Tiny RNAs associated with transcription start sites in animals

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Abstract
John Mattick and Yoshihide Hayashizaki and colleagues report the identifcation of tiny RNAs approximately 18 nucleotides in length that map near transcription start sites in human, chicken and Drosophila genomes. They call them transcription initiation RNAs (tiRNAs) and show that they associate with highly expressed transcripts and sites of RNA polymerase II binding. It has been reported that relatively short RNAs of heterogeneous sizes are derived from sequences near the promoters of eukaryotic genes. As part of 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.