Determination of polycomb group of protein compartmentalization through chromatin fractionation procedure

Epigenetic mechanisms modulate and maintain the transcriptional state of the genome acting at various levels on chromatin. Emerging evidences suggested that the position in the nuclear space and the crosstalk between components of the nuclear architecture play a role in the regulation of epigenetic signatures. We recently described a crosstalk between the epigenetic repressors Polycomb group of proteins (PcG) and the nuclear lamina. This interplay is important for the maintenance of transcriptional repression at muscle specific genes hence for the correct timing of muscle differentiation. To investigate the synergism between PcG factors and nuclear architecture we improved a chromatin fractionation protocol aimed in analyzing the PcG nuclear compartmentalization. We thus separated PcG proteins in different fractions depending on their solubility. We surprisingly found a consistent amount of PcG proteins in the matrix-associated fraction. In this chapter we describe the chromatin fractionation procedure, a method that can be used to study the nuclear compartmentalization of Polycomb group of proteins and/or PcG targets in murine and drosophila cells.