• A Corrigendum to this article was published on 01 July 2009

This article has been updated

Abstract

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.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Change history

  • 26 June 2009

    NOTE: In the version of this article initially published, some author affiliations were incorrectly stated. The error has been corrected in the HTML and PDF versions of the article.

Accessions

References

  1. 1.

    & Small RNAs: regulators and guardians of the genome. J. Cell. Physiol. 213, 412–419 (2007).

  2. 2.

    & Small regulatory RNAs in mammals. Hum. Mol. Genet. 14, R121–R132 (2005).

  3. 3.

    & Accumulation of unstable promoter-associated transcripts upon loss of the nuclear exosome subunit Rrp6p in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 103, 3262–3267 (2006).

  4. 4.

    et al. Genome-wide high-resolution mapping of exosome substrates reveals hidden features in the Arabidopsis transcriptome. Cell 131, 1340–1353 (2007).

  5. 5.

    , , , & A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130, 77–88 (2007).

  6. 6.

    et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316, 1484–1488 (2007).

  7. 7.

    et al. Induction of maturation in cultured human monocytic leukemia cells by a phorbol diester. Cancer Res. 42, 1530–1536 (1982).

  8. 8.

    et al. A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach. Genome Res. 18, 957–964 (2008).

  9. 9.

    et al. Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs. Genome Res. 17, 1850–1864 (2007).

  10. 10.

    , , & Endogenous RNA interference provides a somatic defense against Drosophila transposons. Curr. Biol. 18, 795–802 (2008).

  11. 11.

    et al. An endogenous small interfering RNA pathway in Drosophila. Nature 453, 798–802 (2008).

  12. 12.

    et al. High-efficiency full-length cDNA cloning by biotinylated CAP trapper. Genomics 37, 327–336 (1996).

  13. 13.

    et al. Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc. Natl. Acad. Sci. USA 100, 15776–15781 (2003).

  14. 14.

    et al. Genome-wide analysis of mammalian promoter architecture and evolution. Nat. Genet. 38, 626–635 (2006).

  15. 15.

    & Deep cap analysis gene expression (CAGE): genome-wide identification of promoters, quantification of their expression, and network inference. Biotechniques 44(Suppl.), 627–632 (2008).

  16. 16.

    et al. Accumulation of miR-155 and BIC RNA in human B cell lymphomas. Proc. Natl. Acad. Sci. USA 102, 3627–3632 (2005).

  17. 17.

    et al. Identification and classification of conserved RNA secondary structures in the human genome. PLOS Comput. Biol. 2, e33 (2006).

  18. 18.

    et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15, 1034–1050 (2005).

  19. 19.

    , , & miRBase: tools for microRNA genomics. Nucleic Acids Res. 36, D154–D158 (2008).

  20. 20.

    et al. The UCSC Genome Browser Database: 2008 update. Nucleic Acids Res. 36, D773–D779 (2008).

  21. 21.

    , & Sp1- and Kruppel-like transcription factors. Genome Biol. 4, 206 (2003).

  22. 22.

    The DPE, a core promoter element for transcription by RNA polymerase II. Exp. Mol. Med. 34, 259–264 (2002).

  23. 23.

    et al. A code for transcription initiation in mammalian genomes. Genome Res. 18, 1–12 (2008).

  24. 24.

    , , , & Carbodiimide-mediated cross-linking of RNA to nylon membranes improves the detection of siRNA, miRNA and piRNA by northern blot. Nucleic Acids Res. 35, e60 (2007).

  25. 25.

    , & A glimpse into the epigenetic landscape of gene regulation. Curr. Opin. Genet. Dev. 18, 116–122 (2008).

  26. 26.

    & Poised RNA polymerase II gives pause for thought. Cell 133, 581–584 (2008).

  27. 27.

    et al. RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo. Nat. Genet. 39, 1512–1516 (2007).

  28. 28.

