Identification and functional analysis of long intergenic noncoding RNA genes in porcine pre-implantation embryonic development.

Jingyu Li,Zhengling Gao,Zhonghua Liu,Hongbo Liu,Yan Zhang,Xingyu Wang

doi:10.1038/srep38333

Abstract

Genome-wide transcriptome studies have identified thousands of long intergenic noncoding RNAs (lincRNAs), some of which play important roles in pre-implantation embryonic development (PED). Pig is an ideal model for reproduction, however, porcine lincRNAs are still poorly characterized and it is unknown if they are associated with porcine PED. Here we reconstructed 195,531 transcripts in 122,007 loci, and identified 7,618 novel lincRNAs from 4,776 loci based on published RNA-seq data. These lincRNAs show low exon number, short length, low expression level, tissue-specific expression and cis-acting, which is consistent with previous reports in other species. By weighted co-expression network analysis, we identified 5 developmental stages specific co-expression modules. Gene ontology enrichment analysis of these specific co-expression modules suggested that many lincRNAs are associated with cell cycle regulation, transcription and metabolism to regulate the process of zygotic genome activation. Futhermore, we identified hub lincRNAs in each co-expression modules, and found two lincRNAs TCONS_00166370 and TCONS_00020255 may play a vital role in porcine PED. This study systematically analyze lincRNAs in pig and provides the first catalog of lincRNAs that might function as gene regulatory factors of porcine PED.

Highlights

Genome-wide transcriptome studies have identified thousands of long intergenic noncoding RNAs, some of which play important roles in pre-implantation embryonic development (PED)
We found that the modules in the 4- to 8-cell transition corresponding to zygotic genome activation (ZGA) in pig were enriched for transcription regulation, epigenetic regulation and cell cycle (Fig. 4C and see Supplementary Table S3)
We examined the expression of ten selected lincRNAs obtained from the hub genes sets in 4-cell stage-specific module in seven tissues of pig through quantitative realtime polymerase chainreaction analysis, and found that these lincRNAs as a whole were expressed in reproductive tissues (Fig. 5A and see Supplementary Fig. S4)

Summary

Introduction

Genome-wide transcriptome studies have identified thousands of long intergenic noncoding RNAs (lincRNAs), some of which play important roles in pre-implantation embryonic development (PED). We systematically analyzed genomic signatures, expression patterns and regulatory modules of all lincRNAs. To investigate the potential roles of lincRNAs in porcine PED, we performed weighted gene co-expression network analysis (WGCNA)[19], and revealed that many lincRNAs show strong correlation with specific developmental stages.

Results

Conclusion