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: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: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:We identify the helicase-SANT-associated (HSA) domain as the primary binding platform for nuclear actin-related proteins (ARPs) and actin. Individual HSA domains from chromatin remodelers (RSC, yeast SWI-SNF, human SWI-SNF, SWR1 and INO80) or modifiers (NuA4) reconstitute their respective ARP-ARP or ARP-actin modules. In RSC, the HSA domain resides on the catalytic ATPase subunit Sth1. The Sth1 HSA is essential in vivo, and its omission causes the specific loss of ARPs and a moderate reduction in ATPase activity. Genetic selections for arp suppressors yielded specific gain-of-function mutations in two new domains in Sth1, the post-HSA domain and protrusion 1, which are essential for RSC function in vivo but not ARP association. Taken together, we define the role of the HSA domain and provide evidence for a regulatory relationship involving the ARP-HSA module and two new functional domains conserved in remodeler ATPases that contain ARPs.
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.
Project description:To study the genes regulated by transcription factor SQUAMOSA PROMOTER BINDING PROTEIN-LIKE7 (SPL7) in Arabidopsis thaliana, we conducted chromatin immunoprecipitation-based sequencing (ChIP-seq) in 35S:FALG-SPL7 transgenic plant and spl7 mutant, and genome-wide sequencing-based transcript profiling of Arabidopsis thaliana wild-type plants and of spl7 mutant under MS medium and MS supplement with 5µM CuSO4. These experiments led to the identification of genes that are direct target of SPL7 and genes differentially expressed in an SPL7-dependent or Cu-dependent manner. This study provides a framework for the identification of SPL7 regulated genes towards characterization of SPL7 in copper homeostasis.