Perspective for Studying the Relationship of miRNAs with Transposable Elements

Round 1

Reviewer 1 Report

Mustafin and Khusnutdinova provide an up-to-date account of microRNAs derived from transposable elements. The perspective to establish a database to store this type of microRNAs could be useful for the scientists working in the field. The manuscript is well-constructed in general, easy to follow with useful current information on the topic. I suggest the following minor issues for consideration:

 

1. Line 9, I suggest "an important" instead of "the most"

2. Line 43, please abbreviate "TE" in its first use

3. Lines 223 and 228, please avoid the use of "me" and "I". There are few more such cased in the following parts of the manuscript.

4. Please be consistent in the use of "microRNA" or "miRNA".

Author Response

Hello dear editor. I carefully read all the reviews of our article, I fully agree with all the comments, according to which the article has been corrected. The corrections were made in the review mode in the Word document format, additional corrections were highlighted in the text in accordance with the comments of different reviewers (in different colors) for the convenience of the editors.

Detailed comments step by step, according to different reviewers.

According to reviewer 1 (highlighted in yellow):

Line 9, "the most" corrected to "important".

Line 43 (now 48), "TE" - deciphered the abbreviation on first use in Line 42 (now 47).

In lines 228 and 229 (as well as in other places in the text – lines 22, 247, 248, 293, 294, 345, 349) "me" and "I" are deleted - replaced by other phrases.

Changed "microRNA" to "miRNA" throughout the text.

 

According to reviewer 2 (highlighted in green):

1. I rephrased the introduction section ("the most" corrected to "important"). I also briefly discussed TEs regulation through other mechanisms except for microRNA (TEs' expression is also regulated by epigenetic factors (DNA methylation, histone modifications), SIRT6, cytidine deaminases APOBEC3, APOBEC1, and other catalytic proteins such as ERCC, TREX1, RB1, HELLS, and MEGP2).
2. I corrected the statement “siRNAs are formed mainly through the processing of TEs transcripts” to “siRNAs are generated by degradation of exogenous dsRNAs of transcribed from TEs or from other types of inverted repeats”.
3. Section "FEATURES OF THE... IN PLANTS" has been renamed to "Differences of the Origin of MicroRNAs from Transposons in Plants from Animals" as this section would be interesting for readers to review the differences. I agree with the distinguished reviewer's remarks that it is necessary to discuss which types of TEs are more likely to form miRNAs. Accordingly, I have added this information to the "Conclusion" section: “An analysis of the results presented in the table on the origin of miRNAs from transposons in humans showed that miRNAs are most often formed from LINE elements (108 miRNAs) and SINE elements (94 miRNAs), less often from DNA transposons (64 miRNAs) and LTR-containing retroelements (53 miRNAs)". As recommended by the reviewer, since LINE retroelements are the main sources of miRNAs, in the Conclusion chapter, I also provided evidence that LINE elements play a role in the regulation of embryonic development, which can explain the origin of most miRNAs from them:

“Since, according to the results of the study (table), the main sources of microRNAs in humans are LINE elements, we analyzed the scientific literature on the role of LINEs in the regulation of embryonic development, in which microRNAs play an important role [84-86]. In 2000, Wei et al. described the accumulation of multiple LINE1 insertions in human cell cultures [87]. In 2007, Garcia-Perez et al. revealed the accumulation of LINE1 insertions in human embryonic stem cells, which was accompanied by the suppression of the activity of specific genes required for cell differentiation. On the basis of the obtained data, the researchers suggested that TEs control the work of the genome during the growth and development of organisms [88]. Upon activation of LINE1, their proteins are used to mobilize SINEs. In 2011, Macia et al reported the expression of several subfamilies of Alu elements in undifferentiated human embryonic stem cells. At the same time, activation was detected mainly of LINE1 located within protein-coding genes, which indicates their role in the regulation of these genes [89]. In addition to tissue cultures, consistent transpositions and activation of LINE1, Alu, and SVA have been identified in vivo during early embryogenesis during tissue differentiation. These changes caused large-scale structural variations in the genomes of experimental animals. In 2004, Prak et al. showed in transgenic mouse models that LINE1 can move in vivo during early development [90]. In 2012, organ-specific and stage-specific changes in cell phenotypes were identified in the C57BL/6J mouse line due to structural transformations of their genomes, which were accompanied by changes in the transcriptional activity of certain ERs [91]. Experiments on two-celled mouse embryos have shown that LINE1 is required for the activation of global gene expression during early embryonic development [92]. LINE1 transcripts themselves function as lncRNAs, interacting with KAP1 and Nucleolin, stimulating rDNA gene expression and silencing of other genes in a two-cell embryo by suppressing Dux (a transcription factor that controls the two-cell genetic program) [93].

