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Nucleosome Repositioning via Loop Formation

I. M. Kuli and H. Schiessel

Max-Planck-Institut für Polymerforschung, Theory Group, Mainz, Germany

Correspondence: Address reprint requests to Igor M. Kuli, Max-Planck-Institute for Polymer Research, Ackermannweg 10, Mainz, Germany D-55128. Tel.: 49-06-13-137-9148; E-mail: kulic{at}mpip-mainz.mpg.de.

Active (catalyzed) and passive (intrinsic) nucleosome repositioning is known to be a crucial event during the transcriptional activation of certain eukaryotic genes. Here we consider theoretically the intrinsic mechanism and study in detail the energetics and dynamics of DNA-loop-mediated nucleosome repositioning, as previously proposed by earlier works. The surprising outcome of the present study is the inherent nonlocality of nucleosome motion within this model–being a direct physical consequence of the loop mechanism. On long enough DNA templates the longer jumps dominate over the previously predicted local motion, a fact that contrasts simple diffusive mechanisms considered before. The possible experimental outcome resulting from the considered mechanism is predicted, discussed, and compared to existing experimental findings.