SRA

Genome-wide profiling of rhythmic gene expression has offered new avenues for studying the contribution of circadian clock to diverse biological processes. Sleep has been considered one of the most important physiological processes that are regulated by the circadian clock, however, the effects of chronic sleep loss on rhythmic gene expression remain poorly understood. In the present study, we exploited Drosophila sleep mutants insomniac1 (inc1) and wide awakeD2 (wakeD2) as models for chronic sleep loss. We profiled the transcriptomes of heads collected from 4-week-old wild type flies, inc1 and wakeD2 at timepoints around the clock. Analysis of gene oscillation revealed a substantial loss of rhythmicity in inc1 and wakeD2 compared to wild type flies, with most of the affected genes common to both mutants. The disruption of gene oscillation was not due to changes in average gene expression levels. We also identified a subset of genes whose loss of rhythmicity was shared among animals with chronic sleep loss and old flies, suggesting a contribution of aging to chronic, sleep-loss-induced disruption of gene oscillation. Overall design: RNA sequencing data was collected around the clock every 4 hours over 2 days from Drosophila melanogaster heads of 27-day-old wild type flies, 49-day-old wild type flies, 27-day-old inc1 flies, and 27-day old wakeD2 flies. RNA-seq was conducted on the Illumina NextSeq 500 sequencer to generate 75bp single reads, following manufacturer's protocol. The sequencing depth was about 25 million reads per sample. Reads were aligned to the D. melanogaster reference genome assembly (Release 6.13) (dos Santos et al., 2015) with STAR (Dobin et al., 2013) and read counts were generated with featureCounts (Liao et al., 2014). The raw sequence data are available for samples of all time points except for WT_ZT28 and WT_ZT40. The counts data generated using STAR and featureCounts for all RNA-seq samples are available in supplementary file. The code used for RNA-seq analysis and intermediary results are available at https://github.com/wangzikun329/Wang2022 RNA-seq expression plots for all genes are available at https://zikunwang.shinyapps.io/rna_seq_gene_plot/