I fixed also the minor remarks:

1. In Page 2, line 72: The sentence "TEs make up 45%..." has been moved to the previous paragraph, where we are talking about transposons in the composition of the genomes of various organisms.
2. Figure 2 corrected according to the reviewer's comments: changed the name of the figure to “Scheme of the role of transposable elements in post-transcriptional regulation of protein-coding genes in animals”. I show how miRNA silenced translation. I spell out most of the abbreviations. I spell out PCG as a protein-coding gene. I also show where the 3’UTR.
3. In table 1 I added expressed tissue and their potential targets reported in the original papers (where they have).

 

 

According to reviewer 3 (highlighted in turquoise):

As recommended by the reviewer, I added the information to the article:

1. Methods: added data that in order to find aging-associated microRNAs derived from transposons, a search was made for the association of 52 associated with cancer TEDmiRs, with aging in the databases of articles Scopus, WoS, NCBI, by introducing phrases of specific miRNAs with the words “aging”, "change with age", "senescence", "consenescence" into the search line.

2. Limitations: I noted that the limitations in the methodology are due to the need to search for articles in the Scopus, WoS, NCBI databases, with their careful analysis and interpretation of the results, which are placed in a table in the form of conclusions. Limitations are due to the limited number of articles reporting associations of TEDmiRs with specific diseases and aging. Thus, when searching for aging-associated TEDmiRs out of 467, only 52 were associated with malignant neoplasms, 12 - with idiopathic pulmonary fibrosis.
3. I also fixed the errors noted by the reviewer: In the part of abstract, I corrected the phrase "the most important sources" to “are important soursces”. Additionally, the phrase "serve as sources" corrected to “protein-coding genes and their regulatory elements are derived from transposons”. The phrase "determined features of the expression of noncoding RNAs" rephrased to “detection of expression levels of specific non-coding RNAs”. The statement "Cleavage of the microRNA precursor in animals is caused by two different enzymes" is rephrased to “MiRNA precursor maturation (by cutting out a parts) is caused by specific enzymes”. The statement “miRNAs are partially complementary to the 3'-UTRs of their target mRNAs" is rephrased to “miRNAs interact with the 3'-UTRs of target mRNAs through partial base pairing”. The statement "Binding of microRNAs to the 3'-UTR causes translation silencing" is corrected to “Binding and interaction of microRNAs with the 3'-UTR lead to the repression of gene expression”.

I express my deep gratitude to all the reviewers for a thorough analysis of my article and constructive comments.

 

 

 

 

Author Response File: Author Response.pdf

Reviewer 2 Report

The authors reviewed the recent findings on the discovery of TEs-derived microRNA. The collected list of microRNAs in humans is valuable, although the current manuscript was lack of summary and is not well organized yet. These are some comments that I hope could be helpful.

Major comments:

1. You could probably rephrase the introduction section. It was not well organized and not easy to follow. It would also be helpful to briefly discuss the regulation of TEs through other mechanisms except for microRNA.

2. Please make sure statements like "siRNAs are formed mainly through the processing of TEs transcripts" in page 3 line 44 is correct.

3. Section "FEATURES OF THE... IN PLANTS" does not match well with the manuscript and the main statement focusing on the human microRNAs in aging and other diseases. Instead, the authors could discuss more one which types of TEs are more likely to form microRNAs. Are they mostly expressed in embryonic stem cells or diseased tissues?