    , & Promoter clearance by RNA polymerase II is an extended, multistep process strongly affected by sequence. Mol. Cell. Biol. 21, 5815–5825 (2001).

  29. 29.

    & Transcription elongation factor SII. Bioessays 22, 327–336 (2000).

  30. 30.

    et al. Efficient release from promoter-proximal stall sites requires transcript cleavage factor TFIIS. Mol. Cell 17, 103–112 (2005).

  31. 31.

    , & Evidence that the elongation factor TFIIS plays a role in transcription initiation at GAL1 in Saccharomyces cerevisiae. Mol. Cell. Biol. 25, 2650–2659 (2005).

  32. 32.

    , , & Intrinsic transcript cleavage in yeast RNA polymerase II elongation complexes. J. Biol. Chem. 278, 24189–24199 (2003).

  33. 33.

    , & Combinatorial control of human RNA polymerase II (RNAP II) pausing and transcript cleavage by transcription factor IIF, hepatitis delta antigen, and stimulatory factor II. J. Biol. Chem. 278, 50101–50111 (2003).

  34. 34.

    et al. Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Nature 453, 534–538 (2008).

  35. 35.

    et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454, 766–770 (2008).

  36. 36.

    et al. Inhibiting gene expression at transcription start sites in chromosomal DNA with antigene RNAs. Nat. Chem. Biol. 1, 216–222 (2005).

  37. 37.

    et al. Involvement of AGO1 and AGO2 in mammalian transcriptional silencing. Nat. Struct. Mol. Biol. 13, 787–792 (2006).

  38. 38.

    , , & Small interfering RNA-induced transcriptional gene silencing in human cells. Science 305, 1289–1292 (2004).

  39. 39.

    , , & Short double-stranded RNA induces transcriptional gene silencing in human cancer cells in the absence of DNA methylation. Nat. Genet. 37, 906–910 (2005).

  40. 40.

    et al. Antisense transcripts are targets for activating small RNAs. Nat. Struct. Mol. Biol. 15, 842–848 (2008).

  41. 41.

    et al. CTAB-urea method purifies RNA from melanin for cDNA microarray analysis. Pigment Cell Res. 17, 312–315 (2004).

  42. 42.

    et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376–380 (2005).

  43. 43.

    , , & A highly sensitive method for mapping the 5′ termini of mRNAs. Nucleic Acids Res. 21, 1683–1684 (1993).

  44. 44.

    et al. A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE. Genomics 91, 281–288 (2008).

  45. 45.

    et al. Gene expression during the life cycle of Drosophila melanogaster. Science 297, 2270–2275 (2002).

  46. 46.

    & GeneMerge–post-genomic analysis, data mining, and hypothesis testing. Bioinformatics 19, 891–892 (2003).

  47. 47.

    et al. Hypermethylation and transcriptional downregulation of the CITED4 gene at 1p34.2 in oligodendroglial tumours with allelic losses on 1p and 19q. Oncogene 26, 5010–5016 (2007).

Download references

Acknowledgements

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.

Author information

Affiliations

  1. Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Australia.

    • Ryan J Taft
    • , Nicole Cloonan
    • , Cas Simons
    • , Stuart Stephen
    • , Geoffrey J Faulkner
    • , Sean M Grimmond
    • , Kate Schroder
    • , Katharine Irvine
    • , David A Hume
    •  & John S Mattick
  2. Diamantina Institute for Cancer, Immunology and Metabolic Medicine, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Australia.

    • Evgeny A Glazov
  3. RIKEN Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, Japan.

    • Timo Lassmann
    • , Alistair R R Forrest
    • , Takahiro Arakawa
    • , Mari Nakamura
    • , Atsutaka Kubosaki
    • , Kengo Hayashida
    • , Chika Kawazu
    • , Mitsuyoshi Murata
    • , Hiromi Nishiyori
    • , Shiro Fukuda
    • , Jun Kawai
    • , Carsten O Daub
    • , Harukazu Suzuki
    • , Piero Carninci
    •  & Yoshihide Hayashizaki
  4. The Eskitis Institute for Cell and Molecular Therapies, Griffith University, Nathan, Australia.

