Unwrapping of Nucleosomes Detected by Time-Lapse AFM

Abstract

The dynamics of chromatin provide the access to DNA within nucleosomes and therefore, this process is critically involved into the regulation of chromatin function. The questions, such as the range of opening of the nucleosome, and the mechanism whereby the opening occurs and propagates, remain unknown. Here we applied single molecule time lapse AFM imaging to directly visualize the dynamics of nucleosomes and identify the mechanism of the large range DNA exposure. With this technique, we are able to observe the process of unwrapping of nucleosomes. The unwrapping of nucleosomes proceeds from the ends of the particles, allowing for the unwrapping of DNA regions as large as dozens of base pairs. This process may lead to a complete unfolding of nucleosomes and dissociation of the histone core from the complex. The unwrapping occurs in the absence of proteins involved in the chromatin remodeling that require ATP hydrolysis for their function. This suggests that the inherent dynamics of nucleosomes can contribute to the chromatin unwrapping process. There is an electrostatic interaction of DNA with positively charged histone core and the AFM substrate; therefore a balance between these interactions is a driving force for unwrapping. Transiently unwrapped DNA segments can be trapped by electrostatic interactions with the surface increasing the probability for the next unwrapping step. We speculate that interaction of chromatin with surfaces within the cell including the surfaces of remodeling proteins involved into the interaction with chromatin can contribute to the chromatin dynamics facilitating unwrapping of the chromatin. Therefore, APS-mica can play a role of a model system for elucidating of the role of electrostatic interactions of chromatin with intracellular surfaces in regulation of the chromatin dynamics and genes activity.The work is supported by grants EPS-0701892, PHY-0615590 (both NSF) and GM062235 (NIH).