Dynamics of microRNA expression during mouse prenatal development
- Sorena Rahmanian1,2,7,
- Rabi Murad1,2,7,
- Alessandra Breschi3,
- Weihua Zeng1,2,
- Mark Mackiewicz4,
- Brian Williams5,
- Carrie A. Davis6,
- Brian Roberts4,
- Sarah Meadows4,
- Dianna Moore4,
- Diane Trout5,
- Chris Zaleski6,
- Alex Dobin6,
- Lei-Hoon Sei6,
- Jorg Drenkow6,
- Alex Scavelli6,
- Thomas R. Gingeras6,
- Barbara J. Wold5,
- Richard M. Myers4,
- Roderic Guigó3 and
- Ali Mortazavi1,2
- 1Department of Developmental and Cell Biology, University of California Irvine, Irvine, California 92697, USA;
- 2Center for Complex Biological Systems, University of California Irvine, Irvine, California 92697, USA;
- 3Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Barcelona 08003, Catalonia, Spain;
- 4HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA;
- 5Division of Biology, California Institute of Technology, Pasadena, California 91125, USA;
- 6Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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↵7 These authors contributed equally to this work.
Abstract
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.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.248997.119.
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Freely available online through the Genome Research Open Access option.
- Received January 30, 2019.
- Accepted August 29, 2019.
This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
