Transcription profiling of wild type and hag4 mutant Arabidopsis roots to investigate the role of HAG4 in root development
ABSTRACT: Homeostasis of histone acetylation and the control of transcription. Involvement of histone acetyl transferase HAG4 in the root development. hag4 mutant (with a insertion in HAG4 gene encoding a Histone Acetyl Transferase) and wild-type ecotype (Ws) were grown during 15 days, in vitro. RNA were extrated from roots of seedlings. Each sample (ws or hag4) corresponds to a pool of 3 independant cultures and harvesting.
Project description:Arabidopsis plants are grown for 5 days on MS medium and then we transfer them to a medium supplemented with ACC (5uM) or without ACC. After 3 h of growth, we isolate the RNA of the roots.
Project description:Identification of diacylglycerol pyrophosphate regulated genes in ABA signaling.<br><br> The specific plant phosphorylated form of phosphatidic acid (PA), diacylglycerol pyrophosphate (DGPP) was recently shown to be a second messenger in abscisic acid (ABA) signaling. The aim of the project is to identify among the set of ABA-regulated genes the ones also regulated by DGPP and/or PA.<br> Five ml of 3 days-old suspension cells was incubated with ABA or lipids for 3 h under the conditions of culture. Lipids were emulsified by sonication for 1 mi, four times, at 4°C, in one ml of culture medium then added to 4 ml suspension cells. Cells were filtrated under vacuum, frozen in liquid nitrogen and RNA extracted. Dioleoyl PA and dioctanoyl PA are from Sigma, dioleoyl DGPP and dioctanoyl DGPP are from Avanti Polar Lipids.
Project description:Response of mouse mammary epithelial cells NMuMG to TGF-b1 - time course experiment. Identification of novel gene targets involved in TGF-b1-driven regulation of epithelial-mesenchymal transition (EMT).
Project description:Identification of novel TGF-b1 and BMP-7-regulated genes in epithelial cells.<br> <br> Human mammary epithelial cell line MDA-MB-468 that is lacking endogenous Smad4 was infected with either an adenovirus carrying GFP cDNA (control) or Smad4 cDNA (to restore the Smad4 activity in the cells). Cells were treated with TGF-b1 (0.5 ng/ml) or BMP-7 (300 ng/ml) for 2 or 12h. Smad4-independent vs Smad4-dependent response was measured. Also response to both growth factors was compared.
Project description:The objective of the study was to identify the genes up and down-regulated during the interaction of P. brassicae with a partial resistant genotype of Arabidopsis. The transcriptome pattern of inoculated and non-inoculated plants of Arabidopsis was compared at three time points after inoculation (24 hours, 48 hours and one-week ai).<br> Sixty plants were studied by comparison (inoculated-non inoculated) and by kinetic point. RNAs of the 30 inoculated plants and the RNAs of the 30 non-inoculated plants were pooled to eliminate variability between individual plants and thus to target for genes for which differences in expression were linked to the inoculation by the pathogen. Five comparisons have been performed: inoculated-non inoculated at 24 hours ai; inoculated-non inoculated 48 hours ai; inoculated-non inoculated one-week ai; inoculated 24h ai-inoculated 48h ai; inoculated 48h ai- inoculated one-week ai. The entire experiment was repeated (biological repetition) and each comparison was performed in two independent hybridisations (technical repetition).
Project description:Identification of new genes regulated by RDR6 and SGS3 (two genes involved in PTGS) by analysis of the transcriptome of rdr6-1 and sgs3-1 mutants compared to wild-type plants in different tissues (flower and leaves). The comparison between transcriptome of rdr6-1 and sgs3-1 mutant alleles impaired in PTGS and development (juvenile-to-adult transition) and transcriptome of rdr6-5 and sgs3-3 alleles impaired only in PTGS would allowed identification of genes involved in the developmental default (zip phenotype) of the null alleles (rdr6-1 and sgs3-1 mutants).
