CLK and CYC CUT&RUN in aging Drosophila photoreceptors

Rhythmic changes in the transcriptome are widespread during aging in Drosophila photoreceptors. To investigate the mechanisms underyling these rhythmic changes, we performed CUT&RUN in photoreceptors of the core transcriptional activators that control the circadian rhythm, CLK and CYC, in both young and old flies across the circadian day. Overall design: Drosophila were maintained in population cages in a 25°C incubator with a 12:12 hour light:dark cycle. 200 male flies in triplicate were collected at the indicated days post-eclosion (D10 and D50) and at the indicated Zeitgeber times (ZT4, ZT12, ZT16). 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). For CUT&RUN, 1 ug of either anti-GFP antibody, or IgG was used. MNase digestion was performed for 5 min using 1 ug of antibody.