Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Diversity of microRNAs in human and chimpanzee brain

Abstract

We used massively parallel sequencing to compare the microRNA (miRNA) content of human and chimpanzee brains, and we identified 447 new miRNA genes. Many of the new miRNAs are not conserved beyond primates, indicating their recent origin, and some miRNAs seem species specific, whereas others are expanded in one species through duplication events. These data suggest that evolution of miRNAs is an ongoing process and that along with ancient, highly conserved miRNAs, there are a number of emerging miRNAs.

This is a preview of subscription content

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Figure 1: Human and chimpanzee small RNA libraries.
Figure 2: miRNA cloning frequency and conservation.

References

  1. 1

    Bartel, D.P. Cell 116, 281–297 (2004).

    CAS  Article  Google Scholar 

  2. 2

    Alvarez-Garcia, I. & Miska, E.A. Development 132, 4653–4662 (2005).

    CAS  Article  Google Scholar 

  3. 3

    Griffiths-Jones, S., Grocock, R.J., van Dongen, S., Bateman, A. & Enright, A.J. Nucleic Acids Res. 34, D140–D144 (2006).

    CAS  Article  Google Scholar 

  4. 4

    Bentwich, I. et al. Nat. Genet. 37, 766–770 (2005).

    CAS  Article  Google Scholar 

  5. 5

    Berezikov, E. et al. Cell 120, 21–24 (2005).

    CAS  Article  Google Scholar 

  6. 6

    Margulies, M. et al. Nature 437, 376–380 (2005).

    CAS  Article  Google Scholar 

  7. 7

    Vagin, V.V. et al. Science 313, 320–324 (2006).

    CAS  Article  Google Scholar 

  8. 8

    Stein, A.J., Fuchs, G., Fu, C., Wolin, S.L. & Reinisch, K.M. Cell 121, 529–537 (2005).

    CAS  Article  Google Scholar 

  9. 9

    Bonnet, E., Wuyts, J., Rouze, P. & Van de Peer, Y. Bioinformatics 20, 2911–2917 (2004).

    CAS  Article  Google Scholar 

  10. 10

    Aravin, A. & Tuschl, T. FEBS Lett. 579, 5830–5840 (2005).

    CAS  Article  Google Scholar 

  11. 11

    Allen, E. et al. Nat. Genet. 36, 1282–1290 (2004).

    CAS  Article  Google Scholar 

  12. 12

    Enard, W. et al. Science 296, 340–343 (2002).

    CAS  Article  Google Scholar 

  13. 13

    Schratt, G.M. et al.Nature 439, 283–289 (2006).

    CAS  Article  Google Scholar 

  14. 14

    Ashraf, S.I., McLoon, A.L., Sclarsic, S.M. & Kunes, S. Cell 124, 191–205 (2006).

    CAS  Article  Google Scholar 

  15. 15

    Muotri, A.R. & Gage, F.H. Nature 441, 1087–1093 (2006).

    CAS  Article  Google Scholar 

Download references

Acknowledgements

We thank the various genome sequencing consortia (see Supplementary Methods for full references) for sharing sequence information through Ensembl (http://www.ensembl.org) before publication and thank C. Reijmer (Vrelinghuis, Medical Center Biltstraat, Utrecht) for providing tissue material. This work was supported by grants from the Horizon (E.B.) and BioRange (E.C.) programs of the Netherlands Genomics Initiative, and a TOP grant (R.H.A.P.) from the Netherlands Organization for Scientific Research.

Author information

Affiliations

Authors

Contributions

This study was designed by R.H.A.P., E.C. and E.B.; L.W.L. prepared human tissues; I.K. and R.B. prepared chimpanzee tissues; F.T. generated libraries; E.B. performed the analysis and wrote a first draft of the paper; E.B., E.C. and R.H.A.P. wrote the paper and I.K., R.B. and F.T. contributed critical comments on the manuscript.

Corresponding author

Correspondence to Ronald H A Plasterk.

Ethics declarations

Competing interests

F.T. is founder and Chief Executive Officer of Vertis Biotechnologie AG. Publication of this work may result in an increase in the level of awareness of its services for cloning and analysis of microRNAs.

E.B., E.C. and R.P. are the inventors on a patent application that includes novel miRNA sequences described in this manuscript. This publication may affect the value of this patent.

Supplementary information

Supplementary Fig. 1

Distribution of read densities across the chimpanzee genome. (PDF 140 kb)

Supplementary Table 1

Strand distribution for repeat-derived reads. (PDF 84 kb)

Supplementary Table 2

Sequences of novel human and chimpanzee miRNAs. (PDF 279 kb)

Supplementary Table 3

miRNA families containing novel miRNAs (PDF 64 kb)

Supplementary Table 4

Clusters containing novel human and chimpanzee miRNAs. (PDF 139 kb)

Supplementary Table 5

miRNAs duplicated in human or chimpanzee genomes. (PDF 99 kb)

Supplementary Methods (PDF 494 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Berezikov, E., Thuemmler, F., van Laake, L. et al. Diversity of microRNAs in human and chimpanzee brain. Nat Genet 38, 1375–1377 (2006). https://doi.org/10.1038/ng1914

Download citation

Further reading

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing