Skip to main content
. 2021 Feb 12;10:e64061. doi: 10.7554/eLife.64061

Figure 1. Isw2 is a specialist remodeler that positions single nucleosomes at target sites.

(A) (Left) Clustered heatmap showing differences in nucleosome dyad signal between isw2/isw1/chd1 and ISW2/isw1/chd1 strains at 5942 pre-initiation complex sites (PICs). Black indicates positions where Isw2 preferentially positions nucleosomes compared to the strain lacking Isw2. (Middle) Heatmap of ISW2(K215R) ChIP signal, with rows linked to the PIC data on the left, shows that Isw2-dependent nucleosome changes overlap with regions where Isw2 is present. (Right) Average nucleosome dyad signal for wild type (WT) (black), isw1/chd1 (cyan), and isw2/isw1/chd1 (red) strains for the 178 PIC sites in cluster 3. Black arrows denote Isw2-driven nucleosome shifts. Green arrows indicate rapid decay of positioning at PIC-distal nucleosomes in the ISW2/isw1/chd1 mutant. (B) (Left) Genome Browser image showing nucleosome dyad signal at a unscheduled meiotic gene expression (Ume6) motif (cyan rectangle) for indicated strains. Vertical gray dashed line denotes the motif-proximal WT nucleosome positions while vertical pink dashed line indicates the nucleosome positions in the absence of Ume6 or Isw2. (Center) Clustered heatmap showing the difference in nucleosome dyad signal between isw2/isw1/chd1 and ISW2/isw1/chd1 strains at 202 intergenic Ume6 motifs. Black indicates positions where Isw2 preferentially positions nucleosomes compared to strains lacking Isw2. (Right) Average nucleosome dyad signal for indicated strains at Ume6 motifs in cluster 1. Black arrows indicate direction of nucleosome positioning by Isw2. Green arrows signify decreased positioning of motif-distal nucleosomes in the ISW2/isw1/chd1 strain (cyan) compared to WT (black). (C) (Left) Cartoon depicting the expected activity of Isw2 at barrier elements according to current biochemical data and nucleosome positioning models. Isw2 is thought to move nucleosomes away from bound factors and space nucleosomes with an approximately 200 base pair repeat length. (Right) Cartoon of the observed activity of Isw2 at target sites where only a motif-proximal single nucleosome is precisely positioned but distal nucleosomes are not well-spaced by Isw2.

Figure 1.

Figure 1—figure supplement 1. Isw2 is a precise specialist at target nucleosomes.

Figure 1—figure supplement 1.

Meta-analysis nucleosome dyad signal at all 5942 pre-initiation complex sites (PICs) shows that Isw2 confers no global nucleosome organizing activity throughout yeast cells. WT: wild type.
Figure 1—figure supplement 2. Isw2 is a precise specialist at target nucleosomes.

Figure 1—figure supplement 2.

Example Isw2 target locus where addition of Isw2 in the absence of Isw1 and Chd1 leads to positioning of a single motif-proximal nucleosome at the NTE1 locus. Vertical gray dashed lines indicate the wild-type nucleosome locations while vertical dashed pink lines indicate an alternate isw2 deletion strain position at the motif-proximal nucleosome. The ISW2/chd1/isw1 strain can position the motif-proximal nucleosome, but all distal nucleosomes are disorganized much like the isw2/chd1/isw1 strain.
Figure 1—figure supplement 3. Isw2 is a precise specialist at target nucleosomes.

Figure 1—figure supplement 3.

Heatmaps showing that full-length unscheduled meiotic gene expression (Ume6)-FLAG (left) and Ume6(∆2–763)-FLAG (middle) associate with similar targets. (Right) Clustered heatmap from Figure 1B showing the difference in nucleosome dyad signal between isw2/isw1/chd1 and ISW2/isw1/chd1 strains at 202 intergenic Ume6 motifs. Black indicates positions where Isw2 preferentially positions nucleosomes compared to strains lacking Isw2. All rows are linked, and all 202 intergenic Ume6 motifs are displayed. 
Figure 1—figure supplement 4. Isw2 is a precise specialist at target nucleosomes.

Figure 1—figure supplement 4.

Meta-analysis of nucleosome dyad signal for indicated strains at the 58 unscheduled meiotic gene expression (Ume6) target loci associated with cluster 1 in Figure 1B demonstrates that Isw2 but not Chd1 or Isw1 is necessary and sufficient to position nucleosomes at Ume6 target loci.
Figure 1—figure supplement 5. Isw2 is a precise specialist at target nucleosomes.

Figure 1—figure supplement 5.

Genome Browser image showing nucleosome dyad signal for indicated strains at the MEI4-ACA1 locus, a representative unscheduled meiotic gene expression (Ume6) target locus. The color schemes are shared between Figure 1—figure supplement 1D and E according to the key between figures. Vertical gray lines indicate wild-type nucleosome positions while vertical pink lines indicate ectopic nucleosome positions associated with loss of Isw2 activity.