A Multi-Layered Study on Harmonic Oscillations in Mammalian Genomics and Proteomics
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. Th...
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doaj-5c6ce5141a62446abb4056e816038a382020-11-25T02:48:02ZengMDPI AGInternational Journal of Molecular Sciences1422-00672019-09-012018458510.3390/ijms20184585ijms20184585A Multi-Layered Study on Harmonic Oscillations in Mammalian Genomics and ProteomicsNikolai Genov0Stefano Castellana1Felix Scholkmann2Daniele Capocefalo3Mauro Truglio4Jessica Rosati5Elisa Maria Turco6Tommaso Biagini7Annalucia Carbone8Tommaso Mazza9Angela Relógio10Gianluigi Mazzoccoli11Institute for Theoretical Biology (ITB), Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 1011 Berlin, GermanyBioinformatics Unit, IRCCS “Casa Sollievo della Sofferenza”, 71013 San Giovanni Rotondo (FG), ItalyResearch Office for Complex Physical and Biological Systems (ROCoS), 8006 Zurich, SwitzerlandBioinformatics Unit, IRCCS “Casa Sollievo della Sofferenza”, 71013 San Giovanni Rotondo (FG), ItalyBioinformatics Unit, IRCCS “Casa Sollievo della Sofferenza”, 71013 San Giovanni Rotondo (FG), ItalyCell Reprogramming Unit, Fondazione IRCCS “Casa Sollievo della Sofferenza”, 71013 San Giovanni Rotondo (FG), ItalyCell Reprogramming Unit, Fondazione IRCCS “Casa Sollievo della Sofferenza”, 71013 San Giovanni Rotondo (FG), ItalyBioinformatics Unit, IRCCS “Casa Sollievo della Sofferenza”, 71013 San Giovanni Rotondo (FG), ItalyDivision of Internal Medicine and Chronobiology Unit, Fondazione IRCCS “Casa Sollievo della Sofferenza”, 71013 San Giovanni Rotondo (FG), ItalyBioinformatics Unit, IRCCS “Casa Sollievo della Sofferenza”, 71013 San Giovanni Rotondo (FG), ItalyInstitute for Theoretical Biology (ITB), Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 1011 Berlin, GermanyDivision of Internal Medicine and Chronobiology Unit, Fondazione IRCCS “Casa Sollievo della Sofferenza”, 71013 San Giovanni Rotondo (FG), ItalyCellular, 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.https://www.mdpi.com/1422-0067/20/18/4585biological clockrhythmic gene expressionrhythmic protein expressioncircadian rhythmsultradian rhythmselectrochemical features |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
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 |
spellingShingle |
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 A Multi-Layered Study on Harmonic Oscillations in Mammalian Genomics and Proteomics International Journal of Molecular Sciences biological clock rhythmic gene expression rhythmic protein expression circadian rhythms ultradian rhythms electrochemical features |
author_facet |
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 |
author_sort |
Nikolai Genov |
title |
A Multi-Layered Study on Harmonic Oscillations in Mammalian Genomics and Proteomics |
title_short |
A Multi-Layered Study on Harmonic Oscillations in Mammalian Genomics and Proteomics |
title_full |
A Multi-Layered Study on Harmonic Oscillations in Mammalian Genomics and Proteomics |
title_fullStr |
A Multi-Layered Study on Harmonic Oscillations in Mammalian Genomics and Proteomics |
title_full_unstemmed |
A Multi-Layered Study on Harmonic Oscillations in Mammalian Genomics and Proteomics |
title_sort |
multi-layered study on harmonic oscillations in mammalian genomics and proteomics |
publisher |
MDPI AG |
series |
International Journal of Molecular Sciences |
issn |
1422-0067 |
publishDate |
2019-09-01 |
description |
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. |
topic |
biological clock rhythmic gene expression rhythmic protein expression circadian rhythms ultradian rhythms electrochemical features |
url |
https://www.mdpi.com/1422-0067/20/18/4585 |
work_keys_str_mv |
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