DNA wraps around histones to form nucleosomes, which are compacted into chromatin. DNA-templated processes, including transcription, require chromatin disassembly and reassembly mediated by histone chaperones. Additionally, distinct histone variants can replace core histones to regulate chromatin structure and function. Although replacement of H2A with the evolutionarily conserved H2A.Z via the SWR1 histone chaperone complex has been extensively studied, in plants little is known about how a reduction of H2A.Z levels can be achieved. Here, we show that NRP proteins cause a decrease of H2A.Z-containing nucleosomes in Arabidopsis under standard growing conditions. nrp1-1 nrp2-2 double mutants show an over-accumulation of H2A.Z genome-wide, especially at heterochromatic regions normally H2A.Z-depleted in wild-type plants. Our work suggests that NRP proteins regulate gene expression by counteracting SWR1, thereby preventing excessive accumulation of H2A.Z.
Project description:Arabidopsis thaliana, 14-day-old seedlings grow in 1/2 MS culture medium under short day condition, LC-MS. In this project, two different materials (One is in the wild type background, the other is in the mutant background.) were used to do CoIP experiments, and then mass spectrometry was carried out to compare the number of peptide segments obtained by the two materials.
Project description:In this project, 3XFlag-tagged protein affinity purifications were performed to identify the protein-protein interactors using Cryptococcus neoformans cell lysate. After fractionation with SDS-PAGE, peptide samples for nanoLC-MS/MS were prepared by in-gel digestion. Raw data from Orbotrap Velos pro were processed with MASCOT via Proteome discoverer2.2. Validation of peptide and protein identifications were performed with Scaffold proteome software.
Project description:Endogenous plant signalling peptides regulate developmental and growth-related processes. Recent research indicates that some of these peptides are classified as phytocytokines as they have regulatory functions during plant immune responses. However, the mechanistic basis for phytocytokine-mediated immune modulation remains largely elusive. Here, we identify GOLVEN2 (GLV2) peptides as novel phytocytokines in Arabidopsis thaliana. By peptide application, precursor overexpression and loss-of-function studies we show that GLV2 enhances sensitivity of plants to elicitation with the bacterial flagellin epitope flg22. GLV2 is perceived by ROOT MERISTEM GROWTH FACTOR INSENSITIVE (RGI) receptors and RGI3 forms an flg22-induced complex with the flg22-receptor FLAGELLIN SENSING 2, suggesting that RGIs are part of activated pattern recognition receptor signalling platforms. GLV2 perception increases posttranscriptional FLS2 abundance and RGIs promote FLS2 protein accumulation. Thus, GLV-RGI signalling controls above ground plant immunity via a novel mechanism of phytocytokine activity.
Project description:Genome-wide identification of transcription factor (TF) binding sites is pivotal to our understanding of gene expression regulation. Although much progress has been made in the determination of potential binding regions of proteins by chromatin immunoprecipitation (ChIP), this method has some inherent limitations regarding DNA enrichment efficiency and antibody necessity. Here, we report an alternative strategy for assaying in vivo TF-DNA binding in Arabidopsis thaliana cells by tandem chromatin affinity purification (TChAP). Evaluation of TChAP using the E2Fa TF and comparison with traditional ChIP and single chromatin affinity purification illustrates the suitability of TChAP and provides a resource for exploring the E2Fa transcriptional network. Integration with transcriptome, cis-regulatory element, functional enrichment, and co-expression network analyses demonstrates the quality of the E2Fa TChAP-seq data and validates the identification of new direct E2Fa targets. TChAP enhances both TF target mapping throughput, by circumventing issues related to antibody availability, and output, by improving DNA enrichment efficiency. Illumina Seq analysis of E2Fa bound DNA elements isolated using different chromatin isolation methods. BioProject PRJNA172013; SRA study ID SRP014713
Project description:Proteomic investigation of Arabidopsis thaliana ftsH12 - ftsH12 is one of 17 genes of the FtsH metallo-protease family encoded within the A. thaliana genome.