Project description:Investigation of whole genome gene expression level changes in several Arabidopsis thaliana mutants (nrpd1, nrpe1, ros1 dml2 dml3) compared to wild-type Col-0. The mutants analyzed in this study are further described in Le et al. 'DNA demethylases target promoter transposable elements to positively regulate stress responsive genes in Arabidopsis' . Genome Biology (in press).
Project description:This study used the mutants nrpe1-11 and ros1-4 to assess the impact of RNA-directed DNA methylation (RdDM) and ROS1 on the Arabidopsis thaliana (ecotype Col-0) methylome.
Project description:Whole genome shotgun bisulfite sequencing, small RNA sequencing and transcriptome sequencing of wildtype Arabidopsis plants (Col-0), and met1, drm1 drm2 cmt3, and ros1 dml2 dml3 null mutants using the Illumina Genetic Analyzer. A comparison was performed with regions of the genome containing cytosine DNA methylation identified by methylcytosine immunoprecipitation and whole-genome oligonucleotide tiling microarrays, for wildtype Col-0. Understanding the epigenetic regulatory mechanisms that mediate control of transcription at multiple levels is critical to understanding how plants develop and respond to their environment. We combined next-generation sequencing by synthesis (SBS) technology with novel methods for direct sequencing of the entire cytosine methylome (methylC-seq), transcriptome (RNA-seq), and the small RNA component of the transcriptome (smRNA-seq) to create a set of highly integrated epigenome maps for Arabidopsis thaliana, in conjunction with a set of informative mutants defective in DNA methyltransferase and DNA demethylase activity. At single-base resolution we discovered extensive, previously undetected, DNA methylation, identified the context and level of methylation at each site, and found that local composition has effects upon DNA methylation state. Deep sequencing of the smRNAome exposed a direct relationship between the location and abundance of smRNAs and DNA methylation, perturbation of smRNA biogenesis upon loss of CpG DNA methylation, and a tendency for smRNAs to direct strand-specific DNA methylation in the region of RNA-DNA homology. Finally, strand-specific RNA-seq revealed changes in the transcript abundance of hundreds of genes upon alteration of the DNA methylation state, and enabled the identification of numerous previously unidentified genes regulated by DNA methylation. Keywords: Whole genome shotgun bisulfite sequencing, small RNA sequencing, transcriptome sequencing, methylcytosine immunoprecipitation, whole-genome oligonucleotide tiling microarrays Whole genome shotgun bisulfite sequencing, small RNA sequencing and transcriptome sequencing of wildtype Arabidopsis plants (Col-0), and met1, drm1 drm2 cmt3, and ros1 dml2 dml3 null mutants using the Illumina Genetic Analyzer. A comparison was performed with regions of the genome containing cytosine DNA methylation identified by methylcytosine immunoprecipitation and whole-genome oligonucleotide tiling microarrays, for wildtype Col-0.
Project description:Part of a set of highly integrated epigenome maps for Arabidopsis thaliana. Keywords: Illumina high-throughput bisulfite sequencing Whole genome shotgun bisulfite sequencing of wildtype Arabidopsis plants (Columbia-0), and met1, drm1 drm2 cmt3, and ros1 dml2 dml3 null mutants using the Illumina Genetic Analyzer.
Project description:Investigation of whole genome gene expression level changes in several Arabidopsis thaliana mutants (nrpd1, nrpe1, ros1 dml2 dml3) compared to wild-type Col-0. The mutants analyzed in this study are further described in Le et al. 'DNA demethylases target promoter transposable elements to positively regulate stress responsive genes in Arabidopsis' . Genome Biology (in press). A twelve chip study using total RNA recovered from three week-old plants grown on Murashige Skoog sucrose agar. The number of biological replicates for each plant genotype were as follows: Col-0 (3 biological replicates), rdd (2), nrpd1 (2) and nrpe1 (2) respectively. Each array contains 60-mer probes targeting 39,042 genes (TAIR 9.0) with 4 probes per gene.
Project description:Treatment of Arabidopsis thaliana (ecotype Col-0) seedlings with jasmonic acid (JA) elicits long-term induced resistance (IR) against the chewing herbivore Spodoptera littoralis. We used whole genome bisulfite-seq to profile the methylome associated with this long-lasting JA-IR.
Project description:Active DNA demethylation is an important epigenetic phenomenon in many eukaryotes. In Arabidopsis thaliana, ROS1, a 5-methylcytosine DNA glycosylase, is responsible for active DNA demethylation via a base excision repair process. Here, we found that Bromodomain and ATPase domain-containing protein 1 (BRAT1) associates with BRP1 (BRAT1 Partner 1) and forms a tight BRAT1–BRP1 complex required for DNA demethylation. To identify hypermethylated loci at the whole-genome level in brat1, brp1, and ros1, we performed whole-genome bisulfite sequencing. Compare the DNA methylation profiles of 10-day old seedlings materials of mutants (brat1, brp1, and ros1) to wild type by whole-genome bisulfite sequencing.
