Figure 4. SWR1 mediates histone exchange without net change of nucleosome position.
(A) Left: EMSA (6% native PAGE) shows INO80-mediated nucleosome sliding. An asymmetrically positioned 601 nucleosome with a 43 bp and 0 bp DNA linker was used for the sliding assay. Right: SWR1-mediated incorporation of H2A.Z-H2B dimer (without 3FLAG epitope tag). Incorporation of H2A.Z in nucleosome was confirmed by immunoblotting with anti-H2A.Z antibody. (B) Hydroxyl radical footprinting strategy. A canonical nucleosome with 60 bp and 0 bp linker DNA and fluorescence end-label (bottom strand) was used as substrate for histone replacement, followed by hydroxyl radical treatment and separation by 6% native PAGE. (C) Recovered DNA from gel slices containing AA, AZ, and ZZ states was analyzed on DNA sequencing gels. (D) Intensity plots for AA, AZ, and ZZ nucleosomes.