Tiny RNAs associated with transcription start sites in animals

Ryan J Taft, Evgeny A Glazov, Nicole Cloonan, Cas Simons, Stuart Stephen, Geoffrey J Faulkner, Timo Lassmann, Alistair R R Forrest, Sean M Grimmond, Kate Schroder, Katharine Irvine, Takahiro Arakawa, Mari Nakamura, Atsutaka Kubosaki, Kengo Hayashida, Chika Kawazu, Mitsuyoshi Murata, Hiromi Nishiyori, Shiro Fukuda, Jun Kawai, Carsten O Daub, David A Hume, Harukazu Suzuki, Valerio Orlando, Piero Carninci, Yoshihide Hayashizaki, John S Mattick

It has been reported that relatively short RNAs of heterogeneous sizes are derived from sequences near the promoters of eukaryotic genes. In conjunction with the FANTOM4 project, we have identified tiny RNAs with a modal length of 18 nt that map within -60 to +120 nt of transcription start sites (TSSs) in human, chicken and Drosophila. These transcription initiation RNAs (tiRNAs) are derived from sequences on the same strand as the TSS and are preferentially associated with G+C-rich promoters. The 5' ends of tiRNAs show peak density 10-30 nt downstream of TSSs, indicating that they are processed. tiRNAs are generally, although not exclusively, associated with highly expressed transcripts and sites of RNA polymerase II binding. We suggest that tiRNAs may be a general feature of transcription in metazoa and possibly all eukaryotes.