Overlapping activities of ELAV/Hu family RNA binding proteins specify the extended neuronal 3' UTR landscape in Drosophila [L1 CNS RNA-seq]

The goals of this study are to perform quantitative comparison of whole transcriptome of Drosophila melanogaster 1st instar larvae central neural system (L1CNS) from three genotypes: Canton-S, elav5 single mutant, and elav5/fne double mutant; and the global 3'-end features of Drosophila melanogaster 1st instar larvae central neural system from three genotypes: Canton-S, elav5 single mutant. Total RNAs were extracted from dissected L1CNS of Drosophila melanogaster Canton-S, elav5 single mutant, and elav5/fne double mutant; total RNA-seq libraries were prepared using Illumina TruSeq Stranded Total RNA Sample Prep kit with replicates for each genotype; final cDNA libraries were sequenced on Illumina HiSeq-1000 sequencer with PE-100 mode. Total RNA-seq data were mapped to the corresponding UCSC genome assemblies: Drosophila melanogaster (dm6), HISAT2 aligner was used for the alignment with default parameters. We found that L1CNS from Canton-S expresses neural specific 3' UTR extensions like head, while in L1CNS from elav5 single mutant, global neural specific 3' UTR extensions are not significantly lost, but in elav5/fne double mutant L1CNS, there is a dramatic loss of neural specific 3' UTR extensions. We reported for the first time demonstration of trans-acting factors that globally maintain this very distinctive tissue-specific APA landscape. RNA-seq profiles from dissected Drosophila melanogaster 1st instar larvae central neural system from three genotypes: Canton-S (WT), elav5 single mutant, and elav5/fne double mutant. Elav5 and fne mutants are deletion KO alleles.