Topological Structure of Epigenetic Forests in Flower Morphogenesis

Area of Science:

• Developmental Biology
• Systems Biology
• Genetics

Background:

• Gene regulatory networks (GRNs) govern stable developmental patterns.
• Homeotic mutations in Arabidopsis thaliana provide a model to study disruptions in floral development.
• Understanding the epigenetic landscape is crucial for deciphering GRN dynamics.

Purpose of the Study:

• To investigate how homeotic mutations alter the epigenetic landscape of the floral GRN in Arabidopsis thaliana.
• To quantify the impact of single and double mutants on landscape organization and developmental stability.
• To provide a computational framework for analyzing developmental robustness and epistasis.

Main Methods:

• Development of the Epigenetic Forest framework to model GRN state transitions as basins of attraction.
• Application of the framework to wild-type and various homeotic mutant genotypes (ap1, pi, ag, ap3-pi, ag-pi, ap1-ag).
• Quantification of epigenetic landscape features including basin structure, convergence depth, fate diversity, and divergence from wild type.

Main Results:

• Mutations induce distinct deformations in the epigenetic landscape.
• The ap1 mutant restricts fate accessibility, while pi eliminates B-function identities.
• The ag mutant increases fate diversity, and double mutants show non-additive effects, with ap3-pi being indistinguishable from pi.

Conclusions:

• The Epigenetic Forest framework successfully models canonical floral identities and mutant phenotypes.
• This topology-based approach offers a computable description of developmental robustness and epistasis.
• The study reveals distinct modes of mutant-induced epigenetic landscape deformation in Arabidopsis thaliana floral development.