Minor:

1. Page 2, line 72: The sentence "TEs make up 45%..." does not fit well in the paragraph.

2. Figure 2 was not shown clearly. This is the post-transcriptional regulation rather than changing the epigenetic state of nearby genes. The authors also need to show how they silenced translation. The author should also spell out most of the abbreviations. I also never read papers using "PCG" for "protein-coding gene". The author could show where is the 3'UTR.

3. Table 1: The authors could further add the expressed tissues and their potential targets reported in the original papers if they have.

 

 

Author Response

Hello dear editor. I carefully read all the reviews of our article, I fully agree with all the comments, according to which the article has been corrected. The corrections were made in the review mode in the Word document format, additional corrections were highlighted in the text in accordance with the comments of different reviewers (in different colors) for the convenience of the editors.

Detailed comments step by step, according to different reviewers.

According to reviewer 1 (highlighted in yellow):

Line 9, "the most" corrected to "important".

Line 43 (now 48), "TE" - deciphered the abbreviation on first use in Line 42 (now 47).

In lines 228 and 229 (as well as in other places in the text – lines 22, 247, 248, 293, 294, 345, 349) "me" and "I" are deleted - replaced by other phrases.

Changed "microRNA" to "miRNA" throughout the text.

 

According to reviewer 2 (highlighted in green):

1. I rephrased the introduction section ("the most" corrected to "important"). I also briefly discussed TEs regulation through other mechanisms except for microRNA (TEs' expression is also regulated by epigenetic factors (DNA methylation, histone modifications), SIRT6, cytidine deaminases APOBEC3, APOBEC1, and other catalytic proteins such as ERCC, TREX1, RB1, HELLS, and MEGP2).
2. I corrected the statement “siRNAs are formed mainly through the processing of TEs transcripts” to “siRNAs are generated by degradation of exogenous dsRNAs of transcribed from TEs or from other types of inverted repeats”.
3. Section "FEATURES OF THE... IN PLANTS" has been renamed to "Differences of the Origin of MicroRNAs from Transposons in Plants from Animals" as this section would be interesting for readers to review the differences. I agree with the distinguished reviewer's remarks that it is necessary to discuss which types of TEs are more likely to form miRNAs. Accordingly, I have added this information to the "Conclusion" section: “An analysis of the results presented in the table on the origin of miRNAs from transposons in humans showed that miRNAs are most often formed from LINE elements (108 miRNAs) and SINE elements (94 miRNAs), less often from DNA transposons (64 miRNAs) and LTR-containing retroelements (53 miRNAs)". As recommended by the reviewer, since LINE retroelements are the main sources of miRNAs, in the Conclusion chapter, I also provided evidence that LINE elements play a role in the regulation of embryonic development, which can explain the origin of most miRNAs from them:

“Since, according to the results of the study (table), the main sources of microRNAs in humans are LINE elements, we analyzed the scientific literature on the role of LINEs in the regulation of embryonic development, in which microRNAs play an important role [84-86]. In 2000, Wei et al. described the accumulation of multiple LINE1 insertions in human cell cultures [87]. In 2007, Garcia-Perez et al. revealed the accumulation of LINE1 insertions in human embryonic stem cells, which was accompanied by the suppression of the activity of specific genes required for cell differentiation. On the basis of the obtained data, the researchers suggested that TEs control the work of the genome during the growth and development of organisms [88]. Upon activation of LINE1, their proteins are used to mobilize SINEs. In 2011, Macia et al reported the expression of several subfamilies of Alu elements in undifferentiated human embryonic stem cells. At the same time, activation was detected mainly of LINE1 located within protein-coding genes, which indicates their role in the regulation of these genes [89]. In addition to tissue cultures, consistent transpositions and activation of LINE1, Alu, and SVA have been identified in vivo during early embryogenesis during tissue differentiation. These changes caused large-scale structural variations in the genomes of experimental animals. In 2004, Prak et al. showed in transgenic mouse models that LINE1 can move in vivo during early development [90]. In 2012, organ-specific and stage-specific changes in cell phenotypes were identified in the C57BL/6J mouse line due to structural transformations of their genomes, which were accompanied by changes in the transcriptional activity of certain ERs [91]. Experiments on two-celled mouse embryos have shown that LINE1 is required for the activation of global gene expression during early embryonic development [92]. LINE1 transcripts themselves function as lncRNAs, interacting with KAP1 and Nucleolin, stimulating rDNA gene expression and silencing of other genes in a two-cell embryo by suppressing Dux (a transcription factor that controls the two-cell genetic program) [93].

