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Dynamics of microRNA expression during mouse prenatal development

Rahmanian, Sorena and Murad, Rabi and Breschi, Alessandra and Zeng, Weihua and Mackiewicz, Mark and Williams, Brian and Davis, Carrie A. and Roberts, Brian and Meadows, Sarah and Moore, Dianne and Trout, Diane and Zaleski, Chris and Dobin, Alex and Sei, Lei-Hoon and Drenkow, Jorg and Scavelli, Alex and Gingeras, Thomas R. and Wold, Barbara J. and Myers, Richard M. and Guigó, Roderic and Mortazavi, Ali (2019) Dynamics of microRNA expression during mouse prenatal development. Genome Research, 29 (11). pp. 1900-1909. ISSN 1088-9051. PMCID PMC6836743.

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MicroRNAs (miRNAs) play a critical role as posttranscriptional regulators of gene expression. The ENCODE Project profiled the expression of miRNAs in an extensive set of organs during a time-course of mouse embryonic development and captured the expression dynamics of 785 miRNAs. We found distinct organ-specific and developmental stage–specific miRNA expression clusters, with an overall pattern of increasing organ-specific expression as embryonic development proceeds. Comparative analysis of conserved miRNAs in mouse and human revealed stronger clustering of expression patterns by organ type rather than by species. An analysis of messenger RNA expression clusters compared with miRNA expression clusters identifies the potential role of specific miRNA expression clusters in suppressing the expression of mRNAs specific to other developmental programs in the organ in which these miRNAs are expressed during embryonic development. Our results provide the most comprehensive time-course of miRNA expression as part of an integrated ENCODE reference data set for mouse embryonic development.

Item Type:Article
Related URLs:
URLURL TypeDescription Material CentralArticle Paper
Trout, Diane0000-0002-4928-5532
Wold, Barbara J.0000-0003-3235-8130
Mortazavi, Ali0000-0002-4259-6362
Additional Information:© 2019 Rahmanian et al. Freely available online through the Genome Research Open Access option. This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at Received January 30, 2019; Accepted August 29, 2019; published in Advance October 23, 2019. Data access: All the miRNA-seq, short RNA-seq, and NanoString data from this study can be accessed through the ENCODE data portal ( under the accession numbers listed in Supplemental Table S1. This work was supported by the NIH, National Human Genome Research Institute under grants U54 HG006998 and UM1 HG009443.
Funding AgencyGrant Number
NIHU54 HG006998
NIHUM1 HG009443
National Human Genome Research InstituteUNSPECIFIED
Issue or Number:11
PubMed Central ID:PMC6836743
Record Number:CaltechAUTHORS:20181212-091659236
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:91702
Deposited By: Tony Diaz
Deposited On:12 Dec 2018 17:52
Last Modified:24 Dec 2020 00:34

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