Exploration of Long Non-coding RNAs and Circular RNAs in Porcine Milk Exosomes

Abstract

RNA in milk exosomes can be absorbed in the mammalian intestinal tract and function in gene expression regulations. Our previous work demonstrated that porcine milk exosomes (PME) contain large amounts of miRNAs and mRNAs. Increasing evidence suggests that long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) are of particular interest, given their key role in diverse biological processes of animals. However, the expression profiles and the potential functions of lncRNAs and circRNAs in PME are still unknown. In the present study, we isolated PME by ultracentrifugation and performed a comprehensive analysis of lncRNA and circRNA in PME by using RNA sequencing. As a result, 2,466 novel lncRNAs, 809 annotated lncRNAs, and 61 circRNAs were identified in PME. The lncRNAs shared similar characteristics with other mammals in terms of length, exon number, and open reading frames. However, lncRNAs showed a higher level compared with mRNAs. Eight lncRNAs and five circRNAs in PME were selected for PCR identification. A functional enrichment analysis on the target genes of lncRNAs indicated that these genes were involved in cellular macromolecule metabolic, RNA metabolic, and immune processes. The circRNAs host genes were enriched in nucleic acid binding and adherence junction. We also evaluated the potential interaction targets between miRNAs and PME lncRNAs or circRNAs, and the results showed that the PME lncRNAs and the circRNAs have a high density of miRNA target sites. The top 20 highly expressed lncRNAs were found to interact with the proliferation-related miRNAs, and the circRNAs potentially targeted many miRNAs that are associated with the intestinal barrier. This study is the first to provide a resource for lncRNA and circRNA research of porcine milk. Moreover, the potential interaction between lncRNA/circRNA and miRNA is revealed. The present study expands our knowledge of non-coding RNAs in milk, and additional research is necessary to confirm their exactly physiological functions.

Milk Exosomes: Perspective Agents for Anticancer Drug Delivery

“…Studies of the past decade have shown the content of various noncoding RNA—microRNA, long noncoding RNA, circular RNA [ 60 ]—in bovine [ 61 ], human [ 62 ], panda [ 12 ], porcine [ 7 ], and rat [ 63 ] milk. Exosomal RNAs are stable at low intestinal pH values and in the presence of RNases [ 61 , 64 ].…”

“…It releases mammary epithelial acinus from cell arrest during morphogenesis [ 115 ], suggesting a potential effect of mammary miR-21 on tumor growth processes. Long noncoding RNA of porcine milk exosomes may interact with miRNA related to cell proliferation, and circular RNA may target miRNA associated with intestinal cells [ 60 ]. A recent paper showed that miRNAs from bovine and porcine milk were adsorbed in piglet intestine and transported to the blood serum with different efficiencies [ 92 ].…”

A Two-Dimensional Affinity Capture and Separation Mini-Platform for the Isolation, Enrichment, and Quantification of Biomarkers and Its Potential Use for Liquid Biopsy

“…The role of non-coding RNAs (ncRNAs) in EVs is not fully understood, but their higher abundance in association with cancer and other diseases demonstrated their relevance. Several studies are underway on microRNAs, long ncRNAs, and circular RNA present in exosomes, and evidence exists that non-protein coding genes harbors crucial importance in terms of development, homeostasis, and disease [ 249 , 250 , 251 , 252 , 253 , 254 ].…”

Functional Role of circRNAs in the Regulation of Fetal Development, Muscle Development, and Lactation in Livestock

“…On the one hand, some studies have shown that cir-cRNAs play an important role in regulating the lactation of livestock [3][4][5]. Some studies detected a total of 37,818 circRNAs in goat breast tissue, of which 864 circRNAs were differentially expressed, 611 were upregulated, and 253 were down-regulated [6], so they speculated that these circRNAs may be related to breast development and lactation.…”