Open Access Highly Accessed Research article

Deep sequencing analysis of the developing mouse brain reveals a novel microRNA

King-Hwa Ling123, Peter J Brautigan1, Christopher N Hahn12, Tasman Daish4, John R Rayner1, Pike-See Cheah45, Joy M Raison6, Sandra Piltz4, Jeffrey R Mann7, Deidre M Mattiske7, Paul Q Thomas4, David L Adelson4 and Hamish S Scott12*

Author Affiliations

1 Department of Molecular Pathology, SA Pathology and Centre for Cancer Biology, P.O. Box 14 Rundle Mall Post Office, Adelaide, SA 5000, Australia

2 School of Medicine, Faculty of Health Sciences, University of Adelaide, Adelaide, SA 5005, Australia

3 Department of Obstetrics and Gynaecology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor DE, Malaysia

4 School of Molecular and Biomedical Science, Faculty of Sciences, University of Adelaide, Adelaide, SA 5005, Australia

5 Department of Human Anatomy, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor DE, Malaysia

6 eResearchSA, University of Adelaide, North Terrace, Adelaide, SA 5005, Australia

7 Theme of Laboratory and Community Genetics, Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, VIC 3052, Australia

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BMC Genomics 2011, 12:176  doi:10.1186/1471-2164-12-176

Published: 5 April 2011



MicroRNAs (miRNAs) are small non-coding RNAs that can exert multilevel inhibition/repression at a post-transcriptional or protein synthesis level during disease or development. Characterisation of miRNAs in adult mammalian brains by deep sequencing has been reported previously. However, to date, no small RNA profiling of the developing brain has been undertaken using this method. We have performed deep sequencing and small RNA analysis of a developing (E15.5) mouse brain.


We identified the expression of 294 known miRNAs in the E15.5 developing mouse brain, which were mostly represented by let-7 family and other brain-specific miRNAs such as miR-9 and miR-124. We also discovered 4 putative 22-23 nt miRNAs: mm_br_e15_1181, mm_br_e15_279920, mm_br_e15_96719 and mm_br_e15_294354 each with a 70-76 nt predicted pre-miRNA. We validated the 4 putative miRNAs and further characterised one of them, mm_br_e15_1181, throughout embryogenesis. Mm_br_e15_1181 biogenesis was Dicer1-dependent and was expressed in E3.5 blastocysts and E7 whole embryos. Embryo-wide expression patterns were observed at E9.5 and E11.5 followed by a near complete loss of expression by E13.5, with expression restricted to a specialised layer of cells within the developing and early postnatal brain. Mm_br_e15_1181 was upregulated during neurodifferentiation of P19 teratocarcinoma cells. This novel miRNA has been identified as miR-3099.


We have generated and analysed the first deep sequencing dataset of small RNA sequences of the developing mouse brain. The analysis revealed a novel miRNA, miR-3099, with potential regulatory effects on early embryogenesis, and involvement in neuronal cell differentiation/function in the brain during late embryonic and early neonatal development.