PT  - JOURNAL ARTICLE
AU  - Angela Oliveira Pisco
AU  - Aymeric Fouquier d’Hérouël
AU  - Sui Huang
TI  - Conceptual Confusion: The case of Epigenetics
AID  - 10.1101/053009
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 053009
4099  - http://biorxiv.org/content/early/2016/05/12/053009.short
4100  - http://biorxiv.org/content/early/2016/05/12/053009.full
AB  - 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.