Fig. 4. Characteristics of non-coding transcription during the seed-to-seedling transition.

a Pie chart of annotated TSS types from the csRNA-seq. TSSs associated with an existing Araport11 TSS were annotated as either mRNA, lncRNA or Other ncRNA. The remaining TSSs were annotated as either Putative lncRNA (when a putative transcript could be reconstructed from the RNA-seq) or Unstable TSS (when transcript reconstruction was not possible). b Pie charts of the positional contexts of non-coding TSSs (lncRNA, Putative lncRNA and Unstable TSS). Features which did not overlap any protein coding gene were annotated as Intergenic. Features which overlapped a protein coding gene were annotated as Intragenic, and as either sense or antisense in brackets to denote the relative orientation to the overlapping gene. c Average conservation of promoters by annotated TSS type (mRNA, lncRNA, Putative lncRNA, and Unstable TSS), using PhyloP scores calculated from 63 plant species⁴². The coverage of scores is from 500 bp upstream and downstream of the primary TSS coordinate. d Heatmaps, and accompanying average profiles of external RNAPII¹¹⁰, H3K4me3¹¹⁵, and H3K9ac¹¹⁶ ChIP-seq datasets from Arabidopsis seedlings of the 4 kb area around protein coding TSSs. e A repeat of the plotting from (g), instead showing the non-coding annotated TSS types.