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 KawaiCarsten O. Daub, David A. Hume, Harukazu Suzuki, Valerio Orlando, Piero Carninci, Yoshihide Hayashizaki*, John S. Mattick

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

303 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)572-578
Number of pages7
JournalNature Genetics
Issue number5
StatePublished - May 2009
Externally publishedYes

Bibliographical note

Funding Information:
We thank A. Hasegawa, F. Hori, H. Sano for technical assistance. R.J.T. is supported by a US National Science Foundation Graduate Research Fellowship. N.C. is supported by a University of Queensland Postdoctoral Research Fellowship. A.R.R.F. is supported by a CJ Martin Fellowship from the Australian National Health and Medical Research Council (ID 428261). S.M.G. is supported by Australian NH&MRC Fellowship grant no. 455857. V.O. is supported by Telethon TCP00094, Associazione Italiana Riecrca sul Cancro (AIRC), Compagnia San Paolo. J.S.M. is supported by an Australian Research Council Federation Fellowship (ID FF0561986), the University of Queensland and the Queensland State Government. This work was also supported by grants for the Genome Network Project from the Ministry of Education, Culture, Sports, Science and Technology, Japan (Y.H.), and Research Grant for the RIKEN Genome Exploration Research Project from the Ministry of Education, Culture, Sports, Science and Technology of the Japanese Government, the RIKEN Frontier Research System, Functional RNA Research Program (Y.H.). We thank the reviewers for their insights and suggestions.

ASJC Scopus subject areas

  • Genetics


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