Abstract
BackgroundLong non-coding RNAs (lncRNAs), a type of epigenetic regulator, are thought to play important roles in embryonic development in mice, and several developmental defects are associated with epigenetic modification disorders. The most dramatic epigenetic reprogramming event occurs during somatic cell nuclear transfer (SCNT) when the expression profile of a differentiated cell is abolished, and a newly embryo-specific expression profile is established. However, the molecular mechanism underlying somatic reprogramming remains unclear, and the dynamics and functions of lncRNAs in this process have not yet been illustrated, resulting in inefficient reprogramming.ResultsIn this study, 63 single-cell RNA-seq libraries were first generated and sequenced. A total of 7009 mouse polyadenylation lncRNAs (including 5204 novel lncRNAs) were obtained, and a comprehensive analysis of in vivo and SCNT mouse pre-implantation embryo lncRNAs was further performed based on our single-cell RNA sequencing data. Expression profile analysis revealed that lncRNAs were expressed in a developmental stage-specific manner during mouse early-stage embryonic development, whereas a more temporal and spatially specific expression pattern was identified in mouse SCNT embryos with changes in the state of chromatin during somatic cell reprogramming, leading to incomplete zygotic genome activation, oocyte to embryo transition and 2-cell to 4-cell transition. No obvious differences between other stages and mouse NTC or NTM embryos at the same stage were observed. Gene oncology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and weighted gene co-expression network analysis (WGCNA) of lncRNAs and their association with known protein-coding genes suggested that several lncRNAs and their associated with known protein-coding genes might be involved in mouse embryonic development and cell reprogramming.ConclusionsThis is a novel report on the expression landscapes of lncRNAs of mouse NT embryos by scRNA-seq analysis. This study will provide insight into the molecular mechanism underlying the involvement of lncRNAs in mouse pre-implantation embryonic development and epigenetic reprogramming in mammalian species after SCNT-based cloning.
Highlights
Long non-coding RNAs, a type of epigenetic regulator, are thought to play important roles in embryonic development in mice, and several developmental defects are associated with epigenetic modification disorders
Overview of scRNA-seq To identify Long non-coding RNAs (lncRNAs) expression profiles, we constructed 63 cDNA libraries that were derived from one metaphase II (MII) oocyte, cumulus cell, and Mouse embryonic fibroblasts (MEF) in vivo and two nuclear donor cell mouse nucleus transfer (NT) embryos at different stages prior to implantation
Taken together, many studies have been reported the dynamic mRNA and protein expression landscapes in mouse pre-implantation embryos, little is known about ncRNAs, especially regarding the lncRNAs expression landscapes in cloned embryos
Summary
Long non-coding RNAs (lncRNAs), a type of epigenetic regulator, are thought to play important roles in embryonic development in mice, and several developmental defects are associated with epigenetic modification disorders. The most dramatic epigenetic reprogramming event occurs during somatic cell nuclear transfer (SCNT) when the expression profile of a differentiated cell is abolished, and a newly embryo-specific expression profile is established. Many studies have shown that some somatic cells can be reprogrammed by using somatic cell nuclear transfer (SCNT) [3,4,5], ectopic expression of a defined set of transcription factors ( named Yamanaka factors, OSKM factors) [6] and piggyBac transposons [7]. Cell fate is determined by the cell type-specific gene expression patterns during cell differentiation as well as nuclear reprogramming. While the use of multiple ectopic transcription factors in vitro has provided a more dynamic description of the regulators that coordinate the induction of silent genes, synergistic cooperation potentiates their ability to induce changes in cell fate [13]. The reprogramming efficiency is still very low, especially for somatic cell reprogramming mediated by nuclear transplantation
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