Functional Characterisation of the Ubiquitin-like Core Autophagy Protein ATG12 in Dictyostelium discoideum

Purpose: First global survey of the transcriptome in autophagy-deficient strains of D. discoideum. Results: Our RNAseq analysis of ATG12‾, ATG16‾ and ATG12‾/16‾ cells revealed major transcriptional changes in a large number of genes in comparison to AX2. Conclusions: Our study represents the first detailed analysis of the transcriptome in autophagy-deficient strains of D. discoideum. The data were generated by RNA-seq technology. The optimised data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell. We conclude that RNA-seq based transcriptome characterisation would expedite genetic network analyses and permit the dissection of complex biologic functions. Total RNA from either vegetative or for 3 h starved D. discoideum cells (AX2 wild-type and ATG12‾, ATG16‾, ATG12‾/16‾ mutant strains) was isolated, n=3 or n=6, Illumina HiSeq 4000.