Unmasking ultradian rhythms in gene expression

Biological oscillations with an ultradian time scale of 1 to several hours include cycles in behavioral arousal, episodic glucocorticoid release, and gene expression. Ultradian rhythms are thought to have an extrinsic origin because of a perceived absence of ultradian rhythmicity in vitro and a lack...

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Autores principales: van der Veen, Daan R., Gerkema, Menno P.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Federation of American Societies for Experimental Biology 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5240665/
https://www.ncbi.nlm.nih.gov/pubmed/27871062
http://dx.doi.org/10.1096/fj.201600872R
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author van der Veen, Daan R.
Gerkema, Menno P.
author_facet van der Veen, Daan R.
Gerkema, Menno P.
author_sort van der Veen, Daan R.
collection PubMed
description Biological oscillations with an ultradian time scale of 1 to several hours include cycles in behavioral arousal, episodic glucocorticoid release, and gene expression. Ultradian rhythms are thought to have an extrinsic origin because of a perceived absence of ultradian rhythmicity in vitro and a lack of known molecular ultradian oscillators. We designed a novel, non–spectral-analysis method of separating ultradian from circadian components and applied it to a published gene expression dataset with an ultradian sampling resolution. Ultradian rhythms in mouse hepatocytes in vivo have been published, and we validated our approach using this control by confirming 175 of 323 ultradian genes identified in a prior study and found 862 additional ultradian genes. For the first time, we now report ultradian expression of >900 genes in vitro. Sixty genes exhibited ultradian transcriptional rhythmicity, both in vivo and in vitro, including 5 genes involved in the cell cycle. Within these 60 genes, we identified significant enrichment of specific DNA motifs in the 1000 bp proximal promotor, some of which associate with known transcriptional factors. These findings are in strong support of instrinsically driven ultradian rhythms and expose potential molecular mechanisms and functions underlying ultradian rhythms that remain unknown.—Van der Veen, D. R., Gerkema, M. P. Unmasking ultradian rhythms in gene expression.
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spelling pubmed-52406652017-01-23 Unmasking ultradian rhythms in gene expression van der Veen, Daan R. Gerkema, Menno P. FASEB J Research Biological oscillations with an ultradian time scale of 1 to several hours include cycles in behavioral arousal, episodic glucocorticoid release, and gene expression. Ultradian rhythms are thought to have an extrinsic origin because of a perceived absence of ultradian rhythmicity in vitro and a lack of known molecular ultradian oscillators. We designed a novel, non–spectral-analysis method of separating ultradian from circadian components and applied it to a published gene expression dataset with an ultradian sampling resolution. Ultradian rhythms in mouse hepatocytes in vivo have been published, and we validated our approach using this control by confirming 175 of 323 ultradian genes identified in a prior study and found 862 additional ultradian genes. For the first time, we now report ultradian expression of >900 genes in vitro. Sixty genes exhibited ultradian transcriptional rhythmicity, both in vivo and in vitro, including 5 genes involved in the cell cycle. Within these 60 genes, we identified significant enrichment of specific DNA motifs in the 1000 bp proximal promotor, some of which associate with known transcriptional factors. These findings are in strong support of instrinsically driven ultradian rhythms and expose potential molecular mechanisms and functions underlying ultradian rhythms that remain unknown.—Van der Veen, D. R., Gerkema, M. P. Unmasking ultradian rhythms in gene expression. Federation of American Societies for Experimental Biology 2017-02 2016-11-08 /pmc/articles/PMC5240665/ /pubmed/27871062 http://dx.doi.org/10.1096/fj.201600872R Text en © The Author(s) http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution 4.0 International (CC BY 4.0) (http://creativecommons.org/licenses/by/4.0/) which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research
van der Veen, Daan R.
Gerkema, Menno P.
Unmasking ultradian rhythms in gene expression
title Unmasking ultradian rhythms in gene expression
title_full Unmasking ultradian rhythms in gene expression
title_fullStr Unmasking ultradian rhythms in gene expression
title_full_unstemmed Unmasking ultradian rhythms in gene expression
title_short Unmasking ultradian rhythms in gene expression
title_sort unmasking ultradian rhythms in gene expression
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5240665/
https://www.ncbi.nlm.nih.gov/pubmed/27871062
http://dx.doi.org/10.1096/fj.201600872R
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