Chromatin Structure and “DNA Sequence View”: The Role of Satellite DNA in Ectopic Pairing of the Drosophila X Polytene Chromosome

Round 1

Reviewer 1 Report

I'm sotisfied owith the answers.

Reviewer 2 Report

Dear authors,

The text has been substantially modified and you fulfilled my request. I feel like this manuscript may be accepted of the other referee were to aggree.

Just one "last" comment. At line 544 it reads as "the last version" and should read as "the lastest version".

Best regards,

This manuscript is a resubmission of an earlier submission. The following is a list of the peer review reports and author responses from that submission.

Round 1

Reviewer 1 Report

Dear Authors,

I think you've made a good work and, overall this is a well written manuscript with quite clearly explained results. However, and with due respect and appart from some minor considerations (below), the main issue I have with this manuscript is the abscense of information about the informatic pipeline employed, Homology Segment Analysis, which is not "freely available" at reference 23, as you state at L528, since that reference (Zhuravlev, A.; Zakharov, G. Homology Segment Analysis; 2021) seems to point to a yet to publish manuscript. As such, without a accepted journal or github (or other repository) in where any reviewer could possibly check how this programme works I see no way to accurately judge the results of the current manuscript. Thus, in my view, publication of this manuscript is, right now, premature and should be postponed until the above mentioned reference is available.

Please, see other comments below:

I see no point in mentioning previous results in the abstract. 

"9. (Optional:)" at L560. I deeply appreciate the fact that the authors provide step-by-step guidelines for their method, but if this is nothing more than a mere description of the methods they employed for the current manuscript, I suggest that they refrain from the additional steps and stick to the way they performed. the analysis exactly.

11. Statistical analysis. at L576. I think this should be a section on its own, not within the "bioinformatic analysis". Also, It'd be great for authors to indicate here where they took the data from at this point.

Figs 1 and 2 are a bit hard to swalow as they are. Too many symbols in my view. Also, it is unclear in this figure what is the colours correspondence of each bar.

Reviewer 2 Report

The study of 3D chromatin structure and organization is an interesting and emerging topic. New approach evolving in this filed and more relevant data are available. For this reason I consider this paper interesting. However, if the impact is positive, I find very difficult to read it. The introduction and the results are very hard to be understand. In this form I’m not able to evaluate the discussion.

I suggest you for carefully review the paper and simplify as much as possible the text and clarify some concepts that make reading cumbersome.

Below some comments to help the authors:

The authors use the Homology Segment Analysis software but no detail they do in the introduction. Only in Methods section did they say how it works. I suggest implementing the introduction.

Line 49: “known as transcription factories”, please add a reference for this sentence.

The introduction would be more comprehensive if the authors introduced and explained better the meaning of FEC and FEM. They cite these only in the abstract and no more details they give in the introduction.

Lane 174: The Authors said: “R specific (RSP) varies within 0.18 — 0.3 that correspond to a rather weak positive FEC – FMF correlation”. Why they affirm this? Maybe this sentence needs a reference or a more comprehensive explanation.

Figure1: What represent the different color of the vertical bar in the plot?

Please specify this with a legend or in the text.

Figure1/2: What means “$”? It’s not clear for me.

Why do they use segments up to 50 nt in length? There are more repetitive elements (eg DNA / RNA transposons) that could justify the interaction between two areas of different loci (see Galileo transposon). Also, the locus Agn^ts3 is characterized by a transposon (S element), but is unclear how (and if) it affect the analysis. Why do the authors not consider in the analysis more longer repeats?

Figure 5: “Y value: Ind or R_CORR (for CS and agnts3)” but Ind is plotted in the graph (orange columns).

There are some typos.

• Line 167 “show a high identity percentage of identity with”, please correct.