Fig 2.

Spt6 is required for the repression of cryptic intragenic transcripts on the sense and antisense strands. (A) RNA-seq data was clustered with previous tiling microarray data to determine similarity of antisense profiles of each mutant. The heat map is colored by Pearson correlation value (see Table S4 at http://goo.gl/OEGSsQ) and clustered by similarity. (B) Heat maps display the log₂ expression values on the antisense strand of each transcription unit, sorted by size and aligned by the TTS on the sense strand (vertical green line). The curved green line represents the TSS on the sense strand. (C) Metagene analysis of the RNA-seq antisense signal upstream of the TTS binned by convergent genes, tandem genes, and genes with no neighbor within 0.5 kb (left panel) and for all loci (right panel), with the dashed orange line indicating a linear increase. The vertical dotted lines represent the TTS (pink) and 350 bp (gray). (D) Heat maps display log₂ expression values on the sense strand at each transcription unit sorted by size and aligned by TSS. (E) Three prime enrichment scores were calculated for all genes comparing WT to spt6-1 (top panel) or comparing the first and second replicates as a control, each pooling WT and spt6-1 (bottom panel). Enrichment scores for each transcription unit were plotted by the length of the gene and the red dots represent the averages of 20 bins by length, each containing 5% of the transcripts.