Solution AFM studies of human Swi-Snf and its interactions with MMTV DNA and chromatin

Abstract

ATP-dependent nucleosome remodeling complexes are crucial for relieving nucleosome repression during transcription, DNA replication, recombination, and repair. Remodeling complexes can carry out a variety of reactions on chromatin substrates but precisely how they do so remains a topic of active inquiry. Here, a novel recognition atomic force microscopy (AFM) approach is used to characterize human Swi-Snf (hSwi-Snf) nucleosome remodeling complexes in solution. This information is then used to locate hSwi-Snf complexes bound to mouse mammary tumor virus promoter nucleosomal arrays, a natural target of hSwi-Snf action, in solution topographic AFM images of surface-tethered arrays. By comparing the same individual chromatin arrays before and after hSwi-Snf activation, remodeling events on these arrays can be monitored in relation to the complexes bound to them. Remodeling is observed to be: inherently heterogeneous; nonprocessive; able to occur near and far from bound complexes; often associated with nucleosome height decreases. These height decreases frequently occur near sites of DNA release from chromatin. hSwi-Snf is usually incorporated into nucleosomal arrays, with multiple DNA strands entering into it from various directions, + or - ATP; these DNA paths can change after hSwi-Snf activation. hSwi-Snf appears to interact with naked mouse mammary tumor virus DNA somewhat differently than with chromatin and ATP activation of surface-bound DNA/hSwi-Snf produces no changes detectable by AFM.

FIGURE 1

Images of hSwi-Snf and hSwi-Snf/DNA complexes. Topographic (A) and recognition (B) images of hSwi-Snf are shown. Some representative particles in images A and B are numbered. Particles 1–8 represent complexes in panel A that are recognized by the BRG1 antibody present on the tip during scanning (B). Their heights are: 1, 4.6 nm; 2, 3.7 nm; 3, 4.3 nm; 4, 6.0 nm; 5, 4.6 nm; 6, 3.0 nm; 7, 1.8 nm; 8, 2.2 nm. Particles 9–11 represent particles in panel A that are not (or only weakly) recognized by the BRG1 antibody during scanning. Their heights are: 9, 5.7 nm; 10, 4.2 nm; 11, 2.9 nm. Immediately below Fig 1 A is an image that superimposes recognition events for the numbered complexes in Fig. 1 B on the topographic image from Fig. 1 A (recognition events are identified by blue dots). Note that the sizes of particles in recognition images are often larger than in the corresponding topographic images. The blue dots are not meant to reflect recognition spot size, only the occurrence of strong recognition. The large size of recognition spots may reflect the effect of the antibody tether or other features (25). Higher-magnification topographic and recognition images of some complexes from panel A (1, 3, and 5) are compared side-by-side in panel C. Panel D shows an example of an image of hSwi-Snf plus DNA (1:1 molar ratio). Yellow arrows mark particles that are probably free hSwi-Snf complexes, i.e., not bound to DNA. The heights of the marked, DNA-bound complexes in panel D are: 1, 2.6 nm; 2, 2.3 nm; 3, 7.1 nm (with a 2.1-nm particle to the immediate lower right of the main particle); 4, 1.2 and 1.4 nm. Panel E shows an example of hSwi-Snf bound to DNA (1:6 hSwi-Snf/DNA molar ratio), imaged before (−) and after (+) ATP addition. The heights of the several (presumably) hSwi-Snf blobs in the center of the image are ∼2 nm. The scale bars are 100 nm in images A, B, D, and E and 50 nm in image C.

