WIDESPREAD RECOGNITION OF THE PHENOMENA OF EXTENSIVE AND COMPLEX PATTERNS OF TRANSCRIPTION THROUGHOUT THE GENOMES OF MANY SPECIES

Within the past 5 years, multiple large-scale, unbiased experimental approaches have identified surprisingly large amounts of RNA transcription far exceeding that estimated to be required for the production of messenger RNA for known proteins. This transcriptional “dark mat-ter ” has been observed in (1) large-scale full-length cDNA sequencing (Okazaki et al. 2002; Carninci et al. 2005), (2) mapping of 3 ′ ends with serial analysis of gene expression (Chen et al. 2002; Saha et al. 2002), (3) map-ping of 5 ′ ends by cap analysis of gene expression (Carninci et al. 2005), and (4) analysis of expression by massively parallel signature sequencing (Jongeneel et al. 2005). Whereas these approaches have been key to ana-lyzing widespread transcription, genomic tiling arrays have made substantial contributions by being both unbi