Alex has been pondering the nature of non-protein-coding RNAs. So have the boys at Gene Expression (how appropriate). Coffee Mug and JP have pointed out that a large portion of the human genome is transcribed, and much of it has an unknown function. Now JP describes a paper that takes an evolutionary approach towards studying the function of intergenic transcripts. By comparing human and chimp transcription profiles, the authors "that intergenic transcripts show patterns of tissue-specific conservation of their expression which are comparable to exonic transcripts of known genes." This provides evidence of functional constraints on intergenic transcripts, which means that many of the intergenic transcripts are probably not transcriptional mistakes (or errors in identifying transcripts).