Nucleosome Structures Built from Highly Divergent Histones: Parasites and Giant DNA Viruses

Round 1

Reviewer 1 Report

Nucleosome is the basic unit of chromatin, which containing ~ 146 bp DNA wrapped around histone octamer. This structure is highly conserved in eukaryotes. In this review, the authors summarize two nucleosome structures from parasites and one nucleosome-like structure from giant virus. They compare these structures with nucleosome structure of human and analyze their similarity and difference. Although divergent exist between species, this review confirms that the compacting of DNA by histones is a universal mechanism. The manuscript is well written and organized, I recommend it to be accepted.

There are some small minor errors in the manuscript:

1 As I know, “LECA” (line 145, page 5) is abbreviated for “last eukaryotic common ancestor” but not “ancestral eukaryote” as the authors wrote.

2 The font size of “are transcribed into long polycistronic pre-messenger RNAs” (line 256 & 257, page 8) is different from other text.

3 In Figure 3, figure A and B are not labeled separately.

Author Response

Reviewer 1:

Nucleosome is the basic unit of chromatin, which containing ~ 146 bp DNA wrapped around histone octamer. This structure is highly conserved in eukaryotes. In this review, the authors summarize two nucleosome structures from parasites and one nucleosome-like structure from giant virus. They compare these structures with nucleosome structure of human and analyze their similarity and difference. Although divergent exist between species, this review confirms that the compacting of DNA by histones is a universal mechanism. The manuscript is well written and organized, I recommend it to be accepted.

There are some small minor errors in the manuscript:

1. As I know, “LECA” (line 145, page 5) is abbreviated for “last eukaryotic common ancestor” but not “ancestral eukaryote” as the authors wrote.

Reply: Thank you very much for the comment. In the revised manuscript, "LECA" has been corrected to "last eukaryotic common ancestor" according to the comment.

2. The font size of “are transcribed into long polycistronic pre-messenger RNAs” (line 256 & 257, page 8) is different from other text.

Reply: Thank you very much for pointing this out. The font size for lines 256 and 257 has been corrected in the revised manuscript.

3. In Figure 3, figure A and B are not labeled separately.

Reply: Thank you very much. In the revised manuscript, Figures A and B have been labeled separately and cited appropriately inside the text.

Reviewer 2 Report

It was with great pleasure that I read this manuscript, devoted to a review of data on the features of the structural organization of nucleosomes and core histones in organisms evolutionally distant from eukaryotic cells. The review is well and logically written. I am sure that it will be interesting to a wide range of readers of Epigenomes.  

I have a few minor remarks.

1. Abstract. Line 18. I propose to change "These findings" to "Presented data" or   "Systematized data".

2. Lines 80-81. It would be more correct to write: "These remarkable associations are described as the H2B-H4 four-helix bundle and  the H3-H3´ four-helix 80 bundle, respectively [8]."

3. Lines 91 and 339.   "Electrostatic potential surface of the nucleosome" and "Electrostatic potential of the nucleosomes".  It seems to me that the figures depict the electrostatic potential of the histone octamer, and not the nucleosomes as a whole.

4. Line 172. "H2a, H2b," Is there a reason to use lowercase letters a and b here instead of uppercase letters?

Author Response

Reviewer 2:

It was with great pleasure that I read this manuscript, devoted to a review of data on the features of the structural organization of nucleosomes and core histones in organisms evolutionally distant from eukaryotic cells. The review is well and logically written. I am sure that it will be interesting to a wide range of readers of Epigenomes.  

I have a few minor remarks.

1. Abstract. Line 18. I propose to change "These findings" to "Presented data" or   "Systematized data".

Reply: Thank you very much for the comment. In the revised manuscript, we have changed “These findings” to “The presented data”.

2. Lines 80-81. It would be more correct to write: "These remarkable associations are described as the H2B-H4 four-helix bundle and  the H3-H3´ four-helix 80 bundle, respectively [8]."

Reply: Thank you very much. We have corrected the sentence according to the comment.

3. Lines 91 and 339.   "Electrostatic potential surface of the nucleosome" and "Electrostatic potential of the nucleosomes".  It seems to me that the figures depict the electrostatic potential of the histone octamer, and not the nucleosomes as a whole.

Reply: We agree with this comment. Lines 91 "Electrostatic potential surface of nucleosome" and 339 "Electrostatic potential of nucleosomes" have been replaced by "Electrostatic potential surface of histone octamer" and "Electrostatic potential of histone octamers" in the revised manuscript.

4. Line 172. "H2a, H2b," Is there a reason to use lowercase letters a and b here instead of uppercase letters?

Reply: Thank you very much for pointing this out. Line 172, "H2a, H2b" has been changed to "H2A, H2B".

Reviewer 3 Report

The review by Sato et al. presents a useful synopsis of observations highlighting the structural and biophysical properties of nucleosome particles containing histones from two protozoan parasites and a giant DNA virus. In general, the authors provide a complete and well-presented review.

My only suggestion is to include in the reference list some of the latest review articles regarding background on histone post-translational modifications (reported in section “2.4. Histone tails”). Among others:

- Cavalieri V. Genes 2021. doi: 10.3390/genes12101596

- Chan et al. Trends Genet 2022. doi: 10.1016/j.tig.2022.04.010

Author Response

Reviewer 3:

The review by Sato et al. presents a useful synopsis of observations highlighting the structural and biophysical properties of nucleosome particles containing histones from two protozoan parasites and a giant DNA virus. In general, the authors provide a complete and well-presented review.

My only suggestion is to include in the reference list some of the latest review articles regarding background on histone post-translational modifications (reported in section “2.4. Histone tails”). Among others:

- Cavalieri V. Genes 2021. doi: 10.3390/genes12101596

- Chan et al. Trends Genet 2022. doi: 10.1016/j.tig.2022.04.010

Reply: Thank you very much for this suggestion. In the "2.4 Histone Tails" section of the revised manuscript, we have cited the suggested references (35, 37) as well as the following reference (36):

Millán-Zambrano, G.; Burton, A.; Bannister, A.J.; Schneider, R. Histone post-translational modifications - cause and consequence of genome function. Nat. Rev. Genet. 2022. doi: 10.1038/s41576-022-00468-7. Online ahead of print.