Dear Dr. Chen,

Thank you very much for submitting your manuscript "Critical role of deadenylation in regulating poly(A) rhythms and circadian gene expression" for consideration at PLOS Computational Biology.

As with all papers reviewed by the journal, your manuscript was reviewed by members of the editorial board and by several independent reviewers. In light of the reviews (below this email), we would like to invite the resubmission of a significantly-revised version that takes into account the reviewers' comments.

We cannot make any decision about publication until we have seen the revised manuscript and your response to the reviewers' comments. Your revised manuscript is also likely to be sent to reviewers for further evaluation.

When you are ready to resubmit, please upload the following:

[1] A letter containing a detailed list of your responses to the review comments and a description of the changes you have made in the manuscript. Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out.

[2] Two versions of the revised manuscript: one with either highlights or tracked changes denoting where the text has been changed; the other a clean version (uploaded as the manuscript file).

Important additional instructions are given below your reviewer comments.

Please prepare and submit your revised manuscript within 60 days. If you anticipate any delay, please let us know the expected resubmission date by replying to this email. Please note that revised manuscripts received after the 60-day due date may require evaluation and peer review similar to newly submitted manuscripts.

Thank you again for your submission. We hope that our editorial process has been constructive so far, and we welcome your feedback at any time. Please don't hesitate to contact us if you have any questions or comments.

Sincerely,

Attila Csikász-Nagy

Associate Editor

PLOS Computational Biology

Jason Haugh

Deputy Editor

PLOS Computational Biology

***********************

Reviewer's Responses to Questions

Comments to the Authors:

Please note here if the review is uploaded as an attachment.

Reviewer #1: In this manuscript Yao et al. used mathematical modeling to explore the possible roles of deadenylation in regulating circadian gene expression. I read this work with great interest. It has been an active research area on how circadian rhythm is regulated, and this work shows there is still new mechanism that has not been thoroughly investigated. Through analyzing simple mathematical models that are based on existing experimental observations, these authors convincingly showed that Poly(A) tail length regulation is an important part of circadian gene regulation. I only have a few minor comments for the authors to consider.

1) It took me some efforts to realize that the authors focused on the downstream genes that are regulated by the circadian rhythm network. The authors can make this point more transparent by modifying Fig. 1A. Specifically they can add schematically the circadian rhythm oscillator as an upstream network that affects the four processes, transcription, deadenylation, etc.

2) Figure 3 is probably the most interesting result of this work. I notice the phase plots and some polar coordinate numbers overlap in the figures. The authors may adjust the plotting.

3) It is impressive that some rich information can already deduced from the model given by equations 1 and 2. It is justified to start with such simple models, which are convenient for thorough parameter space examination. There are, however, certain limitations on coarse-graining the poly-A tail length as two discrete states. Mathematically one can treat the process as a reaction-diffusion process, and can write down either a discrete chemical master equation or continuous 1D process (described by Langevin equations or Fokker-Planck equations). The authors may discuss limitation of their formulation and alternative future studies.

Reviewer #2: Attached

Reviewer #3: The authors address a hot topic – the differential regulation of clock-controlled genes (CCGs). It has been found earlier (Naef, Westermark, Robles, Koike, Heyd …) that different stages of gene products display differential rhythmicity. Kojima et al. 2012 provided a rich resource of rhythmic genes associated with mRNA polyadenylation. In the submitted manuscript a theoretical framework is provided to connect different processes to measured quantities.

The paper is clearly written and the selected model type is consistent with the sparse experimental data. Technically speaking, linear non-autonomous differential equations are simulated for 11 randomly selected parameters. Scatter plots and global sensitivity analysis help to quantify the dominant regulations. The theoretical findings are connected to observations (phases of CCGs, phases of deadenylases). Below I list some suggestion to improve the already very good manuscript.

Minor comments:

1. I am aware that redundancy is helpful but abstract, summary, introduction, discussion are quite redundant. Practically identical sentences should be avoided. In the Author Summary a different level of abstraction compared to the abstract might help readers.

2. Regarding posttranscriptional circadian regulations some more references might be of interest: F. Heyd regarding splicing, M. Young, M. Brunner and K. Vanselow regarding nuclear import/export).

