Rhythmic Transcription and Aging: Insights from the Drosophila Photoreceptor Transcriptome and Epigenome

Rhythmic changes in the transcriptome are widespread during aging in Drosophila photoreceptors. To better understand the epigenetic factors underlying these changes, we profiled RNA PolII occupancy and levels of H3K4me1, H3K4me2, and H3K4me3 using CUT&RUN. To profile changes in chromatin accessibility, we also performed ATAC-seq. To obtain robust rhythmic data across age, we collected both young (D10 post-eclosion) and old (D50 post-eclosion) flies every four hours throughout the day in a 12-hour light:12-hour dark cycle in triplicate. Overall design: Drosophila were maintained in population cages in a 25°C incubator with a 12:12 hour light:dark cycle. 400 male flies in triplicate were collected at the indicated days post-eclosion (D10 and D50) and at the indicated Zeitgeber times (ZT0, ZT4, ZT8, ZT12, ZT16, ZT20). GFP-positive photoreceptor nuclei were immunoprecipitated using the nuclei immunoenrichment protocol (dx.doi.org/10.17504/protocols.io.buiqnudw), followed by CUT&RUN (dx.doi.org/10.17504/protocols.io.zcpf2vn) or ATAC-seq.