Abstract
Long intergenic non-coding RNAs (lincRNAs) have been considered to play a key regulatory role in various biological processes. An increasing number of studies have utilized transcriptome analysis to obtain lincRNAs with functions related to cancer, but lincRNAs affecting growth rates in weaned piglets are rarely described. Although lincRNAs have been systematically identified in various mouse tissues and cell lines, studies of lincRNA in pigs remain rare. Therefore, identifying and characterizing novel lincRNAs affecting the growth performance of weaned piglets is of great importance. Here, we reconstructed 101,988 lincRNA transcripts and identified 1,078 lincRNAs in two groups of longissimus dorsi muscle (LDM) and subcutaneous fat (SF) based on published RNA-seq datasets. These lincRNAs exhibit typical characteristics, such as shorter lengths and lower expression relative to protein-encoding genes. Gene ontology analysis revealed that some lincRNAs could be involved in weaned piglet related processes, such as insulin resistance and the AMPK signaling pathway. We also compared the positional relationship between differentially expressed lincRNAs (DELs) and quantitative trait loci (QTL) and found that some of DELs may play an important role in piglet growth and development. Our work details part of the lincRNAs that may affect the growth performance of weaned piglets and promotes future studies of lincRNAs for molecular-assisted development in weaned piglets.
Highlights
Over the past decade, given developments in second-generation sequencing technologies, an increasing number of transcriptome studies have revealed a large number of non-coding transcripts in the genome of mammal (Pauli et al, 2012)
We performed a comprehensive analysis of 36 RNAseq libraries based on the designed pipeline and we identified 1078 lincRNAs in longissimus dorsi muscle (LDM) and subcutaneous fat (SF) of weaned piglets
Compared with the known lincRNA database, we found 198 new putative lincRNAs
Summary
Given developments in second-generation sequencing technologies, an increasing number of transcriptome studies have revealed a large number of non-coding transcripts in the genome of mammal (Pauli et al, 2012). As science and technology have advanced, researchers have gradually realized that non-coding transcripts may possess their own unique regulatory mechanisms; these transcripts are called lincRNAs because they are located between genes and have a structure longer than 200 nt (Mizutani et al, 2012). They have low coding potential, lincRNAs present certain functions in many cellular processes, including gene regulation, apoptosis and embryonic development (Leung et al, 2013). Research involving pig lincRNA is minimal and deserves further exploration (Ran et al, 2016)
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