I fixed also the minor remarks:

1. In Page 2, line 72: The sentence "TEs make up 45%..." has been moved to the previous paragraph, where we are talking about transposons in the composition of the genomes of various organisms.
2. Figure 2 corrected according to the reviewer's comments: changed the name of the figure to “Scheme of the role of transposable elements in post-transcriptional regulation of protein-coding genes in animals”. I show how miRNA silenced translation. I spell out most of the abbreviations. I spell out PCG as a protein-coding gene. I also show where the 3’UTR.
3. In table 1 I added expressed tissue and their potential targets reported in the original papers (where they have).

 

According to reviewer 3 (highlighted in turquoise):

As recommended by the reviewer, I added the information to the article:

1. Methods: added data that in order to find aging-associated microRNAs derived from transposons, a search was made for the association of 52 associated with cancer TEDmiRs, with aging in the databases of articles Scopus, WoS, NCBI, by introducing phrases of specific miRNAs with the words “aging”, "change with age", "senescence", "consenescence" into the search line.

2. Limitations: I noted that the limitations in the methodology are due to the need to search for articles in the Scopus, WoS, NCBI databases, with their careful analysis and interpretation of the results, which are placed in a table in the form of conclusions. Limitations are due to the limited number of articles reporting associations of TEDmiRs with specific diseases and aging. Thus, when searching for aging-associated TEDmiRs out of 467, only 52 were associated with malignant neoplasms, 12 - with idiopathic pulmonary fibrosis.
3. I also fixed the errors noted by the reviewer: In the part of abstract, I corrected the phrase "the most important sources" to “are important soursces”. Additionally, the phrase "serve as sources" corrected to “protein-coding genes and their regulatory elements are derived from transposons”. The phrase "determined features of the expression of noncoding RNAs" rephrased to “detection of expression levels of specific non-coding RNAs”. The statement "Cleavage of the microRNA precursor in animals is caused by two different enzymes" is rephrased to “MiRNA precursor maturation (by cutting out a parts) is caused by specific enzymes”. The statement “miRNAs are partially complementary to the 3'-UTRs of their target mRNAs" is rephrased to “miRNAs interact with the 3'-UTRs of target mRNAs through partial base pairing”. The statement "Binding of microRNAs to the 3'-UTR causes translation silencing" is corrected to “Binding and interaction of microRNAs with the 3'-UTR lead to the repression of gene expression”.

I express my deep gratitude to all the reviewers for a thorough analysis of my article and constructive comments.

Author Response File: Author Response.pdf

Reviewer 3 Report

The article begins by exploring the role of transposable elements (TEs) and microRNAs (miRNAs) in plant and animal genomes. The author explains how the expression patterns of miRNAs can vary in different tissues and conditions due to the species-specific distribution of TEs in genomes. The article highlights the use of existing methods and databases to determine the presence of 467 TE-derived miRNAs in the human genome. The author then proposes to create an online bioinformatics database of microRNAs derived from TEs that can be used to study tissue differentiation during aging and design targeted therapy for various diseases. Overall, the article is effective in conveying the main points and the purpose of the study.

