Comprehensive analysis of long non-coding RNAs highlights their spatio-temporal expression patterns and evolutional conservation in Sus scrofa

Abstract

Despite modest sequence conservation and rapid evolution, long non-coding RNAs (lncRNAs) appear to be conserved in expression pattern and function. However, analysis of lncRNAs across tissues and developmental stages remains largely uncharacterized in mammals. Here, we systematically investigated the lncRNAs of the Guizhou miniature pig (Sus scrofa), which was widely used as biomedical model. We performed RNA sequencing across 9 organs and 3 developmental skeletal muscle, and developed a filtering pipeline to identify 10,813 lncRNAs (9,075 novel). Conservation patterns analysis revealed that 57% of pig lncRNAs showed homology to humans and mice based on genome alignment. 5,455 lncRNAs exhibited typical hallmarks of regulatory molecules, such as high spatio-temporal specificity. Notably, conserved lncRNAs exhibited higher tissue specificity than pigspecific lncRNAs and were significantly enriched in testis and ovary. Weighted co-expression network analysis revealed a set of conserved lncRNAs that are likely involved in postnatal muscle development. Based on the high degree of similarity in the structure, organization, and dynamic expression of pig lncRNAs compared with human and mouse lncRNAs, we propose that these lncRNAs play an important role in organ physiology and development in mammals. Our results provide a resource for studying animal evolution, morphological complexity, breeding, and biomedical research.Intensive transcriptome sequencing, also known as deep sequencing, has led to the discovery that mammalian genomes encode a vast range of non-protein-coding RNAs (ncRNAs) that differ in size and level of conservation 1,2 . The proportion of ncRNAs in an organism's genome has a direct correlation with its developmental complexity 3 . ncRNAs are generally classified into many different RNA types, including microRNA (miRNAs), Piwi-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), small interfering RNAs (siRNAs), and long noncoding RNA (lncRNAs). LncRNAs are defined as transcribed RNA fragments > 200 bp, and they do not have open reading frames of > 100 amino acids. Several recent studies have shown mammalian lncRNAs to be heterogeneous and diverse as well as critically important in cellular function, development, and disease via their transcriptional and posttranscriptional regulation of gene expression 4 . In this study, we aimed to further elucidate the origin, evolution, and function of mammalian ncRNAs, the genome of S. scrofa 5 , a species widely used in medical research, by analyzing the content and function of its lncRNA.LncRNAs have long been ascribed an important role in the evolution of complex traits, and recent studies have revealed that thousands of lncRNAs are evolutionarily conserved in mammals, though not to the same extent as

Systematic identification and characterization of Aedes aegypti long noncoding RNAs

“…Similar to previous reports 1,8,17,23,28 , we discovered that lncRNAs identified in our study 222 exhibited typical characteristics of lncRNAs found in other species including vertebrates 7 . Such 223 characteristics are lower GC content, shorter in length, and low sequence conservation even among 224 closely related species.…”

Effects of melatonin on the synthesis of estradiol and gene expression in pig granulosa cells

“…To maximize the use of splice‐site information, a two iteration mapping strategy was used as in our previous study . In the first iteration, paired‐end clean reads were mapped to the reference genome of Sus scrofa (v10.2) using TopHat2 (v2.1.0) in a reference‐based approach.…”

Reverse-genetics studies of lncRNAs—what we have learnt and paths forward

“…On the other hand, 29% of the former were detected only in one cell line compared to 7% of the latter [3]. Highly cell-type-and temporal-specific lncRNA expression patterns have also been shown in vivo [184][185][186][187]. Analyses of patterns of expression of various lncRNAs in mammalian brains based either on in situ hybridization [184] or RNA-seq analysis [185] revealed highly restricted patterns confined to neuroanatomical regions, cell types, or subcellular compartments in a genderdependent fashion.…”