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Conceptual Confusion: The case of Epigenetics

Angela Oliveira Pisco, Aymeric Fouquier d’Hérouël, Sui Huang
doi: https://doi.org/10.1101/053009
Angela Oliveira Pisco
1Institute for Systems Biology, Seattle, WA, USA
2Systems Biology Program, Faculty of Life Sciences, University of Manchester, Manchester UK
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Aymeric Fouquier d’Hérouël
1Institute for Systems Biology, Seattle, WA, USA
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Sui Huang
1Institute for Systems Biology, Seattle, WA, USA
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  • For correspondence: sui.huang@systemsbiology.org
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ABSTRACT

The observations of phenotypic plasticity have stimulated the revival of ‘epigenetics’. Over the past 70 years the term has come in many colors and flavors, depending on the biological discipline and time period. The meanings span from Waddington’s “epigenotype” and “epigenetic landscape” to the molecular biologists’ “epigenetic marks” embodied by DNA methylation and histone modifications. Here we seek to quell the ambiguity of the name. First we place “epigenetics” in the various historical contexts. Then, by presenting the formal concepts of dynamical systems theory we show that the “epigenetic landscape” is more than a metaphor: it has specific mathematical foundations. The latter explains how gene regulatory networks produce multiple attractor states, the self-stabilizing patterns of gene activation across the genome that account for “epigenetic memory”. This network dynamics approach replaces the reductionist correspondence of molecular epigenetic modifications with concept of the epigenetic landscape, by providing a concrete and crisp correspondence.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted May 12, 2016.
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Conceptual Confusion: The case of Epigenetics
Angela Oliveira Pisco, Aymeric Fouquier d’Hérouël, Sui Huang
bioRxiv 053009; doi: https://doi.org/10.1101/053009
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Conceptual Confusion: The case of Epigenetics
Angela Oliveira Pisco, Aymeric Fouquier d’Hérouël, Sui Huang
bioRxiv 053009; doi: https://doi.org/10.1101/053009

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