Supplemental Movie Files for "Agent-Based Modeling of a Nuclear Chromosome Ensemble Identifies Determinants of Homolog Pairing During Meiosis" by Chriss et al.

This set of Supplemental Information contains two movies made from the simulations from the model developed in the manuscript "Agent-Based Modeling of a Nuclear Chromosome Ensemble Identifies Determinants of Homolog Pairing During Meiosis" by A. Chriss, G. V. Börner, and S. D. Ryan.  

Supplemental Movie S1: WT Chromosome Trajectories during Prophase I. The first file "movie_WT..." contains the file for the results of simulations for the wild-type chromosomes and the exact parameter values can be found in Table 1 of the manuscript. The movie shows one realization of the agent-based model. The simulation movie covers the homology search process from t = 3h to t = 9h. Matching colors correspond to homologous pairs. True chromosome lengths are incorporated and scale the relevant interaction radii. The radius represents the attractive and non-homologous repulsive region.

Supplemental Movie S2: WT Chromosome Trajectories during Prophase I with active dumbbell model.  The second file "movieWT_activedumbbell..." contains the file for the results of the simulations for the modeling of chromosomes as active dumbbells (from polymers) to allow for the study of the effects of elongation, orientation, and flexibility. The movie shows one realization of the agent-based active dumbbell model which is closer to modeling a chromosome as a polymer. The simulation movie covers the homology search process from t = 3h to t = 9h. Matching colors correspond to homologous pairs. True chromosome lengths are incorporated and scale the relevant interaction radii, but are allowed to change in time as the two beads expand and contract. The radius represents the attractive and non-homologous repulsive region.

Supplemental Movie S3: spo11 hypomorph (30% WT DSB levels) Chromosome Trajectories during Prophase I (parameters from Fig 7B). The third file "movie_spo11..." contains the file for the results of the simulations for the spo-11 hypomorph and the associated parameter values can be found in Table 1 of the manuscript.  The movie depicts one realization of the agent-based model for the {\it spo11} hypomorphic mutant. The simulation movie covers the homology search process from t = 3h to t = 9h where mutant spo11 is associated with a weaker attractive and repulsive force (e.g., reduction to 77% of WT values). True chromosome lengths are incorporated and scale the relevant interaction radii. Matching colors correspond to homologous pairs. The radii represent the homologous attractive and the non-homologous repulsive region. Note that the reduction in interaction strength delays homologous pairing consistent with experimental observations in [13]. 

The codes that generated these movies were written in Matlab and freely available via GitHub: https://github.com/sdryan/ChromosomeDynamicsProphase1

For questions please contact the corresponding authors:  G. Valentin Börner g.boerner@csuohio.edu (Biology)  or Shawn D. Ryan s.d.ryan@csuohio.edu (Math).