Pattern formation during development is one of the elegant self-organized phenomena that allow cells to regulate their functions. At all levels, from DNA to a tissue or organ, many developmental processes include the determination of cellular functions through pattern formation. To elucidate the mechanism underlying pattern formation, numerous mathematical models have been developed and applied. However, model simplification has resulted in the role of domains not being seriously considered in pattern formation. Here, we introduce a novel application of the phase-field method for analysis of chromatin dynamics, and a mathematical approach that includes domain information into a biochemical model of pattern formation. Using this new modeling method, here, we consider the role of nuclear and cellular cell shapes on pattern formation.