Project description:ngs2019_18_eplus-eplus-search for mitochondrial editing defect in an arabidopsis PPR mutant Annotation, RNA/Small-RNA quantification: editing quantification. The Mito samples were first enriched with mitochondria by a series of multi-speed centrifugations after grinding with mortar at 4°C.
Project description:We provide sequences of maize chlroplast RNAs associated with non-PPR editing factors through immunoprecipitation. The accumulated sequences indicate expansive role in RNA processing and potential associations of OZ1-ORRM1 complexes with the ribosome and less efficiently translated mRNAs.
Project description:ngs2018_04_half_edit-half_edit - Is there some transcriptomic defects in these different PPR KO mutants? - Identification of RNA editing defects in 3 differents KO mutants for E+ PPR. Results will be compared to different predictive methods in order to find out which one is the more accurate. Also looking for other transcriptomic defects in a pure-PPR.
Project description:In a recent study, we showed that a T-DNA insertional mutation in a mitochondrial PPR protein, POCO1, led to the earlier floral transition (Emami and Kempken 2019). We used RNA-seq analysis to provide an overview of the global transcriptome changes in poco1 mutant during different developmental stages.
Project description:Pentatricopeptide repeat (PPR) proteins, which are characterized by tandem 30-40 amino acid sequence motifs, constitute a large gene family in plants. These known PPR proteins have been identified to play important roles in organellar RNA metabolism and plant development in Arabidopsis and rice. However, functions of PPR genes in woody species remain still largely unknown. Here, we identified and characterized a total of 626 PPR genes containing PPR motifs in the poplar genome. A comprehensive genome-wide analysis of the poplar PPR gene family was performed, including chromosomal location, phylogenetic relationships, gene duplication. Transcriptomic analyses identified that 154 of the PtrPPR genes were induced by biotic and abiotic treatments, including Marssonina brunnea, salicylic acid (SA), methyl jasmonate (MeJA), wounding, cold and salinity. Quantitative RT-PCR analysis further confirmed the expression profiles of 11 PtrPPR genes under different stresses. Our results contribute to a more comprehensive understanding the roles of PPR proteins and provided an insight for improving the stress tolerance in poplar.
Project description:Protein recoding by RNA editing is required for normal health and evolutionary adaptation. However, de novo induction of RNA editing in response to environmental factors is an uncommon phenomenon. While APOBEC3A edits many mRNAs in monocytes/macrophages in response to hypoxia and interferons, the physiological significance of such editing is unclear. Here we show that the related APOBEC3G cytidine deaminase induces site-specific C-to-U RNA editing in natural killer (NK), CD8+ T cells and lymphoma cell lines upon cellular crowding and hypoxia. RNA seq analysis of hypoxic NK cells reveals C-to-U recoding mRNA editing in dozens of genes including multiple translational and ribosomal genes. APOBEC3G promotes Warburg-like metabolic remodeling and reduces proliferation of HuT78 T cells under similar conditions. Hypoxia-induced RNA editing by APOBEC3G can be mimicked by the inhibition of mitochondrial respiration, and occurs independently of HIF-1α. Thus, APOBEC3G induces mRNA editing in lymphocytes to promote adaptation to mitochondrial hypoxic stress.