Diversity of microRNAs in human and chimpanzee brain

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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.

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

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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

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.

Correspondence to Ronald H A Plasterk.

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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)

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