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Genic and Global Functions for Paf1C in Chromatin Modification and Gene Expression in Arabidopsis

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Enrichment of H3K4me3 and H3K36me2 within Genes and Effects of Paf1C Disruption.

(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.

Figure 2

doi: https://doi.org/10.1371/journal.pgen.1000077.g002