Competing Endogenous RNAs (ceRNAs) and Application of Their Regulatory Networks in Complex Traits and Diseases of Ruminants

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

While the paper provides a comprehensive overview of the role of competing endogenous RNAs (ceRNAs) in livestock biology and highlights their potential applications, there are several areas where the manuscript could be improved for better clarity, depth, and impact:

The introduction lacks a clear and concise statement of the problem or research question that the paper aims to address

The literature review is somewhat vague and could benefit from a more detailed exploration of previous studies and key findings in the field of ceRNAs.

The data should be provide in 1-2 tables with suitable references

The paper suggests that ceRNA networks offer a more comprehensive perspective compared to protein-protein interaction (PPI) networks and weighted gene co-expression networks (WGCN). However, this claim lacks detailed comparative analysis.

The conclusion could be more explicit in summarizing the key findings and their implications. Moreover, the conclusion is very long and must be provided with future outlooks.

Don't you think that the current number of references are very few? and does not provide a detailed review on the subject. Please provide a justification

Author Response

Response to Reviewer 1 Comments

The authors greatly appreciate your insightful comments and have taken them into account to revise the manuscript. Changes are highlighted with yellow text.

 

Comments and Suggestions for Authors:

While the paper provides a comprehensive overview of the role of competing endogenous RNAs (ceRNAs) in livestock biology and highlights their potential applications, there are several areas where the manuscript could be improved for better clarity, depth, and impact:

• The introduction lacks a clear and concise statement of the problem or research question that the paper aims to address.

Response: We are grateful for the reviewer’s constructive comments. We applied the mentioned changes in the last paragraph of the introduction.

|Please see page 2, lines 79-82 in the revised manuscript.|

• The literature review is somewhat vague and could benefit from a more detailed exploration of previous studies and key findings in the field of ceRNAs.

Response: We added a suitable explanation as a new section “Literature search strategy to identify studies associated with ceRNA networks in ruminants” in the revised manuscript.

|Please see pages 2 and 3, lines 85-104 in the revised manuscript.|

• The data should be provide in 1-2 tables with suitable references.

Response: We added Table 1 in the revised manuscript according to the response to the previous comment.

|Please see page 3, line 106 in the revised manuscript.|

• The paper suggests that ceRNA networks offer a more comprehensive perspective compared to protein-protein interaction (PPI) networks and weighted gene co-expression networks (WGCN). However, this claim lacks detailed comparative analysis.

Response: We added a suitable explanation along with Table 2 "summary of differences between ceRNA, PPI, and WGC networks" in the revised manuscript.

|Please see pages 8 and 9, lines 306-321 in the revised manuscript.|

• The conclusion could be more explicit in summarizing the key findings and their implications. Moreover, the conclusion is very long and must be provided with future outlooks.

Response: According to your comment, we tried to apply the changes mentioned in the conclusion. In addition, we have written the conclusion and future directions (future outlooks) sections in accordance with the review articles published in the journal, and according to the journal manuscript writing guide (below figure), we have mentioned the conclusion and future directions sections separately.

|Please see page 12, lines 495-496 in the revised manuscript.|

• Don't you think that the current number of references are very few? And does not provide a detailed review on the subject. Please provide a justification.

Response: According to your comment, we inserted additional references according to the added sections and explanations.

|Please see pages 13 and 17, lines 546-757 in the revised manuscript.|

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

Dear Authors,

The manuscript is well-written and comprehensively describes the current state of knowledge on the ceRNA theory in general and in livestock species, with an emphasis on ruminants. It also provides information on future perspectives and potential applications; thus, it will be of value for the researchers in the field. I just have a few minor comments:

line 56: "that pseudogenes, including microRNAs.." - This part should be rewritten since it suggests that miRNAs are pseudogenes.

line 76: "Increasing productive and reproductive capabilities of ruminants..." is not, in my opinion, a "therapeutic application."

line 162: "Schematic illustrating conditions" is not grammatically correct and should be rewritten.

line 390: Please check the author contribution since in the review there are no methodology, validation, or investigation parts.

Best wishes

Author Response

Response to Reviewer 2 Comments

The authors greatly appreciate your insightful comments and have taken them into account to revise the manuscript. Changes are highlighted with pink text.

 

Comments and Suggestions for Authors:

Dear Authors,

The manuscript is well-written and comprehensively describes the current state of knowledge on the ceRNA theory in general and in livestock species, with an emphasis on ruminants. It also provides information on future perspectives and potential applications; thus, it will be of value for the researchers in the field. I just have a few minor comments:

• Line 56: “that pseudogenes, including microRNAs...” - This part should be rewritten since it suggests that miRNAs are pseudogenes.

Response: We are grateful for the reviewer’s constructive comments. We applied the mentioned changes in the revised manuscript.

|Please see page 2, line 57 in the revised manuscript.|

• Line 76: "Increasing productive and reproductive capabilities of ruminants..." is not, in my opinion, a "therapeutic application."

Response: We applied the mentioned changes in the revised manuscript.

|Please see page 2, lines 75-78 in the revised manuscript.|

• Line 162: "Schematic illustrating conditions" is not grammatically correct and should be rewritten.

Response: We applied the mentioned changes in the revised manuscript.

|Please see page 7, lines 252-253 in the revised manuscript.|

• Line 390: Please check the author contribution since in the review there are no methodology, validation, or investigation parts.

Response: We made changes to this section by adding the section "Literature search strategy to identify studies for complex traits and diseases of ruminants" (by the first reviewer's comment), as well as according to the other review articles published in the journal.

|Please see pages 2 and 3, lines 85-105, as well as page 13, lines 536-537 in the revised manuscript.|

Reviewer 3 Report

Comments and Suggestions for Authors

 

The authors tried to provide data on the association between coding an non-coding types of RNA and complex traits as well as disease resistance traits. 1- The review article is well written but i prefer to provide more information about gene expression analysis and its role as biomarker and a monitor for tracking the health status. I mean that the authors should mention previous literature that associate the gene expression analysis with incidence of some economic diseases. As a result the coding mRNA effect on the consequence  of diseases will be prominent. 2- In addition you could provide data on all types of ruminants including buffalo and camels. The authors displayed data on cattle, sheep, and goat.  3- The authors should add the following information with suitable references to give insights about gene expression approach as follows:  Transcript abundance functions as a heritable endophenotype and is associated with chromosomal polymorphisms, in accordance with the genetic genomics theory. This method supported the idea that combining data on gene expression and chromosomal variants could aid in our understanding of the genetics underlying the onset of disease. Quantitative trait loci (QTLs) are polymorphisms connected to gene expression. 4- Please revise subtitles in the review (Some words contain capitalized letters). Please correct.  5- From my expertise, RNA editing is a physiological molecular process that could decipher some physiological conditions on animals. For example, dry period after long period of milk production; it was established that RNA editing in this period could decipher some changes. Any way the authors should provide information on this point.

Author Response

Response to Reviewer 3 Comments

The authors greatly appreciate your insightful comments and have taken them into account to revise the manuscript. Changes are highlighted with green text.

 

Comments and Suggestions for Authors:

The authors tried to provide data on the association between coding and non-coding types of RNA and complex traits as well as disease resistance traits.

• 1- The review article is well written but I prefer to provide more information about gene expression analysis and its role as biomarker and a monitor for tracking the health status. I mean that the authors should mention previous literature that associate the gene expression analysis with incidence of some economic diseases. As a result the coding mRNA effect on the consequence of diseases will be prominent.

Response: We are grateful for the reviewer’s constructive comments. In response, we added some paragraphs with suitable references as a new section “Differential gene expression analysis and its role in economically complex traits and diseases” in the revised manuscript.

|Please see page 4, lines 107-148 in the revised manuscript.|

• 2- In addition you could provide data on all types of ruminants including buffalo and camels. The authors displayed data on cattle, sheep, and goat.

Response: We have added some paragraphs with suitable references about studies regarding buffalo and camels in the revised manuscript.

|Please see pages 11 and 12, lines 446-488, as well as page 1, lines 33-34 in the revised manuscript.|

• 3- The authors should add the following information with suitable references to give insights about gene expression approach as follows: Transcript abundance functions as a heritable endophenotype and is associated with chromosomal polymorphisms, in accordance with the genetic genomics theory. This method supported the idea that combining data on gene expression and chromosomal variants could aid in our understanding of the genetics underlying the onset of disease. Quantitative trait loci (QTLs) are polymorphisms connected to gene expression.

Response: We have added the following information with suitable references according to your comment in the new paragraph about the differential gene expression analysis in the revised manuscript:

“The abundance of transcripts is considered a heritable endophenotype and is linked to chromosomal polymorphisms, according to genetic genomics theory [Jansen and Nap, 2001]. Based on this approach, combining information on chromosomal variants and gene ex-pression could improve our understanding of the genetic basis underlying the onset of a disease in ruminants. Quantitative trait loci (QTLs) are polymorphisms associated with gene expression [Fairfax and Knight, 2014; Cloney, 2016; Essa et al., 2023].”

> Jansen, R.C. and Nap, J.P., 2001. Genetical genomics: the added value from segregation. Trends in Genetics, 17(7), pp. 388-391.

> Fairfax, B.P. and Knight, J.C., 2014. Genetics of gene expression in immunity to infection. Current opinion in immunology, 30, pp. 63-71.

> Cloney, R., 2016. Integrating gene variation and expression to understand complex traits. Nature Reviews Genetics, 17(4), pp. 194-194.

> Essa, B., Al-Sharif, M., Abdo, M., Fericean, L. and Ateya, A., 2023. New insights on nucleotide sequence variants and mRNA levels of candidate genes assessing resistance/susceptibility to mastitis in Holstein and montbéliarde dairy cows. Veterinary Sciences, 10(1), p. 35.

|Please see page 4, lines 130-135 in the revised manuscript.|

• 4- Please revise subtitles in the review (Some words contain capitalized letters). Please correct.

Response: According to the published articles in the journal, all words in the subtitles should contain capital letters.

• 5- From my expertise, RNA editing is a physiological molecular process that could decipher some physiological conditions on animals. For example, dry period after long period of milk production; it was established that RNA editing in this period could decipher some changes. Any way the authors should provide information on this point.

Response: We have added a new paragraph with suitable references according to your comment about RNA editing in the revised manuscript.

|Please see page 6, lines 209-234 in the revised manuscript.|

Author Response File: Author Response.pdf