Abstract
BackgroundLong non-coding RNAs (lncRNAs) regulate embryonic development and cell fate decision in various ways, such as modulation of chromatin modification and post-transcription regulation of gene expression. However, the profiles and roles of lncRNAs in early mammalian development have not yet been demonstrated. Here, we reported a comprehensive analysis of mouse cleavage stage embryonic lncRNA profiles based on public single-cell RNA-seq data.ResultsWe reconstructed 50,006 high-confidence transcripts in 22,827 loci, and identified 5563 novel lncRNAs from 3492 loci expressed in mouse cleavage stage embryos. These lncRNAs share similar characteristics with previously reported vertebrate lncRNAs, such as relatively short length, low exon number, low expression level and low sequence conservation. Expression profile analysis revealed that the profiles of lncRNA vary considerably at different stages of cleavage stage embryos, suggesting that many lncRNAs in cleavage stage embryos are stage-specifically expressed. Co-expression network analysis suggested many lncRNAs in cleavage stage embryos are associated with cell cycle regulation, transcription, translation and oxidative phosphorylation to regulate the process of cleavage stage embryonic development.ConclusionsThis study provides the first catalog of lncRNAs expressed in mouse cleavage stage embryos and gives a revealing insight into the molecular mechanism responsible for early embryonic development.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-845) contains supplementary material, which is available to authorized users.
Highlights
Long non-coding RNAs regulate embryonic development and cell fate decision in various ways, such as modulation of chromatin modification and post-transcription regulation of gene expression
Since our transcriptomes are reconstructed from a non strand-specific RNA-seq dataset, we determined the direction of transcripts based on the splice junction sequences
We provided the first Long non-coding RNAs (lncRNAs) profiles of mouse cleavage stage embryos based on single-cell RNA-seq data, and identified 5563 novel lncRNA transcripts from 3492 loci expressed in mouse cleavage stage embryos
Summary
Long non-coding RNAs (lncRNAs) regulate embryonic development and cell fate decision in various ways, such as modulation of chromatin modification and post-transcription regulation of gene expression. We reported a comprehensive analysis of mouse cleavage stage embryonic lncRNA profiles based on public single-cell RNA-seq data. The beginning of embryogenesis is cleavage stage During this stage, a zygote undergoes several rapid rounds of division, and produces a mass of cells within the zona pellucida. A zygote undergoes several rapid rounds of division, and produces a mass of cells within the zona pellucida Cleavage, such as multinucleation [1] and asynchrony division [2], will lead to poor developmental competence. The expression patterns of messenger RNAs and microRNAs in cleavage stage embryos were discussed in previous studies, the long non-coding RNAs (lncRNAs), which were recently proved to be critical gene regulators of development, are not yet clearly elucidated
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