Figure 1

RNA sequencing and RNA pol ChIP in S. elongatus. (a) Strand-specific RNA sequencing over a representative 40-kb region in the S. elongatus chromosome. Positive strand transcription is shown in blue (positive y-axis), and negative strand transcription in red (negative y-axis). For visualization over full dynamic range, the y-axis shows log₂ transformed reads per nucleotide of RNA sequencing coverage. The position of Joint Genome Institute predicted ORFs for each strand are shown below in black. High RNA sequencing signal is present at nearly all ORFs and anti-sense transcription is extensive. (b) RNA sequencing and RNA pol ChIP sequencing for representative highly expressed transcripts. Top panel: zoomed in view of RNA sequencing coverage of particular mRNA transcripts. Transcripts are color coded by strand as in (a). Transcription units with precise 5' and 3' ends are defined from RNA sequencing data for all mRNAs (black arrow) (Figure S1 in Additional file 2; Materials and methods). Bottom panel: RNA pol ChIP sequencing associated with the transcripts from the top panel. The y-axis is normalized such that the genome average is 200 units per nucleotide. Peaks in RNA pol occupancy are often found near the 5' end of the transcript and occasionally smaller peaks in RNA pol occupancy are located near the 3' ends or inside the transcript. 5' peaks tend to be located within the transcript as opposed to within the promoters.