Transcriptomic analysis of UBQLN2-ALS Drosophila

The goal of this project was to elucidate gene expression changes in flies expressing ALS-associated alleles of the ubiqutin chaperone, UBQLN2. We employed flies expressing wild-type (UBQLN2-WT) or mutant (P497H and 4XALS) human UBQLN2 proteins under the control of an eye-specific GMR driver at room temperature or 29C. The 4XALS allele harbors four different ALS-associated mutations. Total head RNA from all three UBQLN2 genotypes and GMR>Gal4 controls was subjected to RNA-Seq analysis using Novogene. Among other findings, we found that innate immunity genes were strongly upregulated in UBQLN2-4XALS flies and that UBQLN2-WT and UBQLN2-P497H flies have highly similar transcriptional signatures.

Methods
Four different genotypes were reared at 22C or 29C: GMR-Gal4 (control); GMR>UBQLM2-WT; GMR>UBQLN2-P497H; and UBQLN2-4XALS. 100 or more flies of each genotype were collected 1-3 days post eclosion. The heads were removed and stored until RNA extraction and processing. The RNA was then sent to Novogene for cDNA library generation and sequencing.