(A, B) H3 signal profiles associated with gene type and expression level. (A) Mean genic positional signal for H3 was calculated independently for ∼14,500 likely protein-coding genes and ∼3,000 transposon-related or likely pseudogenes from our ∼18,000 gene set, and is depicted across the promoter regions (shown in bp from −300 to 0 relative to the presumed transcriptional start site), transcribed regions (shown proportionally from 0 to 100% of total length), and 3′ regions (shown in bp from 0 to +100 relative to the presumed 3′ end). (B) Protein-coding genes were sorted into ten-percentile bins according to their expression level, as estimated from publicly available microarray data (see Materials and Methods). The averaged positional signals for H3 within each bin were plotted. Data is shown for absolute positions across the 5′ end including the presumed transcriptional start site (TSS). (C–E) Genic patterns of H3 signals associated with Paf1C activity. (C) In the left column, signals for all 17,771 genes evaluated are depicted for wild-type plants (WT) or vip3 mutants across the transcriptional unit as described above for Figure 1A. In the center and right columns, data is shown for absolute positions across the 5′ end including the presumed transcriptional start site (TSS) (center), or across the 3′ end (right) of a subset of 6,180 genes with transcribed regions >2 kb in length. (D) Mean positional H3 signals for transposon-related genes and pseudogenes. (E) Genic patterns of Paf1C-dependent H3 signals with respect to expression level and length. Genic positional signals for H3 were averaged separately for protein coding genes within ten-percentile bins according to expression level (left panel), or twenty-percentile bins according to length of transcribed region (right panel) for vip3 plants relative to wild-type.

(A) Mean genic positional enrichment for H3K27me3 for protein-coding genes or transposon-related/pseudogenes. (B) H3K27me3 enrichment for genes within ten-percentile expression level bins as described for Figure 1B. (C) Mean genic positional enrichment for genes within twenty-percentile bins according to length of transcribed region. (D) Enrichment for H3K27me3 for genes within specific expression level and expression entropy bins as described for Figure 2D. (E) Mean enrichment across the transcriptional unit (left panel) for the ∼18,000-gene set, or across the 5′ end/TSS (center) or 3′ end (right) of genes with transcribed regions >2 kb in length, for wild-type plants (WT) or vip3 mutants. (F) Enrichment for transposon-related genes and pseudogenes. (G) Paf1C-dependent H3K27me3 enrichment with respect to expression level, as determined for Figure 1E. (H) Paf1C-dependent enrichment for H3K27me3 with respect to gene length, as determined for Figure 1E.

Regions of the genome containing substantial enrichment for H3K4me3, H3K36me2 or H3K27me3 were identified using the TileMap package [82] and linked with genome annotation to identify substantially enriched genes. A Venn diagram indicating the number of annotated genes containing substantial enrichment for single or combinatorial modifications is shown. The shaded area represents the subset of genes enriched in both H3K4me3 and H3K27me3, which shows the most significant overrepresentation for Paf1C-regulated genes.

(A) Mean genic positional enrichment for H3K4me3 or H3K36me2 was calculated independently for protein-coding genes or transposon-related/pseudogenes as described above for Figure 1A. (B) H3K4me3 or H3K36me2 enrichment is depicted for genes within ten-percentile expression level bins as described for Figure 1B. (C) H3K4me3 or H3K36me2 enrichment is depicted for genes within twenty-percentile bins according to length of transcribed region. Enrichment is shown across the transcriptional unit (left panels) or the TSS/5′end (for H3K4me3) or 3′ end (for H3K36me2) (right panels) (D) Protein-coding genes were assigned to ten bins according to tissue-specificity of expression, as estimated by Shannon entropy (see Materials and Methods). Genes in Bin 10 (high entropy) show the most ubiquitous expression across various plant parts, whereas genes in Bin 1 (low entropy) show the most specific expression domains. Mean positional signals were calculated for genes within specific ten-percentile expression (Exp) and entropy (Ent) bins, as indicated. Lines were smoothed using a three-point sliding window. (E) Enrichment for all 17,771 genes evaluated are depicted across the transcriptional unit (left panel), or across the 5′ end/TSS (center) or 3′ end (right) of genes with transcribed regions >2 kb in length, for wild-type plants (WT) or vip3 mutants. (F) Enrichment within transposon-related genes and pseudogenes. (G) Paf1C-dependent H3K4me3 or H3K36me2 enrichment with respect to expression level, as determined for Figure 1E. (H) Paf1C-dependent enrichment for H3K4me3 or H3K36me2 with respect to gene length, as determined for Figure 1E.

(A) Genic positional signals for H3 lysine methylations as indicated were averaged separately for genes upregulated in vip3 mutants (top row of panels, red) or downregulated in vip3 mutants (lower panels, green) for both wild-type plants (solid lines) and vip3 mutants (dashed lines). Averaged signals for all genes in the protein-coding gene set presented in Figures 2 and 3 are shown in black. (B) Signals for H3 lysine methylations are shown within a ∼14-kb region encompassing the plant Paf1C-dependent gene FLC from wild-type (WT) plants (top panel). Lower panels show the relative difference in signals between vip3 and wild-type chromatin. Horizontal colored bars in these panels indicate regions where significant (2.5-fold change in vip3/WT; P<10⁻³ in either vip3 or WT) differences in signals were observed. A depiction of the FLC gene within this region is shown at bottom. Data depicted in this figure were corrected for total H3.

(A) Box plots showing the distribution of expression level (left panel), expression entropy (middle panel), and gene size (right panel) for ten-percentile subsets of genes according to misregulation in vip3 mutants. Distribution of genes strongly downregulated in vip3 relative to wild-type is shown in column 1 of each panel; distribution for genes most strongly upregulated in vip3 is shown in column 10 of each panel. Colored boxes indicate the 25^th, 50^th, and 75^th percentiles (bottom, center line, and top of box, respectively). (B) Scatter plot relating gene expression levels with entropy for Arabidopsis genes. Genes strongly upregulated in vip3 mutants are depicted as red circles, whereas strongly downregulated genes are shown as blue triangles. Locally weighted regression (Lowess) fit lines were superimposed onto the scatterplot (gray, all genes; red, upregulated; blue, downregulated).