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Exploration of microRNAs in porcine milk exosomes.

Chen T, Xi QY, Ye RS, Cheng X, Qi QE, Wang SB, Shu G, Wang LN, Zhu XT, Jiang QY, Zhang YL - BMC Genomics (2014)

Bottom Line: Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component.Our findings suggest that porcine milk exosomes contain a large number of miRNAs, which potentially play an important role in information transfer from sow milk to piglets.The predicted miRNAs of porcine milk exosomes in this study provide a basis for future biochemical and biophysical function studies.

View Article: PubMed Central - PubMed

Affiliation: Guandong Provincial Key Lab of Agro-Animal Genomics And Molecular Breeding, College of Animal Science, ALLTECH-SCAU Animal Nutrition Control Research Alliance, National Engineering Research Center For Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China. Zhangyl@scau.edu.cn.

ABSTRACT

Background: Breast milk contains complex nutrients and facilitates the maturation of various biological systems in infants. Exosomes, membranous vesicles of endocytic origin found in different body fluids such as milk, can mediate intercellular communication. We hypothesized that microRNAs (miRNAs), a class of non-coding small RNAs of 18-25 nt which are known to be packaged in exosomes of human, bovine and porcine milk, may play important roles in the development of piglets.

Results: In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). The top 10 miRNAs accounted for 74.5% (67,154 counts) of total counts, which were predicted to target 2,333 genes by RNAhybrid software. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses using DAVID bioinformatics resources indicated that the identified miRNAs targeted genes enriched in transcription, immunity and metabolism processes, and 14 of the top 20 miRNAs possibly participate in regulation of the IgA immune network.

Conclusions: Our findings suggest that porcine milk exosomes contain a large number of miRNAs, which potentially play an important role in information transfer from sow milk to piglets. The predicted miRNAs of porcine milk exosomes in this study provide a basis for future biochemical and biophysical function studies.

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Related in: MedlinePlus

Three distinctive pre-miRNAs identified in porcine milk exosomes. (A) The ssc-miR-27a precursor produced a 3p-arm miRNA sequence and a loop-derived small RNA. (B) The ssc-let-7e precursor produced a 5p-arm sequence, a 3p-arm miRNA sequence and a loop-derived small RNA. (C) The ssc-miR-30a precursor produced a 5p-arm sequence, a 3p-arm miRNA sequence and a loop-derived small RNA. In addition, ssc-moRNA-3, belonging to new type of miRNA termed moRNA, was found at the 5’ end of pre-miR-30.
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Fig10: Three distinctive pre-miRNAs identified in porcine milk exosomes. (A) The ssc-miR-27a precursor produced a 3p-arm miRNA sequence and a loop-derived small RNA. (B) The ssc-let-7e precursor produced a 5p-arm sequence, a 3p-arm miRNA sequence and a loop-derived small RNA. (C) The ssc-miR-30a precursor produced a 5p-arm sequence, a 3p-arm miRNA sequence and a loop-derived small RNA. In addition, ssc-moRNA-3, belonging to new type of miRNA termed moRNA, was found at the 5’ end of pre-miR-30.

Mentions: As described in other studies[51], some small RNAs were generated from the loop or the region between the loop and stem (ssc-let-7e, ssc-miR-27a and ssc-miR-30a) (Figure 10A–C). In addition, we detected another interesting type of small RNAs known as miRNA-offset RNAs, or “moRNAs”, which are derived from the ends of pre-miRNAs, predominantly from the 5’ end, independent of the mature miRNA. A good example of moRNAs and small RNAs generated from the loop was pre-miR-30a (Figure 10C). At the 5’ end of pre-miR-30, a 18 nt RNA sequence was found to be generated from the loop, downstream of ssc-miR-30a-5p (Figure 10C). The findings suggest that these RNAs may be only byproducts of Drosha and Dicer processing, or these small RNAs alternatively may take part in other important regulatory functions different from those of miRNAs.Figure 10


Exploration of microRNAs in porcine milk exosomes.

