Chromatin-remodeling complexes regulate access to nucleosomal DNA by mobilizing nucleosomes in an ATP-dependent manner. In this study, we find that chromatin remodeling by SWI/SNF and ISW2 involves DNA translocation inside nucleosomes two helical turns from the dyad axis at superhelical location-2. DNA translocation at this internal position does not require the propagation of a DNA twist from the site of translocation to the entry/exit sites for nucleosome movement. Nucleosomes are moved in 9- to 11- or approximately 50-base-pair increments by ISW2 or SWI/SNF, respectively, presumably through the formation of DNA loops on the nucleosome surface. Remodeling by ISW2 but not SWI/SNF requires DNA torsional strain near the site of translocation, which may work in conjunction with conformational changes of ISW2 to promote nucleosome movement on DNA. The difference in step size of nucleosome movement by SWI/SNF and ISW2 demonstrates how SWI/SNF may be more disruptive to nucleosome structure than ISW2.

The structure of the SWI/SNF-remodeled nucleosome was characterized with single base-pair resolution by mapping the contacts of specific histone fold residues with nucleosomal DNA. We demonstrate that SWI/SNF peels up to 50 bp of DNA from the edge of the nucleosome, translocates the histone octamer beyond the DNA ends via a DNA bulge propagation mechanism, and promotes the formation of an intramolecular DNA loop between the nucleosomal entry and exit sites. This stable altered nucleosome conformation also exhibits alterations in the distance between contacts of specific histone residues with DNA and higher electrophoretic and sedimentation mobility, consistent with a more compact molecular shape. SWI/SNF converts a nucleosome to the altered state in less than 1 s, hydrolyzing fewer than 10 ATPs per event.

SUMMARY The ATP-dependent chromatin remodeling complex SWI/SNF regulates transcription and has been implicated in promoter nucleosome eviction. Efficient nucleosome disassembly by SWI/SNF alone in biochemical assays has however not been directly observed. Employing a model system of dinucleosomes rather than mononucleosomes, we demonstrate that remodeling leads to ordered and efficient disassembly of one of the two nucleosomes. An H2A/H2B dimer is first rapidly displaced and then in a slower reaction an entire histone octamer is lost. Nucleosome disassembly by SWI/SNF did not require additional factors such as chaperones or acceptors of histones. Observations in single molecules as well as bulk measurement suggest that a key intermediate in this process is one in which a nucleosome is moved towards the adjacent nucleosome. SWI/SNF recruited by the transcriptional activator Gal4-VP16 preferentially mobilizes the proximal nucleosome and destabilizes the adjacent nucleosome.

The imitation switch (ISWI) complex from yeast containing the Isw2 and Itc1 proteins was shown to preferentially slide mononucleosomes with as little as 23 bp of linker DNA from the end to the center of DNA. The contacts of unique residues in the histone fold regions of H4, H2B, and H2A with DNA were determined with base pair resolution before and after chromatin remodeling by a site-specific photochemical cross-linking approach. The path of DNA and the conformation of the histone octamer in the nucleosome remodeled or slid by ISW2 were not altered, because after adjustment for the new translational position, the DNA contacts at specific sites in the histone octamer had not been changed. Maintenance of the canonical nucleosome structure after sliding was also demonstrated by DNA photoaffinity labeling of histone proteins at specific sites within the DNA template. In addition, nucleosomal DNA does not become more accessible during ISW2 remodeling, as assayed by restriction endonuclease cutting. ISW2 was also shown to have the novel capability of counteracting transcriptional activators by sliding nucleosomes through Gal4-VP16 bound initially to linker DNA and displacing the activator from DNA.The process of making DNA more or less accessible in eukaryotes plays a crucial role in the regulation of transcription, replication, recombination, and DNA repair. Several large multisubunit complexes reorganize chromatin in an ATPdependent manner to either activate or repress these cellular processes (26,44,51,53,56,57). ATP-dependent chromatin remodeling complexes contain an ATPase that has a wellconserved seven-domain region, and the ATPase activity is stimulated by DNA and nucleosomes (26). These chromatin remodeling complexes can be divided into four classes: the SWI/SNF and RSC, ISWI (for imitation SWI family), CHD/ Mi-2, and INO80 families (12,26,28,39,43,55). The ISWI protein in Drosophila is assembled into three distinct complexes (NURF, for nucleosome remodeling factor; CHRAC, for chromatin accessibility complex; and ACF, for ATP-utilizing chromatin assembly and remodeling factor), each with different subunit compositions and biochemical activities (9,22,23,47,49,52). In yeast, there are two ISWI proteins, referred to as Isw1p and Isw2p, which are closely related by sequence to the Drosophila ISWI protein and are associated with one to three other polypeptides (48).A general feature of the ISWI family of chromatin remodeling complexes is that they change the translational position of nucleosomes or slide nucleosomes (17,20,28,29). In addition, all of the ISWI complexes except for NURF have been shown to help regularly space nucleosomes. The spacing activities of ISW1 and ISW2 differ in that ISW1 produces more regularly spaced arrays than ISW2, and the spacing varied from ϳ175 to ϳ200 bp for ISW1 and ISW2, respectively (48). ISWI, SWI/SNF, RSC, and Mi-2 have all recently been shown to induce torsional strain on DNA during remodeling (21). A distinguishing characteristic of these complexes is that ISWI requires hist...