Epigenetic regulatory proteins such as transcription factors, chromatin components, and chromatin modification activities alter gene activity during development. The means by which alterations in these factors influence gene expression is poorly understood, but information of this kind is essential if we want to reprogram the epigenotype of specific cell types in a directed fashion. To facilitate chromatin structure-function analysis, we have developed a relatively simple procedure that uses magnetic beads to perform ligation-mediated polymerase chain reaction in solid phase. In this chapter, we describe detailed procedures for the examination of chromatin fine-structure and nucleosome positioning as well as changes in transcription factor binding-site occupancy during cellular differentiation.