DYNAMICS AND FUNCTION OF COMPACT NUCLEOSOME ARRAYS

The packaging of eukaryotic DNA into chromatin sterically occludes polymerases, recombinases and repair enzymes. How chromatin structure changes to allow their actions is unknown. We constructed defined fluorescently labeled trinucleosome arrays, allowing analysis of chromatin conformational dynamics via fluorescence resonance energy transfer (FRET). The arrays undergo reversible Mg(2+)-dependent folding like that of longer arrays studied previously. We define two intermediate conformational states in the reversible folding of the nucleosome arrays, and characterize the microscopic rate constants. Nucleosome arrays are highly dynamic even when compact, undergoing conformational fluctuations on seconds to microseconds timescales. Compact states of the arrays allow binding to DNA within the central nucleosome via site exposure. Protein binding can also drive decompaction of the arrays. Thus, our results reveal multiple modes by which spontaneous chromatin fiber dynamics allows for the invasion and action of DNA processing protein complexes.