    • Alistair R R Forrest
  5. The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Roslin, UK.

    • David A Hume
  6. Dulbecco Telethon Institute, IRCCS Santa Lucia at EBRI, Rome, Italy.

    • Valerio Orlando
  7. Dulbecco Telethon Institute, IGB CNR, Naples, Italy.

    • Valerio Orlando
  8. The FANTOM Consortium.

    • 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
    • , David A Hume
    • , Harukazu Suzuki
    • , Valerio Orlando
    •  & Piero Carninci
  9. RIKEN Omics Science Center.

    • Takahiro Arakawa
    • , Mari Nakamura
    • , Atsutaka Kubosaki
    • , Kengo Hayashida
    • , Chika Kawazu
    • , Mitsuyoshi Murata
    • , Hiromi Nishiyori
    • , Shiro Fukuda
    • , Jun Kawai
    •  & Carsten O Daub
  10. General organizers (of the small RNA group).

    • Yoshihide Hayashizaki
    •  & John S Mattick

Authors

  1. Search for Ryan J Taft in:

  2. Search for Evgeny A Glazov in:

  3. Search for Nicole Cloonan in:

  4. Search for Cas Simons in:

  5. Search for Stuart Stephen in:

  6. Search for Geoffrey J Faulkner in:

  7. Search for Timo Lassmann in:

  8. Search for Alistair R R Forrest in:

  9. Search for Sean M Grimmond in:

  10. Search for Kate Schroder in:

  11. Search for Katharine Irvine in:

  12. Search for Takahiro Arakawa in:

  13. Search for Mari Nakamura in:

  14. Search for Atsutaka Kubosaki in:

  15. Search for Kengo Hayashida in:

  16. Search for Chika Kawazu in:

  17. Search for Mitsuyoshi Murata in:

  18. Search for Hiromi Nishiyori in:

  19. Search for Shiro Fukuda in:

  20. Search for Jun Kawai in:

  21. Search for Carsten O Daub in:

  22. Search for David A Hume in:

  23. Search for Harukazu Suzuki in:

  24. Search for Valerio Orlando in:

  25. Search for Piero Carninci in:

  26. Search for Yoshihide Hayashizaki in:

  27. Search for John S Mattick in:

Contributions

R.J.T. designed the bioinformatic experiments, led the analysis and wrote the manuscript. E.A.G. assisted with the chicken small RNA deep sequencing datasets analysis and helped to write the manuscript. N.C. performed the analysis of THP-1 gene expression. C.S. and S.S. created an in-house database and mapped THP-1 small RNA sequences. G.J.F. analyzed THP-1 promoter architecture. T.L. organized and analyzed THP-1 small RNA sequences. A.R.R.F. and S.M.G. advised on experimental design. K.S., K.I., T.A., M.N., A.K., K.H., C.K., M.M., H.N., S.F., J.K., C.O.D., D.A.H., H.S., V.O., P.C. and Y.H. generated the THP-1 small RNA, deepCAGE, microarray expression, and ChIP-chip data. P.C. and D.A.H. also helped to write the manuscript. J.S.M. helped to design the study and wrote the manuscript. For further information about the small RNA sequencing, contact V.O. (vorlando@vti.telethon.it) or P.C. (carninci@riken.jp). For further information about the bioinformatic analyses, contact R.J.T. (r.taft@imb.uq.edu.au).

Competing interests

A patent application based on this work has been made.

Corresponding authors

Correspondence to Yoshihide Hayashizaki or John S Mattick.

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–12, Supplementary Methods, Supplementary Tables 1 and 2

About this article

Publication history

Received

Accepted

Published

DOI

https://doi.org/10.1038/ng.312

Further reading