ABSTRACT
MicroRNAs (miRNAs) play a critical role as post-transcriptional regulators of gene expression. The ENCODE project profiled the expression of miRNAs in a comprehensive set of tissues during a time-course of mouse embryonic development and captured the expression dynamics of 785 miRNAs. We found distinct tissue and developmental stage specific miRNA expression clusters, with an overall pattern of increasing tissue specific expression as development proceeds. Comparative analysis of conserved miRNAs in mouse and human revealed stronger clustering of expression patterns by tissue types rather than by species. An analysis of messenger RNA gene 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 tissue where these microRNAs are expressed during embryonic development. Our results provide the most comprehensive timecourse of miRNA expression as an integrated part of the ENCODE reference dataset for mouse embryonic development.
Footnotes
Sorena Rahmanian: sorenar{at}uci.edu, Rabi Murad: rmurad{at}uci.edu, Alessandra Breschi: Alessandra.Breschi{at}crg.es, Weihua Zeng: zengw{at}uci.edu, Brian Williams: bawilli{at}caltech.edu, Mark Mackiewicz: mmackiewicz{at}hudsonalpha.org, Brian Roberts: broberts{at}hudsonalpha.org, Sarah Meadows: smeadows{at}hudsonalpha.org Dianne Moore: dmoore{at}hudsonalpha.org Carrie Davis: davisc{at}cshl.edu, Diane Trout: diane{at}caltech.edu Chris Zaleski: zaleski{at}cshl.edu Alex Dobin: dobin{at}cshl.edu, Lei-Hoon Sei: lhsee{at}yahoo.com Jorg Drenkow: drenkow{at}cshl.edu Alex Scavelli: a.t.scavelli{at}gmail.com Thomas Gingeras: gingeras{at}cshl.edu Barbara Wold: woldb{at}caltech.edu Richard M. Myers: rmyers{at}hudsonalpha.org Roderic Guigó: roderic.guigo{at}CRG.CAT Ali Mortazavi: ali.mortazavi{at}uci.edu