Fig. 1: The rhythmic transcriptome of human hepatocytes in vivo.

a Schematic representation for the generation of immunodeficient humanized liver chimeric mice (HLCM). Liver tissues obtained from these HLCM were used to perform RNA-seq and ChIP-seq. PHH primary human hepatocyte. The cartoon was created by the authors using images from freely available online resources. b Mean rhythmic expression pattern of core CC-oscillator genes and CC-output regulators in human and mouse liver cells of HLCM in two independent experiments (Series 1 and 2). Series 1: n = 2/timepoint, Series 2: n = 3/timepoint. Source data are provided as a Source Data file. c Mean expression pattern of genes showing rhythmicity in human and mouse hepatocytes in HLCM as predicted by dryR (n = 5 HLCM/ diurnal timepoint). dryR identified four models of rhythmic genes in HLCM. A fifth model comprising only non-cycling genes is not shown. Phase distribution of respective models is indicated by radial coordinates, where green-human, pink-mice, and gray-overlap of humans and mice. Source data are provided as a Source Data file. d HALLMARK pathways significantly (FDR <0.05) enriched for rhythmic genes in human hepatocytes in HLCM (n = 5 HLCM/ timepoint) as listed in (c) and their expression in WT mice. Similar pathways show overlapping (±1 ZT step) of peak enrichment scores comparing human and WT mice maximum enrichment scores. Source data are provided as a Source Data file. e Rhythmic expression of transcription factors (TFs) in human hepatocytes in HLCM (n = 5 HLCM/ timepoint), as predicted by dryR. Source data are provided as a Source Data file. f Examples of the mean expression pattern of dryR identified TFs as listed in (e). The Y-axis represents the DESeq2 normalized reads. Human hepatocytes (red) and residual murine (green) cells. n = 5 HLCM/timepoint. Bars represent SD. Source data are provided as a Source Data file. g ChIP-seq coverage plots indicate diurnal variations in H3K27ac levels in IRF2 in human hepatocytes and WT mice liver. Human (green) and murine (red) cells. ZT0: represented twice in (b–f) in each panel to maintain conformity.