Figure 7

LUAT-associated promoters are prone to pervasive transcription. A) Average profiles of Total and PolyA RNA-seq signals in DP thymocytes, for the three set of similarly expressed genes. Signals coming from plus and minus strands are indicated by solid and dashed lines, respectively. B) Splicing index calculated for the 5′ and middle exons for the three set of similarly expressed genes in DP thymocytes. C) Boxplots showing the density of Total RNA-seq reads per bp in the same orientation as the matched coding genes and within the first intron of the three group of genes in DP thymocytes. Statistical significance was assessed by the Mann–Whitney U test. D) Intron/exon ratio of individual genes for the three gene sets in DP thymocytes assessed by reverse transcription quantitative PCR. Relative transcript levels at the first intron and the last exon of each gene was estimated based on a standard dilution of genomic DNA. Statistical significance were assessed using Wilcoxon rank sum tests. E) Schematic representation of RNA processing at the three different classes of gene loci. Exons are shown by rectangles (or stripped rectangles in the case of LUATs). Solid and dotted lines represent immature (unspliced) and processed (spliced) transcripts, respectively. Our results suggest that LUAT-associated genes display an increased rate of immature transcripts.