Research Papers:

Identification and functional analysis of long non-coding RNAs in human and mouse early embryos based on single-cell transcriptome data

Jia-jun Qiu, Zhao-rui Ren and Jing-bin Yan _

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Oncotarget. 2016; 7:61215-61228. https://doi.org/10.18632/oncotarget.11304

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Jia-jun Qiu1, Zhao-rui Ren1,2, Jing-bin Yan1,2

1Shanghai Children’s Hospital, Shanghai Institute of Medical Genetics, Shanghai Jiao Tong University School of Medicine, Shanghai 200040, China

2Key Laboratory of Embryo Molecular Biology, Ministry of Health of China and Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai 200040, China

Correspondence to:

Zhao-rui Ren, email: [email protected]

Jing-bin Yan, email: [email protected]

Keywords: long non-coding RNAs (lncRNAs), early embryo, WGCNA, single-cell RNA-seq, human embryogenesis

Received: January 21, 2016     Accepted: August 08, 2016     Published: August 16, 2016


Epigenetics regulations have an important role in fertilization and proper embryonic development, and several human diseases are associated with epigenetic modification disorders, such as Rett syndrome, Beckwith-Wiedemann syndrome and Angelman syndrome. However, the dynamics and functions of long non-coding RNAs (lncRNAs), one type of epigenetic regulators, in human pre-implantation development have not yet been demonstrated. In this study, a comprehensive analysis of human and mouse early-stage embryonic lncRNAs was performed based on public single-cell RNA sequencing data. Expression profile analysis revealed that lncRNAs are expressed in a developmental stage–specific manner during human early-stage embryonic development, whereas a more temporal-specific expression pattern was identified in mouse embryos. Weighted gene co-expression network analysis suggested that lncRNAs involved in human early-stage embryonic development are associated with several important functions and processes, such as oocyte maturation, zygotic genome activation and mitochondrial functions. We also found that the network of lncRNAs involved in zygotic genome activation was highly preservative between human and mouse embryos, whereas in other stages no strong correlation between human and mouse embryo was observed. This study provides insight into the molecular mechanism underlying lncRNA involvement in human pre-implantation embryonic development.

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