Recent analyses based on high-throughput transcriptome data have revealed that the fraction of the genome that is transcribed largely exceeds the fraction encoding protein. Transcription of unconventional genes into noncoding RNAs is widespread and, in mammals, these RNAs comprise at least half the total number of RNAs transcribed by RNA polymerase II. Although the function of the majority of noncoding RNAs has yet to be discovered, many of them are transcribed from both strands of the genome, and evidence points towards a regulatory function for many noncoding RNAs in mammalian cells.