There is an apparent discrepancy between this observed pervasive transcription and the relative paucity of annotated lincRNAs, the most numerous intergenic RNAs. It should be expected that intergenic regions encode far more lincRNAs than are currently annotated. Indeed, here we found that there are many more lincRNAs than previously known, even after aggressive filtering that removed the vast majority of previously annotated long noncoding RNAs and newly discovered intergenic transcripts (Dataset S2). These observations clearly demonstrate that the human genome is pervasively transcribed, and that lincRNAs make up an extremely common class of intergenic transcripts.
