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. 2022 Mar 8;11:e77595. doi: 10.7554/eLife.77595

Figure 3. iswi and acf1 are required for wild-type H3K27me2/3 and H3K36me3 but loss of these methyl marks is not required for transcriptional upregulation.

(A, B) Scatter plots show the correlation of H3K27me2/3 at genes in wild type and ∆iswi or ∆acf1 based on biological replicates of ChIP-seq data. Green points (n=260 in ∆iswi and n=0 in ∆acf1) represent genes with increased H3K27me2/3 levels (at least twofold over wild type) and red points (n=341 in ∆iswi and n=193 in ∆acf1) represent genes with decreased H3K27me2/3 levels (at least twofold relative to wild type) in the indicated mutant. (C, D) Scatter plots show the correlation of H3K36me3 at genes in wild type and ∆iswi or ∆acf1 based on biological replicates of ChIP-seq data. Green points (n=1 in ∆iswi and n=0 in ∆acf1) represent genes with increased H3K36me3 levels (at least twofold over wild type) and red points (n=444 in ∆iswi and n=317 in ∆acf1) represent genes with decreased H3K36me3 levels (at least twofold relative to wild type) in the indicated mutant. (E, F) Scatter plots show the correlation between H3K27me2/3 and gene expression at H3K27-methylated genes (n=836) in the indicated mutants. Pearson correlation coefficient is reported. Red box indicates genes (n=92 in ∆iswi and n=66 in ∆acf1) that are significantly upregulated (log2 fold change>2) but show no significant loss of H3K27me2/3 (log2 fold change>–1). (G, H) Scatter plots show the correlation between H3K36me3 and gene expression at H3K27-methylated genes (n=836) in the indicated mutants. Pearson correlation coefficient is reported. (I) ChIP-seq tracks showing average level of H3K27me2/3 or H3K36me3 merged from two biological replicates for the indicated strains on LG III. Y-axis is 0–1000 RPKM for H3K27me2/3 tracks and 0–100 average read counts for H3K36me3 tracks. (J) Same as in (I), but for LG IV. (K) Enlarged ChIP-seq tracks showing the underlined region on LG IV from (J). Gene expression changes in ∆iswi are shown. (L) ChIP-qPCR data for H3K27me2/3 at the two genes used for the initial mutant selection (NCU05173 and NCU07152) in the indicated strains. Filled bars represent the mean of technical triplicates and error bars show standard deviation (** for p<0.01, * for p<0.05, and ns for not significant; all relative to wild type by unpaired t-test). Data are from one representative experiment that was performed three times.

Figure 3—source data 1. H3K27me2/3 ChIP-seq comparisons (∆iswi and ∆acf1).
Figure 3—source data 2. H3K36me3 ChIP-seq comparisons.
Figure 3—source data 3. Comparison of H3K27me2/3 ChIP-seq data and RNA-seq data in ∆iswi and ∆acf1.
elife-77595-fig3-data3.xlsx (965.6KB, xlsx)

Figure 3.

Figure 3—figure supplement 1. iswi and acf1 are not required for H3K36me2.

Figure 3—figure supplement 1.

(A, B) Scatter plots show the correlation of H3K36me2 at genes in wild type and ∆iswi or ∆acf1 based on biological replicates of ChIP-seq data. Green points (n=9 in ∆iswi and n=1 in ∆acf1) represent genes with increased H3K36me2 levels (at least twofold over wild type) and red points (n=25 in ∆iswi and n=7 in ∆acf1) represent genes with decreased H3K36me2 levels (at least twofold relative to wild type) in the indicated mutant.
Figure 3—figure supplement 1—source data 1. H3K36me2 ChIP-seq comparisons.
Figure 3—figure supplement 2. Loss of iaf-3, iaf-1, and iaf-2 results in minor changes in H3K27me2/3.

Figure 3—figure supplement 2.

(A) Scatter plot showing the correlation of H3K27me2/3 at all genes in wild type and ∆iaf-3 based on biological replicates of ChIP-seq data. Green points represent genes with increased H3K27me2/3 (at least twofold over wild type) and red points represent genes with decreased H3K27me2/3 levels (at least twofold relative to wild type) in ∆iaf-3 strains. (B) Same as in (A), but for ∆iaf-1 strains. (C) Same as in (A), but for ∆iaf-2 strains. (D) ChIP-seq tracks showing average levels of H3K27me2/3 merged from two biological replicates for the indicated strains on the indicated chromosomes (linkage groups). Y-axis is 0–1000 RPKM for all tracks.
Figure 3—figure supplement 2—source data 1. H3K27me2/3 ChIP-seq comparisons (∆iswi, ∆acf1, ∆iaf-3, ∆iaf-1, and ∆iaf-2).