title: Messenger RNA and microRNA profiling during early mouse EB formation.
abstract: Embryonic stem (ES) cells can be induced to differentiate into embryoid bodies (EBs) in a synchronised manner when plated at a fixed density in hanging drops. This differentiation procedure mimics post-implantation development in mouse embryos and also serves as the starting point of protocols used in differentiation of stem cells into various lineages. Currently, little is known about the potential influence of microRNAs (miRNAs) on mRNA expression patterns during EB formation. We have measured mRNA and miRNA expression in developing EBs plated in hanging drops until day 3, when discrete structural changes occur involving their differentiation into three germ layers. We observe significant alterations in mRNA and miRNA expression profiles during this early developmental time frame, in particular of genes involved in germ layer formation, stem cell pluripotency and nervous system development. Computational target prediction using Pictar, TargetScan and miRBase Targets reveals an enrichment of binding sites corresponding to differentially and highly expressed miRNAs in stem cell pluripotency genes and a neuroectodermal marker, Nes. We also find that members of let-7 family are significantly down-regulated at day 3 and the corresponding up-regulated genes are enriched in let-7 seed sequences. These results depict how miRNA expression changes may affect the expression of mRNAs involved in EB formation on a genome-wide scale. Understanding the regulatory effects of miRNAs during EB formation may enable more efficient derivation of different cell types in culture.
authors: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom.
authors: Rashmi
authors: R
authors: Tripathi
authors: Harpreet Kaur
authors: HK
authors: Saini
authors: Roland
authors: R
authors: Rad
authors: Cei
authors: C
authors: Abreu-Goodger
authors: Stijn
authors: S
authors: van Dongen
authors: Anton J
authors: AJ
authors: Enright
mesh_terms: D000818:Animals; D002454:Cell Differentiation / Q000235:genetics; D058732:Embryoid Bodies / Q000166:cytology / Q000378:metabolism*; D053595:Embryonic Stem Cells / Q000166:cytology / Q000378:metabolism; D020869:Gene Expression Profiling; D016678:Genome; D051379:Mice; D035683:MicroRNAs / Q000737:chemistry / Q000378:metabolism*; D012333:RNA, Messenger / Q000737:chemistry / Q000378:metabolism*
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger; C542687:mirnlet7 microRNA, mouse