Project description:We evaluated differential RNA-seq coverage of all TAIR10-annotated introns in Arabidopsis seedlings subjected to heat stress. Transcriptome analyses of plants infected with bacteria suggested the untreated upf1-5 mutant was enriched not only with pathogen defense-associated mRNAs but also with transcripts encoding genes involved in the general abiotic stress responses. Therefore, we reasoned that global IR events in the upf1-5 mutant and in environmentally stressed wild-type plants may show similarities. Indeed, the transcriptomes of upf1-5 mutant and the heat-stressed wild-type seedlings shared an overlapping set of differentially expressed introns
Project description:We obtained an Arabidopsis mutant from the Arabidopsis Biological Resource Center stock collection and verified that it was homozygous for a T-DNA insertion in the first exon of ORRM1 (SALK_072648, designated here as orrm1). The homozygous mutant did not show any phenotypic defect when grown under growth room conditions. We examined the organelle transcriptome of the mutant for editing defects because other proteins carrying RIP domains have been shown to be editing factors. We analyzed the plastid RNA editing extent with a new methodology based on RNA-seq. Briefly, total RNA is isolated from leaves and RT-PCR products corresponding to known organelle genes are obtained by using gene-specific primers. The products are mixed in equimolar ratio, sheared, and used as templates to produce an Illumina TruSeq library. This RNA-seq analysis demonstrated that ORRM1 is a plastid editing factor; 12 among 34 plastid sites exhibit a severe reduction of editing extent in the mutant relative to the wild-type
Project description:Small RNA sequences from Arabidopsis thaliana Col-0 inflorescence tissues of three biological replicates. The data were analyzed to identify non-templated nucleotides in Arabidopsis small RNAs.
Project description:Transcriptional profiling of the vegetative part of Arabidopsis comparing wild type with the shr scl23 scr triple mutant. The latter is produced by crossing the strong null alleles of shr (shr-2), scl23 (scl23-1) and scr (scr-5). The goal was to determine the effects of the GRAS transcription factors SHR, SCL23 and SCR on growth and development of the Arabidopsis shoot system by global transcriptome analysis.
