Long non-coding RNAs involved in the regulatory network during porcine pre-implantation embryonic development and iPSC induction

Liang Zhong,Jianyong Han,Haiyuan Mu,Bingqiang Wen,Qingqing Wei,Ge Gao,Suying Cao,Wei Zhang

doi:10.1038/s41598-018-24863-5

Abstract

Long non-coding RNAs (lncRNA) play a key role in the orchestration of transcriptional regulation during development and many other cellular processes. The importance of the regulatory co-expression network was highlighted in the identification of the mechanism of these processes in humans and mice. However, elucidation of the properties of porcine lncRNAs involved in the regulatory network during pre-implantation embryonic development and fibroblast reprogramming to induced pluripotent stem cell (iPSC) has been limited to date. Using a weighted gene co-expression network analysis, we constructed the regulatory network and determined that the novel lncRNAs were functionally involved in key events of embryonic development during the pre-implantation period; moreover, reprogramming could be delineated by a small number of potentially functional modules of co-expressed genes. These findings indicate that lncRNAs may be involved in the transcriptional regulation of zygotic genome activation, first lineage segregation and somatic reprogramming to pluripotency. Furthermore, we performed a conservation and synteny analysis with the significant lncRNAs involved in these vital events and validated the results via experimental assays. In summary, the current findings provide a valuable resource to dissect the protein coding gene and lncRNA regulatory networks that underlie the progressive development of embryos and somatic reprogramming.

Highlights

Long non-coding RNA is a type of non-protein coding transcript longer than 200 nucleotides that represents a large and diverse class of non-coding RNA
To identify potentially functional Long non-coding RNAs (lncRNA) and the regulatory network involved in porcine pre-implantation embryos and induced pluripotent stem cell (iPSC), we first aligned clean reads to the porcine genome using TopHat and assembled them subsequently into 621,085 transcripts to form 227,625 loci in all samples using Cufflinks, which include 27 RNA-seq samples composing of oocyte, 7 consecutive embryonic stages and iPSC
We subsequently performed a weighted gene co-expression network and predicted the potentially functional regulatory network of stage-specific lncRNAs based on their associations with known protein coding genes involved in pre-implantation embryonic development and reprogramming to pluripotency

Summary

Introduction

Long non-coding RNA (lncRNA) is a type of non-protein coding transcript longer than 200 nucleotides that represents a large and diverse class of non-coding RNA. To date, no authentic porcine embryonic stem cells have been derived; a comprehensive analysis of pre-implantation embryos and induced pluripotent stem cells (iPSCs) would facilitate the understanding of the mechanism of pluripotency in pigs. Porcine transcriptome data have indicated that zygotic genome activation (ZGA) occurs during the period from 4-cell stage to 8-cell stage, and there are shared molecular determinants and pathways among pigs, mice and humans involved in first lineage segregation and primitive endoderm differentiation[27]. We report the genome-wide characterization of iPSCs and all stage-embryonic lncRNAs and define a stringent set of 207 (563 transcripts) novel lncRNA genes from RNA-seq data of porcine embryos. Our genome-wide annotation of embryonic lncRNAs may improve our understanding of the molecular mechanisms that underlie porcine embryogenesis as well as reprogramming and provide several regulatory networks during developmental process

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Results

Conclusion