High throughput sequencing of microRNAs in chicken somites

Rathjen, Tina; Pais, Helio; Sweetman, Dylan; Moulton, Vincent; Munsterberg, Andrea; Dalmay, Tamas

doi:10.1016/j.febslet.2009.03.048

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Volume 583, Issue 9 , Pages 1422-1426, 6 May 2009

High throughput sequencing of microRNAs in chicken somites

Edited by Shou-Wei Ding

Tina Rathjen
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
- These authors contributed equally to this work.
Helio Pais
- School of Computing Science, University of East Anglia, Norwich NR4 7TJ, UK
- These authors contributed equally to this work.
Dylan Sweetman
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
Vincent Moulton
- School of Computing Science, University of East Anglia, Norwich NR4 7TJ, UK
Andrea Munsterberg
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
- Corresponding authors. Fax: +44 1603 592250.
Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
- Corresponding authors. Fax: +44 1603 592250.

Received 11 September 2008; received in revised form 25 February 2009; accepted 19 March 2009. published online 27 March 2009.

Abstract

High throughput Solexa sequencing technology was applied to identify microRNAs in somites of developing chicken embryos. We obtained 651273 reads, from which 340415 were mapped to the chicken genome representing 1701 distinct sequences. Eighty-five of these were known microRNAs and 42 novel miRNA candidates were identified. Accumulation of 18 of 42 sequences was confirmed by Northern blot analysis. Ten of the 18 sequences are new variants of known miRNAs and eight short RNAs are novel miRNAs. Six of these eight have not been reported by other deep sequencing projects. One of the six new miRNAs is highly enriched in somite tissue suggesting that deep sequencing of other specific tissues has the potential to identify novel tissue specific miRNAs.