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

BACKGROUND: 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,...

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Autores principales: Ling, King-Hwa, Brautigan, Peter J, Hahn, Christopher N, Daish, Tasman, Rayner, John R, Cheah, Pike-See, Raison, Joy M, Piltz, Sandra, Mann, Jeffrey R, Mattiske, Deidre M, Thomas, Paul Q, Adelson, David L, Scott, Hamish S
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3088569/
https://www.ncbi.nlm.nih.gov/pubmed/21466694
http://dx.doi.org/10.1186/1471-2164-12-176
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author Ling, King-Hwa
Brautigan, Peter J
Hahn, Christopher N
Daish, Tasman
Rayner, John R
Cheah, Pike-See
Raison, Joy M
Piltz, Sandra
Mann, Jeffrey R
Mattiske, Deidre M
Thomas, Paul Q
Adelson, David L
Scott, Hamish S
author_facet Ling, King-Hwa
Brautigan, Peter J
Hahn, Christopher N
Daish, Tasman
Rayner, John R
Cheah, Pike-See
Raison, Joy M
Piltz, Sandra
Mann, Jeffrey R
Mattiske, Deidre M
Thomas, Paul Q
Adelson, David L
Scott, Hamish S
author_sort Ling, King-Hwa
collection PubMed
description BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: 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.
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spelling pubmed-30885692011-05-06 Deep sequencing analysis of the developing mouse brain reveals a novel microRNA Ling, King-Hwa Brautigan, Peter J Hahn, Christopher N Daish, Tasman Rayner, John R Cheah, Pike-See Raison, Joy M Piltz, Sandra Mann, Jeffrey R Mattiske, Deidre M Thomas, Paul Q Adelson, David L Scott, Hamish S BMC Genomics Research Article BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: 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. BioMed Central 2011-04-05 /pmc/articles/PMC3088569/ /pubmed/21466694 http://dx.doi.org/10.1186/1471-2164-12-176 Text en Copyright ©2011 Ling et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Ling, King-Hwa
Brautigan, Peter J
Hahn, Christopher N
Daish, Tasman
Rayner, John R
Cheah, Pike-See
Raison, Joy M
Piltz, Sandra
Mann, Jeffrey R
Mattiske, Deidre M
Thomas, Paul Q
Adelson, David L
Scott, Hamish S
Deep sequencing analysis of the developing mouse brain reveals a novel microRNA
title Deep sequencing analysis of the developing mouse brain reveals a novel microRNA
title_full Deep sequencing analysis of the developing mouse brain reveals a novel microRNA
title_fullStr Deep sequencing analysis of the developing mouse brain reveals a novel microRNA
title_full_unstemmed Deep sequencing analysis of the developing mouse brain reveals a novel microRNA
title_short Deep sequencing analysis of the developing mouse brain reveals a novel microRNA
title_sort deep sequencing analysis of the developing mouse brain reveals a novel microrna
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3088569/
https://www.ncbi.nlm.nih.gov/pubmed/21466694
http://dx.doi.org/10.1186/1471-2164-12-176
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