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J. Biol. Chem., Vol. 279, Issue 38, 39933-39941, September 17, 2004

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Spatial Contacts and Nucleosome Step Movements Induced by the NURF Chromatin Remodeling Complex^*

Ralf Schwanbeck, Hua Xiao, and Carl Wu

From the Laboratory of Molecular Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892-4255

The nucleosome remodeling factor NURF is a four-subunit, ISWI-containing chromatin remodeling complex that catalyzes nucleosome sliding in an ATP-dependent fashion, thereby modulating the accessibility of the DNA. To elucidate the mechanism of nucleosome sliding, we have investigated by hydroxyl radical footprinting how NURF makes initial contact with a nucleosome positioned at one end of a DNA fragment. NURF binds to two separate locations on the nucleosome: a continuous stretch of linker DNA up to the nucleosome entry site and a region asymmetrically surrounding the nucleosome dyad within the minor grooves, close to residues of the histone H4 tail that have been implicated in the activation of ISWI activity. Kinetic analysis reveals that nucleosome sliding occurs in apparent increments or steps of 10 bp. Furthermore, single nucleoside gaps as well as nicks about two helical turns before the dyad interfere with sliding, indicating that structural stress at this region assists the relative movement of DNA. These findings support a sliding model in which the position-specific tethering of NURF forces a translocating ISWI ATPase to pump a DNA distortion over the histone octamer, thereby changing the translational position of the nucleosome.

Received for publication, June 1, 2004 , and in revised form, July 6, 2004.

^* The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

The on-line version of this article (available at http://www.jbc.org) contains a supplemental movie.

Supported by a European Molecular Biology Organization Long Term Fellowship and a National Institutes of Health Visiting Fellowship.

To whom correspondence should be addressed: Laboratory of Molecular Cell Biology, Center for Cancer Research, NCI, NIH, Bldg. 37, Rm. 6068, Bethesda, MD 20892-4255. Tel.: 301-496-3029; Fax: 301-435-3697; E-mail: carlwu{at}helix.nih.gov.

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