There has been a recent debate about whether there is pervasive transcription of the human genome and what the number and abundance of intergenic transcripts is [9]–[12]. Until recently, a key missing component to this debate has been an analysis of ultra deep RNA-seq data sampling a wide array of tissue types. Without this, insufficient read depth can result in a failure to identify low abundance intergenic transcripts, and limited tissue sampling results in missed tissue specific expression. During the course of this study, the ENCODE project released a large scale analysis of RNA-seq data that provided clear evidence that the human genome is pervasively transcribed [14]. We analyzed a distinct, complementary set of RNA-seq data that also fulfills these requirements of read depth and tissue breadth, covering both polyadenylated and nonpolyadenylated RNA fractions. In strong agreement with the ENCODE results, we observed that approximately 85% of the genome is transcribed, supporting prior observations of pervasive transcription based on tiling arrays that have been recently questioned [2]–[5].
