SMARCAD1 and TOPBP1 contribute to heterochromatin maintenance at the transition from the 2C-like to the pluripotent state

Reviewer #1 (Public Review):

In the present work the authors explore the molecular driving events involved in the establishment of constitutive heterochromatin during embryo development. The experiments have been carried out in a very accurate manner and clearly fulfill the proposed hypotheses.

Regarding the methodology, the use of: i) an efficient system for conversion of ESCs to 2C-like cells by Dux overexpression; ii) a global approach through IPOTD that reveals the chromatome at each stage of development and iii) the STORM technology that allows visualization of DNA decompaction at high resolution, helps to provide clear and comprehensive answers to the conclusion raised.

The contribution of the present work to the field is very important as it provides valuable information on chromatin-bound proteins at key stages of embryonic development that may help to understand other relevant processes beyond heterochromatin maintenance.

The study could be improved through a more mechanistic approach that focuses on how SMARCAD1 and TOPBP1 cooperate and how they functionally connect with H3K9me3, HP1b and heterochromatin regulation during embryonic development. For example, addressing why topoisomerase activity is required or whether it connects (or not) to SWI/SNF function and the latter to heterochromatin establishment, are questions that would help to understand more deeply how SMARCAD1 and TOPBP1 operate in embryonic development.

Reviewer #2 (Public Review):

The manuscript by Sebastian-Perez describes determinants of heterochromatin domain formation (chromocenters) at the 2-cell stage of mouse embryonic development. They implement an inducible system for transition from ESC to 2C-like cells (referred to as 2C+) together with proteomic approaches to identify temporal changes in associated proteins. The conversion of ESCs to 2C+ is accompanied by dissolution of chromocenter domains marked by HP1b and H3K9me3, which reform upon transition back to the 2C-like state. The innovation in this study is the incorporation of proteomic analysis to identify chromatin-associated proteins, which revealed SMARCAD1 and TOPBP1 as key regulators of chromocenter formation.

In the model system used, doxycycline induction of DUX leads to activation of EGFP reporter regulated by the MERVL-LTR in 2C+ cells that can be sorted for further analysis. A doxycycline-inducible luciferase cell line is used as a control and does not activate the MERVL-LTR GFP reporter. The authors do see groups of proteins anticipated for each developmental stage that suggest the overall strategy is effective.

The major strengths of the paper involve the proteomic screen and initial validation. From there, however, the focus on TOPBP1 and SMARCAD1 is not well justified. In addition, how data is presented in the results section does not follow a logical flow. Overall, my suggestion is that these structural issues need to be resolved before engaging in comprehensive review of the submission. This may be best achieved by separating the proteomic/morphological analyses from the characterization of TOPBP1 and SMARCAD1.

Reviewer #3 (Public Review):

The manuscript entitled "SMARCAD1 and TOPBP1 contribute to heterochromatin maintenance at the transition from the 2C-like to the pluripotent state" by Sebastian-Perez et al. adopted the iPOTD method to compare the chromatin-bound proteome in ESCs and 2C-like cells generated by Dux overexpression. The authors identified 397 chromatin-bound proteins enriched only in ESC and 2C- cells, among which they further investigated TOPBP1 due to its potential role in controlling chromocenter reorganization. SMARCD1, a known interacting protein of TOPBP1, was also investigated in parallel. The authors observed increased size and decreased number of H3K9me3-heterochromatin foci in Dux-induced 2C+ cells. Interestingly, depletion of TOPBP1 or SMARCD1 also led to increased size and decreased number of H3K9me3 foci. However, depletion of these proteins did not affect entry into or exit from the 2C-like state. Nevertheless, the authors showed that both TOPBP1 and SMARCD1 are required for early embryonic development.

Although this manuscript provides new insights into the features of 2C-like cells regarding H3K9me3-heterochromatin reorganization, it remains largely descriptive at this stage. It does not provide new insights into the following important aspects: 1) how SMARCD1 associates with H3K9me3 and contributes to heterochromatin maintenance, 2) how TOPBP1 regulates the expression of SMARCD1 and facilitates its localization in heterochromatin foci, 3) whether the remodelling of chromocenter is causally related to the mutual transitions between ESCs and 2C-like cells. Furthermore, some results are over-interpreted. Additional experiments and analyses are needed to increase the strength of mechanistic insights and to support all claims in the manuscript.