Abstract
ObjectiveWe investigated the temporal expression profiles of long noncoding RNA (lncRNA) and mRNA in the peripheral blood of pigs during development and identified the lncRNAs that are related to the blood-based immune system.MethodsPeripheral blood samples were obtained from the pigs at 0, 7, 28, and 180 days and 2 years of age. RNA sequencing was performed to survey the lncRNA and mRNA transcriptomes in the samples. Short time-series expression miner (STEM) was used to show temporal expression patterns in the mRNAs and lncRNAs. Gene ontology and Kyoto encyclopedia of genes and genomes analyses were performed to assess the genes’ biological relevance. To predict the functions of the identified lncRNAs, we extracted mRNAs that were nearby loci and highly correlated with the lncRNAs.ResultsIn total of 5,946 lncRNA and 12,354 mRNA transcripts were identified among the samples. STEM showed that most lncRNAs and mRNAs had similar temporal expression patterns during development, indicating the expressional correlation and functional relatedness between them. The five stages were divided into two classes: the suckling period and the late developmental stage. Most genes were expressed at low level during the suckling period, but at higher level during the late stages. Expression of several T-cell-related genes increased continuously during the suckling period, indicating that these genes are crucial for establishing the adaptive immune system in piglets at this stage. Notably, lncRNA TCONS-00086451 may promote blood-based immune system development by upregulating nuclear factor of activated T-cells cytoplasmic 2 expression.ConclusionThis study provides a catalog of porcine peripheral blood-related lncRNAs and mRNAs and reveals the characteristics and temporal expression profiles of these lncRNAs and mRNAs during peripheral blood development from the newborn to adult stages in pigs.
Highlights
A better understanding of porcine immune system development is needed because of the agricultural importance of pigs, the role of pigs as potential reservoir hosts for zoonotic diseases, and increasing awareness of the benefits of using pigs as preclinical models for human disease and therapy [1]
We considered a mRNA to be expressed if it had an expression value greater than 0.5 fragments per kilobase per million mapped reads (FPKM) (FPKM >0.5) in at least one
We considered a long noncoding RNA (lncRNA) transcript to be expressed if it had an expression value greater than 0.1 FPKM (FPKM >0.1) in at least one sample
Summary
A better understanding of porcine immune system development is needed because of the agricultural importance of pigs, the role of pigs as potential reservoir hosts for zoonotic diseases, and increasing awareness of the benefits of using pigs as preclinical models for human disease and therapy [1]. Previous research has reported that mammals experience a critical stage in development that extends from late gestation to weaning [2]. Piglets suffer high mortality and morbidity during this stage due to various diseases [3], likely because this stage is a critical window when the adaptive immune system is developing, and the temporary protection provided by passive immunity and pre-adaptive antibodies is being replaced [4]. Accurate knowledge of the immune system development after birth, www.ajas.info
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