Chen T, Xi QY, Ye RS, Cheng X, Qi QE, Wang SB, Shu G, Wang LN, Zhu XT, Jiang QY, Zhang YL - BMC Genomics (2014)

Three distinctive pre-miRNAs identified in porcine milk exosomes. (A) The ssc-miR-27a precursor produced a 3p-arm miRNA sequence and a loop-derived small RNA. (B) The ssc-let-7e precursor produced a 5p-arm sequence, a 3p-arm miRNA sequence and a loop-derived small RNA. (C) The ssc-miR-30a precursor produced a 5p-arm sequence, a 3p-arm miRNA sequence and a loop-derived small RNA. In addition, ssc-moRNA-3, belonging to new type of miRNA termed moRNA, was found at the 5’ end of pre-miR-30.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4008308&req=5

Fig10: Three distinctive pre-miRNAs identified in porcine milk exosomes. (A) The ssc-miR-27a precursor produced a 3p-arm miRNA sequence and a loop-derived small RNA. (B) The ssc-let-7e precursor produced a 5p-arm sequence, a 3p-arm miRNA sequence and a loop-derived small RNA. (C) The ssc-miR-30a precursor produced a 5p-arm sequence, a 3p-arm miRNA sequence and a loop-derived small RNA. In addition, ssc-moRNA-3, belonging to new type of miRNA termed moRNA, was found at the 5’ end of pre-miR-30.
Mentions: As described in other studies[51], some small RNAs were generated from the loop or the region between the loop and stem (ssc-let-7e, ssc-miR-27a and ssc-miR-30a) (Figure 10A–C). In addition, we detected another interesting type of small RNAs known as miRNA-offset RNAs, or “moRNAs”, which are derived from the ends of pre-miRNAs, predominantly from the 5’ end, independent of the mature miRNA. A good example of moRNAs and small RNAs generated from the loop was pre-miR-30a (Figure 10C). At the 5’ end of pre-miR-30, a 18 nt RNA sequence was found to be generated from the loop, downstream of ssc-miR-30a-5p (Figure 10C). The findings suggest that these RNAs may be only byproducts of Drosha and Dicer processing, or these small RNAs alternatively may take part in other important regulatory functions different from those of miRNAs.Figure 10

Bottom Line: Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component.Our findings suggest that porcine milk exosomes contain a large number of miRNAs, which potentially play an important role in information transfer from sow milk to piglets.The predicted miRNAs of porcine milk exosomes in this study provide a basis for future biochemical and biophysical function studies.

View Article: PubMed Central - PubMed

Affiliation: Guandong Provincial Key Lab of Agro-Animal Genomics And Molecular Breeding, College of Animal Science, ALLTECH-SCAU Animal Nutrition Control Research Alliance, National Engineering Research Center For Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China. Zhangyl@scau.edu.cn.

ABSTRACT

Background: Breast milk contains complex nutrients and facilitates the maturation of various biological systems in infants. Exosomes, membranous vesicles of endocytic origin found in different body fluids such as milk, can mediate intercellular communication. We hypothesized that microRNAs (miRNAs), a class of non-coding small RNAs of 18-25 nt which are known to be packaged in exosomes of human, bovine and porcine milk, may play important roles in the development of piglets.

Results: In this study, exosomes of approximately 100 nm in diameter were isolated from porcine milk through serial centrifugation and ultracentrifugation procedures. Total RNA was extracted from exosomes, and 5S ribosomal RNA was found to be the major RNA component. Solexa sequencing showed a total of 491 miRNAs, including 176 known miRNAs and 315 novel mature miRNAs (representing 366 pre-miRNAs), which were distributed among 30 clusters and 35 families, and two predicted novel miRNAs were verified targeting 3'UTR of IGF-1R by luciferase assay. Interestingly, we observed that three miRNAs (ssc-let-7e, ssc-miR-27a, and ssc-miR-30a) could be generated from miRNA-offset RNAs (moRNAs). The top 10 miRNAs accounted for 74.5% (67,154 counts) of total counts, which were predicted to target 2,333 genes by RNAhybrid software. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses using DAVID bioinformatics resources indicated that the identified miRNAs targeted genes enriched in transcription, immunity and metabolism processes, and 14 of the top 20 miRNAs possibly participate in regulation of the IgA immune network.

Conclusions: Our findings suggest that porcine milk exosomes contain a large number of miRNAs, which potentially play an important role in information transfer from sow milk to piglets. The predicted miRNAs of porcine milk exosomes in this study provide a basis for future biochemical and biophysical function studies.

Show MeSH
Related in: MedlinePlus