Morphogenesis Software based on Epigenetic Code Concept

TL;DR

This paper introduces Morphogenesis Software that simulates 3D embryo development based on a novel epigenetic code concept, providing a proof-of-concept for epigenetic regulation in morphogenesis.

Contribution

It formalizes a mathematical model of morphogenesis driven by epigenetic information and implements software to simulate embryo development from zygote to shape.

Findings

Software successfully simulates embryo development

Variation in rules affects embryo shape

Supports hypothesis of epigenetic regulation in morphogenesis

Abstract

The process of morphogenesis is an evolution of the shape of an organism together with the differentiation of its parts. This process encompasses numerous biological processes ranging from embryogenesis to regeneration following crisis such as amputation or transplantation. A fundamental theoretical question is where exactly do these instructions for (re-)construction reside and how are they implemented? We have recently proposed a set of concepts, aiming to respond to these questions and to provide an appropriate mathematical formalization of the geometry of morphogenesis [1]. First, we consider the possibility that evolution of shape is determined by epigenetic information, responsible for realization of different types of cell events. Second, we suggest a set of rules for converting this epigenetic information into instructive signals for cell events for each cell, as well as for transforming it after each cell event. Next we give notions of cell state, determined by its epigenetic array, and cell event, which is a change of cell state, and formalize development as a graph (tree) of cell states connected by 5 types of cell events, corresponding to the processes of cell division, cell growth, cell death, cell movement and cell differentiation. Here we present a Morphogenesis Software capable of simulating the evolution of a 3D embryo starting from zygote, following a set of rules based on our theoretical assumptions, and thus to provide a proof-of-concept for the hypothesis of epigenetic code regulation. The software creates a developing embryo and a corresponding graph of cell events according to the zygotic epigenetic spectrum and chosen parameters of the developmental rules. Variation of rules influencing the resulting shape of an embryo may help elucidating the principal laws underlying pattern formation.