Review Reports

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

In this review, the authors aim to provide an overview of nuclear mechanisms contributing to cellular quiescence in eukaryotes, building on numerous recent publications that found nuclear pathways essential to maintain viability in G0. After presenting the key unicellular organisms used as G0 models (S. cerevisiae and S. pombe), the authors highlight parallels with several mammalian models of quiescence (stem cells) and dormancy (mouse embryo), and provide strong evidence that across organisms, quiescence is an actively and dynamically-maintained cell state.

 

Overall, the review is well-written, and provides an excellent overview of the subject and recent research on quiescence. It will likely be of wide interest to both the G0 community and the chromatin field.

 

A few minor points that can be clarified or improved:

1) p12 with ref 57, near “3% of coding genes are still active”: The precision that “seven detected in more than 80% of single-cell transcript analyses” is a bit unclear – this could be interpreted either as heterogenous expression, or as very high-level of expression in Q cells resulting in detection in most cells (due to the data sparsity problem in scRNA-seq). If significant, this observation should be clarified a bit more.

 

2) Likewise, in S. pombe it is said that 97% of the genome is repressed and only 16 genes retain high-expression. The word “repressed” (and the mention of only very few high-expression genes) seem to imply a full repression with no transcription, but Q cells still express, at low levels, a wide variety of transcripts (see Marguerat 2012, or even Fig 5 in this review!); the “number of genes expressed” metric is highly dependent on thresholds used. This is also important because later in the text (p16) this global genome downregulation could be interpreted as genome-wide full repression by H3K9me, which has not been observed. A simple clarification would be to mention that most of the genome is “down-regulated” rather than “fully repressed”.

 

3) p18, the paragraph about H3K79me should mention that this is in S cerevisiae, and that H3K79 methylation is absent in S. pombe; the authors may also add a note that H3K79me is not quiescence-specific, but a multifaceted mark with roles in meiosis and G2/M for example (see Farooq et al, 2016 for an example review).

 

4) in Fig 5 yellow dots (mRNA) are quite hard to see. While the figure focuses on ncRNAs, it may still be a good idea to enhance the contrast for mRNAs as well (darker yellow/orange?).

 

Minor typos:

line 1 of p16: “cell lacking Dcr1, Ago1 or Rpd3” -> this is a typo, the authors most likely meant “Rdp1” in this list (RNAi core factor).

typo in Table 1: “Pac1C” should be “Paf1C”.

For “RRPE”, note that equivalent motifs (with small sequence differences) are also present at ribosomal synthesis genes in S. pombe, namely HomolD and HomolE motifs (see for example Montes et al, 2017, FEBS).

typo in Table 2 legend: both 1 and 2 are in superscript.

“strong reduction in total mRNA levels” (currently “levesl”)

p16 first paragraph: reference not converted (Joh 2016) next to “Figure 3”.

p19 third paragraph: “expresino” -> “expression”

p29 second paragraph: “Ntur2”->”Ntu2”

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

This manuscript presents a comprehensive, well-structured, and timely review of nuclear remodeling during cellular quiescence, integrating mechanistic insights from yeast models with conserved principles in multicellular systems. The authors convincingly convey that quiescence is an actively maintained and highly regulated cellular state rather than a passive default, and they provide a thorough synthesis of transcriptional, epigenetic, post-transcriptional, and nuclear architectural mechanisms underlying quiescence entry, maintenance, and exit.

Overall, the review is scientifically sound, clearly written, and exceptionally well referenced. The figures, tables, and glossary are informative and add substantial value for readers from diverse backgrounds. The manuscript will be of broad interest to researchers in chromatin biology, metabolism, stem cell biology, and disease.

The following suggestions are intended to further strengthen clarity and conceptual integration:

1. Conceptual clarity of quiescent states
   While the manuscript emphasizes the distinction between quiescence, senescence, and terminal differentiation, a concise conceptual overview explicitly contrasting quiescence with related arrested states (e.g., diapause, dormancy, persister states) would help orient non-specialist readers early in the review.

2. Cross-species synthesis
   The mechanistic depth of the yeast sections is excellent. Where possible, more explicit mapping of yeast-derived mechanisms to mammalian or metazoan systems (or a clear statement when such conservation is unknown) would further reinforce the “conserved mechanisms” theme of the review.

3. Integration of nuclear architecture with function
   Sections describing nucleolar condensation, telomere clustering, condensin-mediated chromosome reorganization, and 3D genome remodeling are informative but could benefit from a brief synthesis highlighting how these structural changes directly support genome stability, transcriptional repression, and rapid reversibility upon quiescence exit.

4. Post-transcriptional regulation in metazoans
   The discussion of intron retention, alternative polyadenylation, RNA storage, and non-coding RNAs is strong in yeast models. Expanding the integration of these mechanisms with mammalian quiescent stem cell systems, where data are available, would enhance translational relevance.

5. Disease and therapeutic relevance
   The manuscript briefly touches on cancer persister cells and therapy resistance. A short, focused paragraph discussing how quiescence-associated nuclear features may contribute to disease persistence—and potentially represent therapeutic vulnerabilities—would broaden the impact of the review.

6. Minor presentation points

   • Consider adding brief “key takeaway” statements to selected figure legends to guide readers.

   • Ensure consistent terminology (e.g., G0 cells, Q cells, quiescent cells) across sections.

   • A small number of typographical and formatting issues can be addressed during revision.

In summary, this is a high-quality and authoritative review that makes a significant contribution to the field. The suggested revisions are minor and primarily aimed at enhancing conceptual clarity and cross-system integration. I believe the manuscript will be an excellent resource for the community.

Comments on the Quality of English Language

The manuscript is written in clear, fluent, and professional English. The language accurately conveys complex concepts and does not hinder comprehension. Only minimal copy-editing, if any, would be sufficient.

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Reviewer 3 Report

Comments and Suggestions for Authors

Submitted manuscript is a well written and comprehensive review of epigenetic regulation of cellular quiescence in eukaryotic cells. To improve the work I would suggest to address the following points:

1. The title is a bit misleading as the review discuss more than just nuclear remodelation, it discuss also the role of non coding RNAs or alternative splicing. I would suggest to tweak the title or remove parts that are not relevant for nuclear reorganization.
2. The authors stress out the role of TOR signaling in regulation of quiescence in the introduction but then in the body of the manuscript there is only limited information on how TOR mediated signaling regulates nuclear remodeling in quiescence. I would suggest to re-frame the introduction or add additional connections of TOR to nuclear remodeling. 
3. Some parts are quite unbalanced and really focused on yeasts while not discussing mammalian regulation of the same processes. There is a lot of studies on mammalian quiescence regulation so I was expecting to read more on mammalian quiescence regulation. Especially the section 3 "What drives transcriptional reprogramming in quiescent cells?" is heavily focused on yeast, but rest of the sections also contain only limited information on mammalian quiescence regulation. I would suggest complement yeasts studies with mammalian studies throughout the manuscript.

Author Response

Please see the attachment.

Author Response File: Author Response.pdf