To analyze the effects of HFD feeding on circadian transcriptomic profiles in murine ELGs, we investigated the expression of cycling transcripts in ELGs collected at eight time points at 3-hour intervals. We identified 2663 (14.14%) and 1553 (8.54%) circadian transcripts (
Supplementary Table S2) from all ELG transcripts of HFD (18,829) and NC-1 (18,181) mice, respectively (
Figs. 4A,
4B;
Supplementary Table S3). In total, 516 cycling transcripts were shared between the two groups, 1037 were unique to NC-1 ELGs, and 2147 were unique to HFD-fed ELGs (
Fig. 4B;
Supplementary Table S4). Although the expression of unique transcripts in NC-1 mice peaked during the light phase, they did not display a significant circadian rhythmic pattern in HFD ELGs (
Supplementary Figs. S2A,
S2C). In contrast, the unique cycling transcripts in HFD mice were mainly expressed during the dark phase but did not show a significant circadian rhythmic expression pattern in NC-1 ELGs (
Supplementary Figs. S2B,
S2C). To evaluate the temporal effect of an HFD on the circadian transcriptome, we calculated the phase, period, and Rayleigh vector of the cycling transcripts in the shared, NC-1–specific, and HFD-specific cycling transcripts using Oriana software. The results showed that the expression phase of NC-1–specific cycling transcripts was mainly during the daytime (
Fig. 4C). The mean vector (µ) was approximately ZT6:07, and its length (
r) was 0.463 (
Fig. 4C). In contrast, the expression phase of HFD-specific cycling transcripts occurred during the dark phase (µ = ZT18:37;
r = 0.309) (
Fig. 4D). Interestingly, the shared cycling transcripts were mainly distributed from ZT3 to ZT13.5 in the NC-1 group (µ = ZT7:59;
r = 0.484) and throughout the circadian cycle in the HFD group (µ = ZT9:47;
r = 0.155) (
Figs. 4E,
4F). Of the shared transcripts in HFD ELGs, 79.85% were phase shifted and only 20.15% were in phase (
Fig. 4G). Of these shifted rhythmic transcripts, 64.32% were delayed in phase, and 35.68% were advanced (
Figs. 4G–
4I). The amplitude of oscillation in HFD unique cycling transcripts was lower than that in the NC-1 group (
Supplementary Fig. S2D, top). Similarly, the amplitude of oscillation of shared transcripts was lower in the HFD group than in the NC-1 group (
Supplementary Fig. S2D, bottom). Thus, HFD intervention dramatically altered the composition, number, and oscillation phase of rhythm transcripts in mouse ELGs.