Systematic Identification and Molecular Characteristics of Long Noncoding RNAs in Pig Tissues.

Yalan Yang,Hua Li,Kui Li,Rong Zhou,Xunbi Li,Shiyun Zhu,Hui Yu

doi:10.1155/2017/6152582

Abstract

Long noncoding RNAs (lncRNAs) are non-protein-coding RNAs that are involved in a variety of biological processes. The pig is an important farm animal and an ideal biomedical model. In this study, we performed a genome-wide scan for lncRNAs in multiple tissue types from pigs. A total of 118 million paired-end 90 nt clean reads were obtained via strand-specific RNA sequencing, 80.4% of which were aligned to the pig reference genome. We developed a stringent bioinformatics pipeline to identify 2,139 high-quality multiexonic lncRNAs. The characteristic analysis revealed that the novel lncRNAs showed relatively shorter transcript length, fewer exons, and lower expression levels in comparison with protein-coding genes (PCGs). The guanine-cytosine (GC) content of the protein-coding exons and introns was significantly higher than that of the lncRNAs. Moreover, the single nucleotide polymorphism (SNP) density of lncRNAs was significantly higher than that of PCGs. Conservation analysis revealed that most lncRNAs were evolutionarily conserved among pigs, humans, and mice, such as CUFF.253988.1, which shares homology with human long noncoding RNA MALAT1. The findings of our study significantly increase the number of known lncRNAs in pigs.

Highlights

The discovery of new classes of regulatory noncoding RNAs, which constitute a majority of transcriptional products, challenges the central dogma of biology [1]
Noncoding RNAs are generally classified as small RNAs, a group that includes microRNAs, piwiinteracting RNAs, and small nucleolar RNAs, or as long noncoding RNAs. Long noncoding RNAs (lncRNAs) share many similar features with mRNA, such as multiexonic structures, 5󸀠 caps, and polyadenylation, but the former group lacks coding potential [2]
LncRNAs are generally evolutionarily conserved to a lesser degree than are protein-coding genes, thousands of lncRNAs are conserved across species [15,16,17,18,19]

Summary

Introduction

The discovery of new classes of regulatory noncoding RNAs (ncRNAs), which constitute a majority of transcriptional products, challenges the central dogma of biology [1]. It may be possible to predict the functions of lncRNAs by analyzing their expression signatures and examining the genomic context of lncRNAs relative to that of protein-coding genes with known functions [14]. The domestic pig (Sus scrofa) is a major animal protein source for human and has significant advantages over other biomedical models [20, 21]. TncRNA, a porcine lncRNA isolated from long SAGE libraries, may perform complex and critical functions in pig fetal development [24]. Systematic identification of pig lncRNAs and analysis of their characteristics are necessary to provide a foundation for further studies of the biological functions of noncoding RNAs in this important model species. To gain insight into the characteristics of Sus scrofa lncRNAs, total RNA, excluding rRNA, was isolated and pooled from different tissues at different developmental stages and sequenced using strand-specific RNA sequencing. This study provides a catalog of porcine lncRNAs to serve as a foundation for further studies on the functions and evolutionary history of noncoding RNAs in mammals

Materials and Methods

Results

Findings

Discussion