A Multi-Layered Study on Harmonic Oscillations in Mammalian Genomics and Proteomics

Int J Mol Sci. 2019 Sep 17;20(18):4585. doi: 10.3390/ijms20184585.


Cellular, organ, and whole animal physiology show temporal variation predominantly featuring 24-h (circadian) periodicity. Time-course mRNA gene expression profiling in mouse liver showed two subsets of genes oscillating at the second (12-h) and third (8-h) harmonic of the prime (24-h) frequency. The aim of our study was to identify specific genomic, proteomic, and functional properties of ultradian and circadian subsets. We found hallmarks of the three oscillating gene subsets, including different (i) functional annotation, (ii) proteomic and electrochemical features, and (iii) transcription factor binding motifs in upstream regions of 8-h and 12-h oscillating genes that seemingly allow the link of the ultradian gene sets to a known circadian network. Our multifaceted bioinformatics analysis of circadian and ultradian genes suggests that the different rhythmicity of gene expression impacts physiological outcomes and may be related to transcriptional, translational and post-translational dynamics, as well as to phylogenetic and evolutionary components.

Keywords: biological clock; circadian rhythms; electrochemical features; rhythmic gene expression; rhythmic protein expression; ultradian rhythms.

MeSH terms

  • Animals
  • Binding Sites
  • Biomarkers
  • Chromosome Mapping
  • Computational Biology / methods
  • Epigenesis, Genetic
  • Gene Expression Profiling
  • Genomics* / methods
  • Humans
  • Mammals / genetics*
  • Mammals / metabolism*
  • Molecular Sequence Annotation
  • Phylogeny
  • Promoter Regions, Genetic
  • Proteome
  • Proteomics* / methods
  • Time Factors
  • Transcription Factors


  • Biomarkers
  • Proteome
  • Transcription Factors