MicroRNAs Regulating Human and Mouse Naïve Pluripotency.

Damien Detraux,Julie Mathieu,Abdiasis M Hussein,Logeshwaran Somasundaram,Yuliang Wang,Hannele Ruohola-Baker,Rithika Sankar

doi:10.3390/ijms20235864

Damien Detraux, Julie Mathieu + Show 5 more

Open Access

https://doi.org/10.3390/ijms20235864

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Abstract

microRNAs are ~22bp nucleotide non-coding RNAs that play important roles in the post-transcriptional regulation of gene expression. Many studies have established that microRNAs are important for cell fate choices, including the naïve to primed pluripotency state transitions, and their intermediate state, the developmentally suspended diapause state in early development. However, the full extent of microRNAs associated with these stage transitions in human and mouse remain under-explored. By meta-analysis of microRNA-seq, RNA-seq, and metabolomics datasets from human and mouse, we found a set of microRNAs, and importantly, their experimentally validated target genes that show consistent changes in naïve to primed transitions (microRNA up, target genes down, or vice versa). The targets of these microRNAs regulate developmental pathways (e.g., the Hedgehog-pathway), primary cilium, and remodeling of metabolic processes (oxidative phosphorylation, fatty acid metabolism, and amino acid transport) during the transition. Importantly, we identified 115 microRNAs that significantly change in the same direction in naïve to primed transitions in both human and mouse, many of which are novel candidate regulators of pluripotency. Furthermore, we identified 38 microRNAs and 274 target genes that may be involved in diapause, where embryonic development is temporarily suspended prior to implantation to uterus. The upregulated target genes suggest that microRNAs activate stress response in the diapause stage. In conclusion, we provide a comprehensive resource of microRNAs and their target genes involved in naïve to primed transition and in the paused intermediate, the embryonic diapause stage.

Highlights

MicroRNAs are highly conserved small non coding RNA that post-transcriptionally regulate their target genes by binding mainly to the 3 UTR region of protein-coding mRNA, resulting in translational repression or transcript destabilization [1]
Disruption of enzymes involved in microRNA biogenesis (Drosha, DGCR8, Dicer) leads to the failure of embryonic stem cells (ESC) to downregulate pluripotency markers and to differentiate after exposure to a differentiation signals [9,10,11,12,13,14]
OicfrothReN6A47-ttaarrggeett gceonnense,c2t4io3nasreasriegnciafisceasntwlyhheirgehear minicnraoïRveNhAEiSsCupco(mdopwarne)d-retoguplraitmede,dahnEdSiCts; t4a0r4gettagrgeentegiesndeoswanre(usipg)n-rifiegcuanlattleydlo(Fwigerurine 1nAaï,vBe). hOEfStChes. 6A4l7thtoaurggeht tgheenmesi,cr2o4R3NarAe-tsaigrgneifticgaenntelyinhteigrahcetrioinnsnhaaïvvee phEriSoCr ecxopmerpiamreedntatol spurpimpoerdt fhrEoSmCm; 4i0rT4atraBragseet, genes are significantly lower in naïve hESCs

Summary

Introduction

MicroRNAs are highly conserved small non coding RNA that post-transcriptionally regulate their target genes by binding mainly to the 3 UTR region of protein-coding mRNA, resulting in translational repression or transcript destabilization [1]. Mouse and human ESC have been stabilized in culture at different pluripotency states corresponding to pre- and post-implantation stages in vivo and are referred as naïve and primed cells, respectively [30,31,32] (Figure 1A) Even though these cells are close in a developmental timeline, they are very different in terms of signaling requirements, gene expression, epigenetic landscape, and metabolic signature [26,30,31,32]. We identified 115 microRNAs that significantly change in the same direction in naïve to primed transition in both human and mouse, many of which have not been previously reported, and serve as a resource for future studies These microRNAs and their target genes regulate developmental (e.g., Hedgehog pathway) and metabolic pathways (e.g., fatty acid oxidation, OXPHOS) important for pluripotency. Grereenen √mmeeaannssththeemmiiccrrooRRNNAA--ggeenneeccoonnnneeccttiioonn iiss ccoonnssiiddeerreedd ccoonnssiisstteenntt;; rreedd ××mmeeaannsstthheeccoonnnneeccttiioonniiss nnoott ccoonnssiisstteenntt.. ((CC))GGeenneeoonnttoollooggyyeennrriicchhmmeennttooffmmiiccrrooRRNNAA ttaarrggeett ggeenneesswwitihthlolwowererexepxrpersessiosnioinn ihnumhuamn annaïvneaïEvSeCEsS(Cthse(mthiecrmoRicNrAoRrNegAulraetogruslaatroerhsigahreerhiinghnearïvien). nx-aaïvxies).isx-naexgisatiisvneelgoagt1i0veofloegn1r0icohfmeennrticph-mvaelnutep(-lvaragluere m(laeragnesrmmoeraenssigmnoifirecasnigt)n.ificant)

Results

Hh Pathway in Naïve-to-Primed Transition

Metabolism in Naïve-to-Primed Transition

Grow ElfAF Sperber H1

MicroRNAs showing

Materials and Methods

Culture of Naïve and Primed Human Pluripotent Stem Cells

Generation of GPR161 Mutant hESC

Immunofluorescence Staining and Confocal Imaging

RT-qPCR Analysis of GPR161 Mutant

Conclusions