Nuclear Proteomics Uncovers Diurnal Regulatory Landscapes in Mouse Liver

Cell Metab. 2017 Jan 10;25(1):102-117. doi: 10.1016/j.cmet.2016.10.003. Epub 2016 Nov 3.


Diurnal oscillations of gene expression controlled by the circadian clock and its connected feeding rhythm enable organisms to coordinate their physiologies with daily environmental cycles. While available techniques yielded crucial insights into regulation at the transcriptional level, much less is known about temporally controlled functions within the nucleus and their regulation at the protein level. Here, we quantified the temporal nuclear accumulation of proteins and phosphoproteins from mouse liver by SILAC proteomics. We identified around 5,000 nuclear proteins, over 500 of which showed a diurnal accumulation. Parallel analysis of the nuclear phosphoproteome enabled the inference of the temporal activity of kinases accounting for rhythmic phosphorylation. Many identified rhythmic proteins were parts of nuclear complexes involved in transcriptional regulation, ribosome biogenesis, DNA repair, and the cell cycle and its potentially associated diurnal rhythm of hepatocyte polyploidy. Taken together, these findings provide unprecedented insights into the diurnal regulatory landscape of the mouse liver nucleus.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cell Nucleus / metabolism*
  • Circadian Clocks / genetics
  • Circadian Rhythm* / genetics
  • DNA Repair
  • Gene Expression Regulation
  • Isotope Labeling
  • Liver / metabolism*
  • Mass Spectrometry
  • Mice
  • Mice, Knockout
  • Nuclear Proteins / metabolism
  • Organelle Biogenesis
  • Phosphoproteins / metabolism
  • Phosphorylation
  • Polyploidy
  • Protein Kinases / metabolism
  • Proteome / metabolism
  • Proteomics / methods*
  • Ribosomes / metabolism
  • Time Factors
  • Transcription Factors / metabolism
  • Transcription, Genetic


  • Nuclear Proteins
  • Phosphoproteins
  • Proteome
  • Transcription Factors
  • Protein Kinases