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

Abstract

BackgroundMicroRNAs (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.ResultsWe 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.ConclusionsWe 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.

Identification and characterization of microRNAs expressed in the African malaria vector Anopheles funestus life stages using high throughput sequencing

“…The predicted novel miRNAs exhibited much lower expression levels, consistent with the evidence that non-conserved miRNAs are often expressed at a lower level than conserved miRNAs [97–99]. …”

Sex-Biased miRNA Expression in Atlantic Halibut <b><i>(Hippoglossus hippoglossus)</i></b> Brain and Gonads

“…Previously they were found enriched in mammalian brain [Sempere et al, 2004;Linsen et al, 2010;Ling et al, 2011]. Other miRNAs, such as let-7a, miR-103 and miR-107, were also expressed abundantly, though not exclusively, in Atlantic halibut brain.…”

“…numbers of reads remained unmapped. However, a large proportion of deep sequencing data remains uncharacterized or discarded because of sequencing errors in model species [Morin et al, 2008;Ling et al, 2011]. SOLiD sequencing technology has an advantage over other similar technologies in discriminating single nucleotide polymorphisms from sequencing errors by interrogating each nucleotide in 2 different ligation steps.…”

Developmental and Activity-Dependent miRNA Expression Profiling in Primary Hippocampal Neuron Cultures

“…The central nervous system is a rich source of miRNA expression [12], [13], [14], with a diversity of miRNA functions that affect many neuronal genes. A large number of miRNAs have been identified in the brain [12], [13], [14], [15], [16], [17], [18] including several miRNAs that are specifically expressed in glia cells and neurons [14], [19], [20]. Recent studies have shown that miRNA function is essential for the development of the zebrafish nervous system [21] and plays a role in neuronal plasticity in the rodent brain [7], [9].…”