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