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 Stanley Mattick

doi:10.1038/ng.312

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 Stanley Mattick

Research output: Contribution to journal › Article › Research › peer-review

307 Citations (Scopus)

Abstract

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 language	English
Pages (from-to)	572 - 578
Number of pages	7
Journal	Nature Genetics
Volume	41
Issue number	5
DOIs	https://doi.org/10.1038/ng.312
Publication status	Published - 2009
Externally published	Yes

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Taft, R. J., Glazov, E. A., Cloonan, N., Simons, C., Stephen, S., Faulkner, G. J., Lassmann, T., Forrest, A. R. R., Grimmond, S. M., Schroder, K., Irvine, K., Arakawa, T., Nakamura, M., Kubosaki, A., Hayashida, K., Kawazu, C., Murata, M., Nishiyori, H., Fukuda, S., ... Mattick, J. S. (2009). Tiny RNAs associated with transcription start sites in animals. Nature Genetics, 41(5), 572 - 578. https://doi.org/10.1038/ng.312

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title = "Tiny RNAs associated with transcription start sites in animals",

abstract = "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.",

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

year = "2009",

doi = "10.1038/ng.312",

language = "English",

volume = "41",

pages = "572 -- 578",

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Taft, RJ, Glazov, EA, Cloonan, N, Simons, C, Stephen, S, Faulkner, GJ, Lassmann, T, Forrest, ARR, Grimmond, SM, Schroder, K, Irvine, K, Arakawa, T, Nakamura, M, Kubosaki, A, Hayashida, K, Kawazu, C, Murata, M, Nishiyori, H, Fukuda, S, Kawai, J, Daub, CO, Hume, DA, Suzuki, H, Orlando, V, Carninci, P, Hayashizaki, Y & Mattick, JS 2009, 'Tiny RNAs associated with transcription start sites in animals', Nature Genetics, vol. 41, no. 5, pp. 572 - 578. https://doi.org/10.1038/ng.312

TY - JOUR

T1 - Tiny RNAs associated with transcription start sites in animals

AU - Taft, Ryan J

AU - Glazov, Evgeny A

AU - Cloonan, Nicole

AU - Simons, Cas

AU - Stephen, Stuart

AU - Faulkner, Geoffrey J

AU - Lassmann, Timo

AU - Forrest, Alistair R R

AU - Grimmond, Sean M

AU - Schroder, Kate

AU - Irvine, Katharine

AU - Arakawa, Takahiro

AU - Nakamura, Mari

AU - Kubosaki, Atsutaka

AU - Hayashida, Kengo

AU - Kawazu, Chika

AU - Murata, Mitsuyoshi

AU - Nishiyori, Hiromi

AU - Fukuda, Shiro

AU - Kawai, Jun

AU - Daub, Carsten O

AU - Hume, David A

AU - Suzuki, Harukazu

AU - Orlando, Valerio

AU - Carninci, Piero

AU - Hayashizaki, Yoshihide

AU - Mattick, John Stanley

PY - 2009

Y1 - 2009

N2 - 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.

AB - 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.

UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19377478

U2 - 10.1038/ng.312

DO - 10.1038/ng.312

M3 - Article

SN - 1061-4036

VL - 41

SP - 572

EP - 578

JO - Nature Genetics

JF - Nature Genetics

IS - 5

ER -

Tiny RNAs associated with transcription start sites in animals

Abstract

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