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

Nikolai Genov, Stefano Castellana, Felix Scholkmann, Daniele Capocefalo, Mauro Truglio, Jessica Rosati, Elisa Maria Turco, Tommaso Biagini, Annalucia Carbone, Tommaso Mazza, Angela Relógio, Gianluigi Mazzoccoli

Research output: Contribution to journalArticle

Abstract

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.

Original languageEnglish
JournalInternational Journal of Molecular Sciences
Volume20
Issue number18
DOIs
Publication statusPublished - Sep 17 2019

Fingerprint

harmonic oscillation
Genomics
genes
Proteomics
Genes
set theory
gene expression
Periodicity
Gene expression
annotations
Animal Structures
physiology
Transcription factors
Physiology
Gene Expression Profiling
Bioinformatics
Computational Biology
liver
organs
Liver

Keywords

  • biological clock
  • circadian rhythms
  • electrochemical features
  • rhythmic gene expression
  • rhythmic protein expression
  • ultradian rhythms

ASJC Scopus subject areas

  • Catalysis
  • Molecular Biology
  • Spectroscopy
  • Computer Science Applications
  • Physical and Theoretical Chemistry
  • Organic Chemistry
  • Inorganic Chemistry

Cite this

A Multi-Layered Study on Harmonic Oscillations in Mammalian Genomics and Proteomics. / Genov, Nikolai; Castellana, Stefano; Scholkmann, Felix; Capocefalo, Daniele; Truglio, Mauro; Rosati, Jessica; Turco, Elisa Maria; Biagini, Tommaso; Carbone, Annalucia; Mazza, Tommaso; Relógio, Angela; Mazzoccoli, Gianluigi.

In: International Journal of Molecular Sciences, Vol. 20, No. 18, 17.09.2019.

Research output: Contribution to journalArticle

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