However, while the result of perspect provides a clear line of reasoning and conclusion based on a review of the scientific literature, there are a few things that could be added to provide a more complete picture of the topic:

1. Methods: there was no mention of the methods used to collect and analyze the data. For example, how were the data analyzed for 16 of the 56 TEDmiRs that were found to be associated with aging?
2. Limitations: It would be helpful to acknowledge any limitations or uncertainties in the evidence presented in the results. For example, the conclusion relies on the assumption that the results of the literature review are robust and accurate, but it would be useful to note any limitations in the methodology or data that could affect the validity of the conclusion.

In addition, there are few errors that could be rephrased.

In the part of abstract, the use of "the most important sources" oversimplifies the contribution of TEs to the production of microRNA and long non-coding RNA genes. Additionally, the phrase "serve as sources" implies that this is a current occurrence, when in fact it is a phenomenon that has occurred over time. The phrase "determined features of the expression of noncoding RNAs" is also unclear and could be rephrased to provide a clearer idea of what is being suggested.

In the part of transposon miRNAs in animals, it has a few errors and unclear statements. The statement "Cleavage of the microRNA precursor in animals is caused by two different enzymes" is unclear and could be rephrased to better explain the process; The statement "miRNAs are partially complementary to the 3'-UTRs of their target mRNAs" is not accurate and could be rephrased to clarify that miRNAs interact with the 3'-UTRs of target mRNAs through partial base pairing; The statement "Binding of microRNAs to the 3'-UTR causes translation silencing" is not entirely accurate, as it is not just binding of miRNAs to the 3'-UTR that causes translation silencing, but the interaction of miRNAs with the 3'-UTR can lead to the repression of gene expression.

Author Response

Hello dear editor. I carefully read all the reviews of our article, I fully agree with all the comments, according to which the article has been corrected. The corrections were made in the review mode in the Word document format, additional corrections were highlighted in the text in accordance with the comments of different reviewers (in different colors) for the convenience of the editors.

Detailed comments step by step, according to different reviewers.

According to reviewer 1 (highlighted in yellow):

Line 9, "the most" corrected to "important".

Line 43 (now 48), "TE" - deciphered the abbreviation on first use in Line 42 (now 47).

In lines 228 and 229 (as well as in other places in the text – lines 22, 247, 248, 293, 294, 345, 349) "me" and "I" are deleted - replaced by other phrases.

Changed "microRNA" to "miRNA" throughout the text.

 

According to reviewer 2 (highlighted in green):

1. I rephrased the introduction section ("the most" corrected to "important"). I also briefly discussed TEs regulation through other mechanisms except for microRNA (TEs' expression is also regulated by epigenetic factors (DNA methylation, histone modifications), SIRT6, cytidine deaminases APOBEC3, APOBEC1, and other catalytic proteins such as ERCC, TREX1, RB1, HELLS, and MEGP2).
2. I corrected the statement “siRNAs are formed mainly through the processing of TEs transcripts” to “siRNAs are generated by degradation of exogenous dsRNAs of transcribed from TEs or from other types of inverted repeats”.
3. Section "FEATURES OF THE... IN PLANTS" has been renamed to "Differences of the Origin of MicroRNAs from Transposons in Plants from Animals" as this section would be interesting for readers to review the differences. I agree with the distinguished reviewer's remarks that it is necessary to discuss which types of TEs are more likely to form miRNAs. Accordingly, I have added this information to the "Conclusion" section: “An analysis of the results presented in the table on the origin of miRNAs from transposons in humans showed that miRNAs are most often formed from LINE elements (108 miRNAs) and SINE elements (94 miRNAs), less often from DNA transposons (64 miRNAs) and LTR-containing retroelements (53 miRNAs)". As recommended by the reviewer, since LINE retroelements are the main sources of miRNAs, in the Conclusion chapter, I also provided evidence that LINE elements play a role in the regulation of embryonic development, which can explain the origin of most miRNAs from them:

