Operon gene regulation across development. (A) A box plot of the ratio of SL2 reads to all splice leader reads for all second genes in operons across the embryonic time series 0223. Well-expressed second genes in operons (dcpm ≥0.1) were divided into eight equally sized bins (105 genes) based on the overall SL2 fraction. Outliers may indicate stage-specific usage of the two promoters. (B) The same eight bins showing average SL1 (top) and SL2 (bottom) expression in dcpm across development for the second genes. (C) Average H3K27ac signal across the transcript start site of the first (left) and second (right) gene in operons, divided into the same eight bins as in A. Marks of open chromatin may serve to maintain open chromatin for polymerase read-through during transcription of the operon. Average H3K79me2 signal across the transcription start site of the first (left) and second (right) gene in operons, divided into the same eight bins as in A. Promoter areas of these second genes are sites of active regulation.
