Fig. 3
From: SMRT-Cappable-seq reveals complex operon variants in bacteria
Transcriptional context. a Distribution of genes according to the number of transcriptional contexts from RegulonDB (left Bar chart), individual SMRT-Cappable-seq (Center Bar charts), and combined SMRT-Cappable-seq data set (Right Bar chart). Only genes having at least one context are considered (n = the number of genes). The number of transcriptional contexts for a given gene X is the number of unique combinations of genes co-transcribed with gene X. b Individual reads (Rich condition) mapping across the frr gene ordered by TSS location and decreased read size. Read colors represent TSS positions. Reads derived from major and minor TSS are divided into two panels offering different scale for clarity. The frr gene is transcribed from eight different gene contexts when the cells are grown in Rich medium. These contexts are altering the gene content of the transcripts encoding the frr protein. The eight possible combinations are: rpsB-tsf-pyrH-frr, tsf-pyrH-frr-dxr, tsf-pyrH-frr, pyrH-frr-dxr, pyrH-frr, frr-dxr-ispU-cdsA, frr-dxr-ispU, and frr alone. RegulonDB only annotates frr alone. c Number of contexts in M9 medium (x-axis) compared to the number of contexts in Rich medium for each selected genes. The point size represents the average expression level between the two growth conditions while the color represents the ratio between the expression level in Rich medium compared to M9 medium. d Example of the rplB gene coding for the 50S ribosomal subunit protein L2 showing a change in the number of transcriptional context from 13 contexts (Rich medium) to only three contexts (M9 medium). * indicates the SMRT-Cappable-seq defined TTSs downstream of rpsS and rplB, and red arrow indicates the previously known TTS downstream of rpsQ. The number of reads supporting each context is shown in blue