Project description:Title : Characterization of genes differentially expressed in roots of transgenic arabidopsis lines expressing the p25 protein of beet necrotic yellow vein virus.<br> <br> Biological question : <br> Rhizomania ("crazy root") is a severe disease of sugar beet caused by beet necrotic yellow vein virus (BNYVV), which is transmitted by the soil-inhabiting fungus Polymyxa betae. Symptoms of virus infection are characterized by a constricted tap root and a massive proliferation of fine rootlets that often undergo necrosis. BNYVV RNA-3 encodes a 25 kDa (p25) which is an important determinant of leaf symptom phenotype. It also governs BNYVV invasion of the plant root system and induction of rootlet proliferation in sugar beet.<br> In order to obtain a better understanding of molecular aspects of disease development in roots and to characterize specific host genes involved in response to viral infection, transgenic Arabidopsis overexpressors of p25 viral protein was obtained and better characterized. It was shown that transgenic plants that efficiently expressed p25 protein produced more lateral roots. <br> Comparative analysis (microarray) was performed between wild type Arabidopsis roots and transgenic Arabidopsis roots expressing p25 protein, in order to identify Arabidopsis genes differentially expressed in response to p25 viral protein.<br> <br> Experiment description: <br> Seeds were surface sterilized, chilled at 4C for 4 days, and then germinated and grown on square Petri plates containing sterilized Murashige and Skoog (MS) medium with 1% sucrose. Such stock plates were arranged vertically in plastic racks and placed into growth chamber. After 5 days, plants were transferred carefully onto fresh MS medium big round plates. On each plate, 60 Wild Type (WT) plantlets were transferred on the half right of the plate, and 60 transgenic plantlets (B, E or T lines) were transferred on the half left of the plate. Plates were arranged horizontally and placed into growth chamber. <br> <br>Experiment 1 : 5 plates containing WT0A control plants and B0A transgenic plants. <br> <br>Experiment 2 : 5 plates containing WT1 control plants and B transgenic plants. <br>5 plates containing WT2 control plants and E transgenic plants. <br>5 plates containing WT3 control plants and T transgenic plants. <br> <br>Plants were harvested after 7 days (experiment 1) or 12 days (experiment 2), and WT roots or transgenic roots were pooled and conserved at -80C.
Project description:Arabidopsis thaliana transcriptome analysis in response to plant growth promoting rhizobacteria (PGPR)<br> Experiment 1 : Changes in gene expression profile triggered during root architecture response to Phyllobacterium.<br> Biological question : Which genes are up- or down-regulated in Arabidopsis thaliana cultivated in vitro with increased lateral root development in response to Phyllobacterium STM196 inoculation.<br> Experiment description: Seeds of wild-type Arabidopsis thaliana (ecotype Columbia) were surface-sterilized and sown on agar mineral medium (see below). 4 days after storage in the dark at 4C, seedling were cultivated 6 days in a growth chamber (16 h daily, 20-22C) and then transferred on a fresh agar mineral medium inoculated or not with Phyllobacterium STM196 (2.108 cfu/ml). 6 days later, root and leaves were collected, froze on liquid nitrogen and stored at -80C.<br> <br> Experiment 2 : Changes in gene expression profile triggered during induced systemic resistance (ISR)<br> Biological question : Which genes are up- or down-regulated during the ISR triggered by a rhizobacteria, in comparison with those affected by a pathogenic interaction. <br> Experiment description: Seeds were sown on 0.8% (W/V) agar mineral medium (see below). 4 days after storage in the dark at 4C, seedling were cultivated 6 days in a growth chamber (16 h daily, 20-22C) and then transferred on soil inoculated or not with 107 cfu.g-1 of Bradyrhizobium strain ORS278. Three weeks later, 3 leaves per plant were infiltrated with a suspension of Pseudomonas syringae pv. tomato (2.105 cfu.ml-1) or with MgSO4 10 mM alone for control plants. Infiltrated leaves were collected 24h later.<br> <br> Experiment 3 : Comparison of the effects of 3 rhizobacteria on Arabidopsis thaliana transcriptome<br> Biological question : which genes are specifically induced or repressed in Arabidopsis thaliana by inoculation of the soil with a PGPR vs a bacteria that has the ability to trigger nodule formation in a Legume. <br> Experiment description: Seeds of wild-type Arabidopsis thaliana (ecotype Columbia) were surface-sterilized and sown on agar mineral medium. Four days after storage in the dark at 4C, seedlings were cultivated 6 days in a growth chamber (16 h daily, 20-22C) and then transferred on soil inoculated or not with 108 cfu.g-1 of Mesorhizobium loti, or 108 cfu.g-1 of Phyllobacterium STM196, or 107 cfu.g-1 of Bradyrhizobium ORS278.