FIGURE 2

Heights of hSwi-Snf alone, heights of hSwi-Snf bound to chromatin near sites of significant remodeling, and nucleosome heights. Panel A shows the distribution of hSwi-Snf heights in images such as those in Fig. 1 A. The open bars are particles imaged only topographically. The solid bars are particles in topographic images for which a corresponding particle was found in a recognition image obtained by scanning using an AFM tip containing the BRG1 antibody. Only some of the topographic images were checked for recognition; thus the larger numbers of open bars do not reflect low recognition efficiency. The efficiency of BRG1 recognition in these images is estimated to be ∼60%. Panel B shows heights for particles identified as hSwi-Snf (height ≥4.2 nm, width and shape characteristic of hSwi-Snf; see text) in images of hSwi-Snf plus MMTV nucleosomal arrays that show major remodeling changes after ATP addition to the in situ sample. The striped bars are heights measured in images before the addition of ATP to the deposited samples and the open bars are heights after ATP addition. Panel C shows the height distribution for nucleosomes measured in all 18 high-resolution fields analyzed. Heights were measured in the −ATP image to avoid remodeling effects. The average height value for this set of nucleosomes is 2.7 ± 0.4 nm. In each of the three panels, the y axis is the number of particles (hSwi-Snf or nucleosomes) with a particular height value and the x axis is height, binned in 0.2-nm intervals. Error bars are ± 1 SD.

FIGURE 3

Examples of hSwi-Snf complexes bound to MMTV nucleosomal arrays and the remodeling events that occur near these identified complexes. Images of the same fields before (−) and after (+) in situ ATP addition to deposited hSwi-Snf + MMTV nucleosomal arrays are compared. The hSwi-Snf complexes identified in each pair of images (using the criteria described in the text) are designated as S1, S2, etc. Nucleosomes are numbered. Yellow arrows identify features involving DNA changes, such as newly released DNA, that are present after ATP addition. These various features are discussed in the text. The heights of the hSwi-Snf complexes shown in this figure are tabulated, − and + ATP, in Table 1 and the average nucleosome heights in the high-magnification image from which this example was taken are also given in Table 1. The pair of images to the immediate right of the +ATP image in panel D are from the region around S1 in image D, using an image presentation adjusted (contrast, etc.) to enhance DNA visibility. All samples shown in this figure were checked in this way to insure the correctness of the identified DNA paths. The leveling algorithm necessary to maximize contrast causes the dark horizontal streaks in these images. They are unavoidable but clear indications of taller particles. The middle streak in panel A is due to a tall complex just off right of the field shown.

FIGURE 4

The lengths of DNA released during remodeling events. The lengths of DNA released in remodeling events, from either terminal (open bars) or internal nucleosomes (solid bars), for the entire set of 18 high-resolution images are shown versus the number of times that release length was observed in the data set. These lengths were obtained by measuring DNA pathlengths before and after ATP addition. Values were binned in 2-nm intervals. Error bars are ± 1 SD.

FIGURE 5

Possible bulge propagation during a nucleosome sliding event. After ATP addition, the nucleosome in this image has slid almost to the adjacent DNA terminus (with no other change in the rest of the molecule; not shown) and the DNA now appears bifurcated on the left side of the nucleosome with the lower “branch” (yellow arrow, +ATP image) broader than the upper. This breadth could reflect a doubled “bulge” of DNA; if doubled, its length (25 nm × 2 = 50 nm) equals the difference in length from this nucleosome to the DNA terminus in the − versus + ATP images. Thus, this branch could be a trapped bulge of DNA generated during nucleosome sliding.

FIGURE 6

The particle height distribution for hSwi-Snf bound to DNA. This figure shows the histogram of heights measured for hSwi-Snf complexes bound to MMTV promoter DNA. Only particles actually bound to DNA were included. The y axis is the number of particles with a particular height value and heights are binned in 0.2-nm intervals. Data from all stoichiometries of hSwi-Snf/DNA (see text) are included. Error bars are ± 1 SD.

FIGURE 7

Nucleosome height decreases after ATP addition. Histograms of nucleosome heights before (A) and after (B) ATP addition for the images analyzed in Fig. 3 are shown. Values are binned in 0.25-nm intervals. The peak falls from just below 3 nm in the −ATP images to just above 2 nm in the +ATP images, an average decrease of ∼25%.