3. K. Thurley (PNAS 2017) developed a general theory of rhythmic fluxes along chains and introduced circadian response analysis (CRA). These results are highly relevant to interpret the model in Figure 1.

4. Page 5: …recently …. 2012???

5. Linear systems as in Equations 1-3 can be treated analytically using e.g. variation of constants (see also Luck & Westermark and Thurley 2017). I am aware that the resulting expressions with 4 periodic terms become very complicated. Anyway, the authors should discuss why they prefer numerical solutions.

6. I appreciate the analysis of random parameters since few quantitative details are available. This approach of studying parameter sets instead of specific parameters became popular in chronobiology and the authors might cite papers using this approach: J. Locke BMC 2008, P. Pett LSA 2018, B. Ananthasubramaniam JMB 2020).

7. Regarding Figure 2 I am surprised that DeA controls L/S and L strongly but S only weakly. Typically, an oscillating denominator (S in case of L/S) has a strong impact. Is there any explanation why L seems more relevant regarding DeA regulation.

8. Looking at Figure 1, I am not surprised that Deadenylation plays a major role. It has a central position and modulates the decay of L and the production of S. If this is the correct interpretation I would expect for constant DeA a major control of Polyadenylation on the L/S ratio since this reaction is also at the center of the chain and effects L and S.

**********

Have all data underlying the figures and results presented in the manuscript been provided?

Large-scale datasets should be made available via a public repository as described in the PLOS Computational Biology data availability policy, and numerical data that underlies graphs or summary statistics should be provided in spreadsheet form as supporting information.

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

**********

PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: No

Reviewer #2: No

Reviewer #3: No

Figure Files:

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email us at figures@plos.org.

Data Requirements:

Please note that, as a condition of publication, PLOS' data policy requires that you make available all data used to draw the conclusions outlined in your manuscript. Data must be deposited in an appropriate repository, included within the body of the manuscript, or uploaded as supporting information. This includes all numerical values that were used to generate graphs, histograms etc.. For an example in PLOS Biology see here: http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001908#s5.

Reproducibility:

To enhance the reproducibility of your results, PLOS recommends that you deposit laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. For instructions, please see http://journals.plos.org/compbiol/s/submission-guidelines#loc-materials-and-methods

Attachments

Attachment

Submitted filename: PC_Yao.pdf

Dear Dr. Chen,

We are pleased to inform you that your manuscript 'Critical role of deadenylation in regulating poly(A) rhythms and circadian gene expression' has been provisionally accepted for publication in PLOS Computational Biology.

Before your manuscript can be formally accepted you will need to complete some formatting changes, which you will receive in a follow up email. A member of our team will be in touch with a set of requests.

Please note that your manuscript will not be scheduled for publication until you have made the required changes, so a swift response is appreciated.

IMPORTANT: The editorial review process is now complete. PLOS will only permit corrections to spelling, formatting or significant scientific errors from this point onwards. Requests for major changes, or any which affect the scientific understanding of your work, will cause delays to the publication date of your manuscript.

Should you, your institution's press office or the journal office choose to press release your paper, you will automatically be opted out of early publication. We ask that you notify us now if you or your institution is planning to press release the article. All press must be co-ordinated with PLOS.

Thank you again for supporting Open Access publishing; we are looking forward to publishing your work in PLOS Computational Biology. 

Best regards,

Attila Csikász-Nagy

Associate Editor

PLOS Computational Biology

Jason Haugh

Deputy Editor

PLOS Computational Biology

***********************************************************

Reviewer's Responses to Questions

Comments to the Authors:

Please note here if the review is uploaded as an attachment.

Reviewer #1: The authors have satisfactorily addressed my concerns.

Reviewer #2: The authors have fully answered to comments.

Reviewer #3: The authors addressed carefully all comments. Congratulations to such an interesting combination of data, insight, modeling, and statistics.

**********

Have all data underlying the figures and results presented in the manuscript been provided?

Large-scale datasets should be made available via a public repository as described in the PLOS Computational Biology data availability policy, and numerical data that underlies graphs or summary statistics should be provided in spreadsheet form as supporting information.

Reviewer #1: None

Reviewer #2: Yes

Reviewer #3: None

**********

PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: No

Reviewer #2: No

Reviewer #3: No