Retinoic Acid Induces Embryonic Stem Cell Differentiation by Altering Both Encoding RNA and microRNA Expression

Jingcheng Zhang; Yang Gao; Mengying Yu; Haibo Wu; Zhiying Ai; Yongyan Wu; Hongliang Liu; Juan Du; Zekun Guo; Yong Zhang

doi:10.1371/journal.pone.0132566

Retinoic Acid Induces Embryonic Stem Cell Differentiation by Altering Both Encoding RNA and microRNA Expression

PLoS One. 2015 Jul 10;10(7):e0132566. doi: 10.1371/journal.pone.0132566. eCollection 2015.

Authors

Jingcheng Zhang¹, Yang Gao², Mengying Yu², Haibo Wu², Zhiying Ai³, Yongyan Wu², Hongliang Liu², Juan Du³, Zekun Guo², Yong Zhang²

Affiliations

¹ College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China; Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China; College of Veterinary Medicine, China Agricultural University, Beijing, 100094, China.
² College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China; Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
³ Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China; College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China.

Abstract

Retinoic acid (RA) is a vitamin A metabolite that is essential for early embryonic development and promotes stem cell neural lineage specification; however, little is known regarding the impact of RA on mRNA transcription and microRNA levels on embryonic stem cell differentiation. Here, we present mRNA microarray and microRNA high-output sequencing to clarify how RA regulates gene expression. Using mRNA microarray analysis, we showed that RA repressed pluripotency-associated genes while activating ectoderm markers in mouse embryonic stem cells (mESCs). Moreover, RA modulated the DNA methylation of mESCs by altering the expression of epigenetic-associated genes such as Dnmt3b and Dnmt3l. Furthermore, H3K4me2, a pluripotent histone modification, was repressed by RA stimulation. From microRNA sequence data, we identified two downregulated microRNAs, namely, miR-200b and miR-200c, which regulated the pluripotency of stem cells. We found that miR-200b or miR-200c deficiency suppressed the expression of pluripotent genes, including Oct4 and Nanog, and activated the expression of the ectodermal marker gene Nestin. These results demonstrate that retinoid induces mESCs to differentiate by regulating miR-200b/200c. Our findings provide the landscapes of mRNA and microRNA gene networks and indicate the crucial role of miR-200b/200c in the RA-induced differentiation of mESCs.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Biomarkers / metabolism
Cell Differentiation / drug effects*
Cell Differentiation / genetics
Cell Self Renewal / drug effects
Cell Self Renewal / genetics
Ectoderm / drug effects
Ectoderm / metabolism
Epigenesis, Genetic / drug effects
Gene Expression Regulation / drug effects*
Mice
MicroRNAs / genetics*
MicroRNAs / metabolism
Molecular Sequence Annotation
Mouse Embryonic Stem Cells / cytology*
Mouse Embryonic Stem Cells / drug effects
Mouse Embryonic Stem Cells / metabolism
Oligonucleotide Array Sequence Analysis
Pluripotent Stem Cells / cytology
Pluripotent Stem Cells / drug effects
Pluripotent Stem Cells / metabolism
RNA, Messenger / genetics
RNA, Messenger / metabolism
Signal Transduction / drug effects
Signal Transduction / genetics
Tretinoin / pharmacology*

Substances

Biomarkers
MicroRNAs
RNA, Messenger
Tretinoin

Associated data

GEO/GSE43405
GEO/GSE54145

Grants and funding

This work was supported by the National High Technology Research and Development Program of China (863 Program) (No. 2011AA100303) (http://www.863.gov.cn/), partly by a grant from the National Natural Science Foundation of China (No. 31172279) (http://www.nsfc.gov.cn/), and Key Science and Technology Innovation Team in Shaanxi Province (2014KCT-26) (http://www.sninfo.gov.cn/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.