Unknown,Transcriptomics,Genomics,Proteomics

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

ABSTRACT: 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 22-23nt miRNAs: mm_br_e15_1181, mm_br_e15_279920, mm_br_e15_96719 and mm_br_e15_294354 each with a 70-76nt 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. Deep sequencing analysis of small RNAs isolated from an E15.5 mouse brain.

ORGANISM(S): Mus musculus

SUBMITTER: King Ling

PROVIDER: E-GEOD-22653 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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

Ling King-Hwa KH Brautigan Peter J PJ Hahn Christopher N CN Daish Tasman T Rayner John R JR Cheah Pike-See PS Raison Joy M JM Piltz Sandra S Mann Jeffrey R JR Mattiske Deidre M DM Thomas Paul Q PQ Adelson David L DL Scott Hamish S HS

BMC genomics 20110405

<h4>Background</h4>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.<h4>R ...[more]

PMID: 21466694

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Project description:Background: In humans, cleft palate (CP) accounts for one of the largest number of birth defects with a complex genetic and environmental etiology. TGFM-NM-23 has been established as an important regulator of palatal fusion in mice and it has been shown that TGFM-NM-23-null mice exhibit CP without any other major deformities. However, the genes that regulate cellular decisions and molecular mechanisms maintained by the TGFM-NM-23 pathway throughout palatogenesis are predominantly unexplored. Our objective in this study was to analyze global transcriptome changes within the palate during different gestational ages within TGFM-NM-23 knockout mice to identify TGFM-NM-23-associated genes previously unknown to be associated with the development of cleft palate. We used deep sequencing technology, RNA-Seq, to analyze the transcriptome of TGFM-NM-23 knockout mice at crucial stages of palatogenesis, including palatal growth (E14.5), adhesion (E15.5), and fusion (E16.5). Results: The overall transcriptome analysis of TGFM-NM-23 wildtype mice (C57BL/6) reveals that almost 6000 genes were upregulated during the transition from E14.5 to E15.5 and more than 2000 were downregulated from E15.5 to E16.5. Using bioinformatics tools and databases, we identified the most comprehensive list of CP genes (n = 322) in which mutations cause CP either in humans or mice, and analyzed their expression patterns. The expression motifs of CP genes between TGFM-NM-23+/M-bM-^HM-^R and TGFM-NM-23M-bM-^HM-^R/M-bM-^HM-^R were not significantly different from each other, and the expression of the majority of CP genes remained unchanged from E14.5 to E16.5. Using these patterns, we identified 8 unique genes within TGFM-NM-23M-bM-^HM-^R/M-bM-^HM-^R mice (Chrng Foxc2, H19, Kcnj13, Lhx8, Meox2, Shh, and Six3), which may function as the primary contributors to the development of cleft palate in TGFM-NM-23M-bM-^HM-^R/M-bM-^HM-^R mice. When the significantly altered CP genes were overlaid with TGFM-NM-2 signaling, all of these genes followed the Smad-dependent pathway. Conclusions: Our study represents the first analysis of the palatal transcriptome of the mouse, as well as TGFM-NM-23 knockout mice, using deep sequencing methods. In this study, we characterized the critical regulation of palatal transcripts that may play key regulatory roles through crucial stages of palatal development. We identified potential causative CP genes in a TGFM-NM-23 knockout model, which may lead to a better understanding of the genetic mechanisms of palatogenesis and provide novel potential targets for gene therapy approaches to treat cleft palate. Palatal mRNA profiles of wild type (WT), TGFM-NM-23+/-, and TGFM-NM-23-/- mice at E14.5, E15.5, and E16.5 were generated by deep sequencing, in triplicate, using Illumina HiSeq2000

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

Publications

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

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