Analytical ultracentrifugation and agarose gel electrophoresis as tools for studying chromatin folding in solution

Analytical ultracentrifugation and agarose gel electrophoresis each can be used to accurately quantify changes in structure that accompany chromatin folding in solution. Analytical ultracentrifugation directly measures the extent of compaction of each species present in a chromatin sample under a wide range of solution conditions. Agarose gel electrophoresis yields information about changes in the average surface charge density, size and/or shape, and conformational flexibility during chromatin folding. When used together, these methodologies are particularly powerful. Protocols for the characterization of chromatin folding by analytical ultracentrifugation and agarose gel electrophoresis are described. Discussion focuses on analysis and interpretation of experimental chromatin folding data.