“Since, according to the results of the study (table), the main sources of microRNAs in humans are LINE elements, we analyzed the scientific literature on the role of LINEs in the regulation of embryonic development, in which microRNAs play an important role [84-86]. In 2000, Wei et al. described the accumulation of multiple LINE1 insertions in human cell cultures [87]. In 2007, Garcia-Perez et al. revealed the accumulation of LINE1 insertions in human embryonic stem cells, which was accompanied by the suppression of the activity of specific genes required for cell differentiation. On the basis of the obtained data, the researchers suggested that TEs control the work of the genome during the growth and development of organisms [88]. Upon activation of LINE1, their proteins are used to mobilize SINEs. In 2011, Macia et al reported the expression of several subfamilies of Alu elements in undifferentiated human embryonic stem cells. At the same time, activation was detected mainly of LINE1 located within protein-coding genes, which indicates their role in the regulation of these genes [89]. In addition to tissue cultures, consistent transpositions and activation of LINE1, Alu, and SVA have been identified in vivo during early embryogenesis during tissue differentiation. These changes caused large-scale structural variations in the genomes of experimental animals. In 2004, Prak et al. showed in transgenic mouse models that LINE1 can move in vivo during early development [90]. In 2012, organ-specific and stage-specific changes in cell phenotypes were identified in the C57BL/6J mouse line due to structural transformations of their genomes, which were accompanied by changes in the transcriptional activity of certain ERs [91]. Experiments on two-celled mouse embryos have shown that LINE1 is required for the activation of global gene expression during early embryonic development [92]. LINE1 transcripts themselves function as lncRNAs, interacting with KAP1 and Nucleolin, stimulating rDNA gene expression and silencing of other genes in a two-cell embryo by suppressing Dux (a transcription factor that controls the two-cell genetic program) [93].

I fixed also the minor remarks:

1. In Page 2, line 72: The sentence "TEs make up 45%..." has been moved to the previous paragraph, where we are talking about transposons in the composition of the genomes of various organisms.
2. Figure 2 corrected according to the reviewer's comments: changed the name of the figure to “Scheme of the role of transposable elements in post-transcriptional regulation of protein-coding genes in animals”. I show how miRNA silenced translation. I spell out most of the abbreviations. I spell out PCG as a protein-coding gene. I also show where the 3’UTR.
3. In table 1 I added expressed tissue and their potential targets reported in the original papers (where they have).

 

 

According to reviewer 3 (highlighted in turquoise):

As recommended by the reviewer, I added the information to the article:

1. Methods: added data that in order to find aging-associated microRNAs derived from transposons, a search was made for the association of 52 associated with cancer TEDmiRs, with aging in the databases of articles Scopus, WoS, NCBI, by introducing phrases of specific miRNAs with the words “aging”, "change with age", "senescence", "consenescence" into the search line.

2. Limitations: I noted that the limitations in the methodology are due to the need to search for articles in the Scopus, WoS, NCBI databases, with their careful analysis and interpretation of the results, which are placed in a table in the form of conclusions. Limitations are due to the limited number of articles reporting associations of TEDmiRs with specific diseases and aging. Thus, when searching for aging-associated TEDmiRs out of 467, only 52 were associated with malignant neoplasms, 12 - with idiopathic pulmonary fibrosis.
3. I also fixed the errors noted by the reviewer: In the part of abstract, I corrected the phrase "the most important sources" to “are important soursces”. Additionally, the phrase "serve as sources" corrected to “protein-coding genes and their regulatory elements are derived from transposons”. The phrase "determined features of the expression of noncoding RNAs" rephrased to “detection of expression levels of specific non-coding RNAs”. The statement "Cleavage of the microRNA precursor in animals is caused by two different enzymes" is rephrased to “MiRNA precursor maturation (by cutting out a parts) is caused by specific enzymes”. The statement “miRNAs are partially complementary to the 3'-UTRs of their target mRNAs" is rephrased to “miRNAs interact with the 3'-UTRs of target mRNAs through partial base pairing”. The statement "Binding of microRNAs to the 3'-UTR causes translation silencing" is corrected to “Binding and interaction of microRNAs with the 3'-UTR lead to the repression of gene expression”.

I express my deep gratitude to all the reviewers for a thorough analysis of my article and constructive comments.

Author Response File: Author Response.pdf