Environmental circadian disruption re-programs liver circadian gene expression

Abstract

Circadian gene expression is fundamental to the establishment and functions of the circadian clock, a cell-autonomous and evolutionary-conserved timing system. Yet, how it is affected by environmental-circadian disruption (ECD) such as shiftwork and jetlag, which impact millions of people worldwide, are ill-defined. Here, we provided the first comprehensive description of liver circadian gene expression under normal and after ECD conditions. We found that post-transcription and post-translation processes are dominant contributors to whole-cell or nuclear circadian proteome, respectively. Furthermore, rhythmicity of 64% transcriptome, 98% whole-cell proteome and 95% nuclear proteome is re-written by ECD. The re-writing, which is associated with changes of circadian cis-regulatory elements, RNA-processing and protein trafficking, diminishes circadian regulation of fat and carbohydrate metabolism and persists after one week of ECD-recovery.

Fig. 1:. A topography of circadian gene expression in mouse liver.

(A, A’) Relative-abundance heatmap (normalized to series average; log2 scale) of rhythmic transcripts (mRNA), rhythmic whole-cell proteins (TE) and rhythmic nuclear proteins (NE) (A), and their Venn diagram of rhythmic overlaps (A’). (B) Percentages of rhythmic time series and their phase distribution of transcripts, whole cell proteins and nuclear proteins. (C-F) Percentage of transcripts with or without proteins (C), proteins with or without transcripts (D), rhythmic transcripts with or without rhythmic whole-cell proteins, (E) rhythmic whole-cell proteins with or without rhythmic transcripts (F) in the 6937 sub-population. (G) Examples of differential transcript (transcription), whole-cell protein (translation) and nuclear (post-translation) circadian patterns. (H-I) Percentages of rhythmic whole-cell proteins with or without rhythmic nuclear proteins (H), or rhythmic nuclear proteins with or without rhythmic whole-cell proteins (I) in the 6937 sub-population. TE – total extract; NE – nuclear extract; RHY – rhythmic; “★” – rhythmic portion; – corresponding groups between (A) and (A’).

Fig. 2:. ECD re-writes rhythmicity of 4179 transcripts.

(A) Relative-abundance heatmap (normalized to series average; log2 scale) of rhythmic transcripts in 21061 transcripts that were quantified under both standard (STD) and ECD conditions. (B) Percent rhythmic transcript time series and the corresponding phase distribution of transcripts that are either rhythmic under ECD, rhythmic under STD but not under ECD (LOR_R), not rhythmic under STD but rhythmic under ECD (GOR_R) or rhythmic under both STD and ECD (ROR_R). (C) The total amount of transcripts that switch their rhythmicity in response to ECD. (D) Core clock transcripts that showed a change in their circadian pattern in response to ECD as quantified by RNA-seqs. (E) Weight matrix of enriched cis-elements within 20kb upstream of the either STD or ECD rhythmic transcripts ranked by Normalized Enrichment Score (NES); “★“ – rhythmic portion.

Fig. 3:. ECD re-writes rhythmicity of circadian whole-cell (TE) and nuclear (NE) proteomes.

(A-B) Relative-abundance heatmap (normalized to series average; log2 scale) of rhythmic proteins in whole-cell (A) or nuclear (B) circadian proteomes under ECD in comparison with STD. (C-D) Percent rhythmic protein time series and the corresponding phase distribution of proteins that either loss rhythmicity (LOR), retain rhythmicity (ROR) or gain rhythmicity (GOR) in the whole-cell (C) or nuclear (D) circadian proteomes. (E) Percent of all proteins that change their rhythmicity at the whole-cell or nuclear compartment levels. (F) Estimate percentages of rhythmic proteins, collectively; “★“ – rhythmic portion.

Fig. 4:. Contributions of post-transcription and post-translation in circadian gene expression under ECD.

(A) Relative abundance heatmap (log2) of rhythmic transcripts, rhythmic whole-cell protein and rhythmic nuclear proteins in 5028 genes of which both transcript and protein were quantified under ECD. (A’) Venn diagram shows overlaps between each population shown in A. (B-C) Percent of transcripts with or without proteins and vice versa. (D-E) Percent of rhythmic transcripts with or without rhythmic whole-cell proteins and vice versa. (F-G) Percent of rhythmic whole-cell proteins with or without rhythmic nuclear proteins and vice versa. (H) Percent of genes with the phase of transcript leads or lags the phase of whole-cell protein under STD or ECD. (I) Percent of genes with the amplitude of whole-cell protein rhythms is lower or higher than that of the transcript rhythms under STD or ECD; “★“ – rhythmic portion; – corresponding groups between (A) and (A’)

Fig. 5:. Comparative functional G.O. enrichment analyses.

(A-B) Heatmap of G.O. enrichment analysis of (A) ECD whole-cell rhythmic proteins peaking during day-time, night-time or both, (B) whole-cell circadian proteome under ECD in comparison with STD. (C) Comparative whole-cell protein abundance throughout a circadian cycle of representative factors in mRNA processing, translation initiation, RTK/Ras signaling and protein transport under STD versus ECD conditions. (D) Reactome enrichment analysis of (B). (E) G.O. Slim map of changes in enrichment of terms related to fatty acid, carboxylic acid and amino acid, as circled in C, in response to ECD.