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Research Article
Non-Coding RNA in Raw and Commercially Processed Milk and Putative Targets Related to Growth and Immune-Response
E. Testroet
University of Vermont
Corresponding Author
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background:
Bovine milk contains extracellular vesicles (EVs) that play a role in cellular communication, acting in either an autocrine, paracrine, or an exocrine manner. The unique properties of the EVs protect the cargo against degradation. We profiled the ncRNAs (non-coding RNA) present in the EVs from five fluid dairy products - raw whole milk, heat-treated skim milk, homogenized heat-treated skim milk, pasteurized homogenized skim milk, and pasteurized heavy whipping cream (four replicates each) obtained at different processing steps from a commercial dairy plant. EVs and their cargo were extracted by using a validated commercial kit that has been shown to be efficient and specific for EVs. Because many ncRNAs and the ncRNAs of bovine are less well characterized that human but are generally highly conserved, both human and Bos taurus databases were probed for putative targets.
Results:
Thirty microRNAs (miRNAs), isolated from milk, with their corresponding 1546 putative gene targets have functions associated with immune response and growth and development, indicating the potential for these ncRNAs to beneficially support mammary health and growth for the cow as well as neonatal gut maturation. The most abundant miRNAs were miR-125, which is involved in host bacterial and viral immune response, and human homolog miR-718 in the regulation of p53, VEGF, and IGF signaling pathways, respectively. Sixty-two miRNAs were enriched and 121 miRNAs were diluted throughout all the milk samples when compared to raw whole milk. In addition, our study explored the putative roles of other ncRNAs which included 88 piRNAs (piwi-interacting RNA), 64 antisense RNAs, and 105 long-intergenic ncRNAs contained in the bovine exosomes.
Conclusion:
Together, the results indicate that bovine milk contains significant numbers of ncRNAs with putative regulatory targets associated with immune- and developmental-functions important for neonatal bovine health, and that processing significantly increases the abundance of these ncRNA species. It is worth noting, however, that these gene regulatory targets are putative, and, though not necessary, further evidence could be generated through experimental validation.
Keywords
miRNA, ncRNA, piRNA, exosome, mammary health, gut maturation
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This is a list of supplementary files associated with this preprint. Click to download.
- Supplementaltable1.xlsx
Supplemental Table 1: Detailed results from Statistical testing of total miRNA abundance levels using DESeq2 in different milk samples against the raw whole milk as the control group.
- Supplementaltable2.xlsx
Supplemental Table 2: Gene ontology (GO) IDS over-represented in list of gene targets (specific to Bos taurus) for which miRNAs have been found in the milk samples.
- Supplementaltable3.xlsx
Supplemental Table 3: Gene ontology (GO) IDS over-represented in list of gene targets (specific to Homo sapiens) for which miRNAs have been found in the milk samples.
- Supplementaltable4.xlsx
Supplemental Table 4: List of miRNAs with associated gene targets when compared with miRbase.
- Supplementaltable5.xlsx
Supplemental Table 5: List of other RNA (tRNAs, lincRNAs, protein-coding regions) found from milk samples.
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CURRENT STATUS: Under Review
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Posted 30 Dec, 2020
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Reviewer #4 agreed
On 08 Jan, 2021
Reviewer #3 agreed
On 08 Jan, 2021
Reviewer #2 agreed
On 08 Jan, 2021
Reviewer #1 agreed
On 08 Jan, 2021
Reviewers invited
Invitations sent on 08 Jan, 2021
Editor assigned
On 08 Jan, 2021
Editor invited
On 28 Dec, 2020
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On 28 Dec, 2020
First submitted
On 22 Dec, 2020
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Subject Areas
Epigenetics & Genomics
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This preprint is under consideration at BMC Genomics. A preprint is a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research Article
Non-Coding RNA in Raw and Commercially Processed Milk and Putative Targets Related to Growth and Immune-Response
E. Testroet
University of Vermont
Corresponding Author
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Under Review
Version 1
Posted 30 Dec, 2020
No community comments so far
Reviewer #4 agreed
On 08 Jan, 2021
Reviewer #3 agreed
On 08 Jan, 2021
Reviewer #2 agreed
On 08 Jan, 2021
Reviewer #1 agreed
On 08 Jan, 2021
Reviewers invited
Invitations sent on 08 Jan, 2021
Editor assigned
On 08 Jan, 2021
Editor invited
On 28 Dec, 2020
Submission checks complete
On 28 Dec, 2020
First submitted
On 22 Dec, 2020
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Epigenetics & Genomics
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background:
Bovine milk contains extracellular vesicles (EVs) that play a role in cellular communication, acting in either an autocrine, paracrine, or an exocrine manner. The unique properties of the EVs protect the cargo against degradation. We profiled the ncRNAs (non-coding RNA) present in the EVs from five fluid dairy products - raw whole milk, heat-treated skim milk, homogenized heat-treated skim milk, pasteurized homogenized skim milk, and pasteurized heavy whipping cream (four replicates each) obtained at different processing steps from a commercial dairy plant. EVs and their cargo were extracted by using a validated commercial kit that has been shown to be efficient and specific for EVs. Because many ncRNAs and the ncRNAs of bovine are less well characterized that human but are generally highly conserved, both human and Bos taurus databases were probed for putative targets.
Results:
Thirty microRNAs (miRNAs), isolated from milk, with their corresponding 1546 putative gene targets have functions associated with immune response and growth and development, indicating the potential for these ncRNAs to beneficially support mammary health and growth for the cow as well as neonatal gut maturation. The most abundant miRNAs were miR-125, which is involved in host bacterial and viral immune response, and human homolog miR-718 in the regulation of p53, VEGF, and IGF signaling pathways, respectively. Sixty-two miRNAs were enriched and 121 miRNAs were diluted throughout all the milk samples when compared to raw whole milk. In addition, our study explored the putative roles of other ncRNAs which included 88 piRNAs (piwi-interacting RNA), 64 antisense RNAs, and 105 long-intergenic ncRNAs contained in the bovine exosomes.
Conclusion:
Together, the results indicate that bovine milk contains significant numbers of ncRNAs with putative regulatory targets associated with immune- and developmental-functions important for neonatal bovine health, and that processing significantly increases the abundance of these ncRNA species. It is worth noting, however, that these gene regulatory targets are putative, and, though not necessary, further evidence could be generated through experimental validation.
Figure 1
Figure 2
Figure 3
Figure 4