Disordered regions and folded modules in CAF-1 promote histone deposition in S. pombe

Reviewer #1 (Public Review):

Summary:
This paper makes important contributions to the structural analysis of the DNA replication-linked nucleosome assembly machine termed Chromatin Assembly Factor-1 (CAF-1). The authors focus on the interplay of domains that bind DNA, histones, and replication clamp protein PCNA.

Strengths:
The authors analyze soluble complexes containing full-length versions of all three fission yeast CAF-1 subunits, an important accomplishment given that many previous structural and biophysical studies have focused on truncated complexes. New data here supports previous experiments indicating that the KER domain is a long alpha helix that binds DNA. Via NMR, the authors discover structural changes at the histone binding site, defined here with high resolution. Most strikingly, the experiments here show that for the S. pombe CAF-1 complex, the WHD domain at the C-terminus of the large subunit lacks DNA binding activity observed in the human and budding yeast homologs, indicating a surprising divergence in the evolution of this complex. Together, these are important contributions to the understanding of how the CAF-1 complex works.

Weaknesses:
1. There are some aspects of the experimentation that are incompletely described:

In the SEC data (Fig. S1C) it appears that Pcf1 in the absence of other proteins forms three major peaks. Two are labeled as "1a" (eluting at ~8 mL) and "1b" (~10-11 mL). It appears that Pcf1 alone or in complex with either or both of the other two subunits forms two different high molecular weight complexes (e.g. 4a/4b, 5a/5b, 6a/6b). There is also a third peak in the analysis of Pcf1 alone, which isn't named here, eluting at ~14 mL, overlapping the peaks labeled 2a, 4c, and 5c.

The text describing these different macromolecular complexes seems incomplete (p. 3, lines 32-33): "When isolated, both Pcf2 and Pcf3 are monomeric while Pcf1 forms large soluble oligomers". Which of the three Pcf1-alone peaks are oligomers, and how do we know? What is the third peak? The gel analysis across these chromatograms should be shown.

More importantly, was a particular SEC peak of the three-subunit CAF-1 complex (i.e. 4a or 4b) characterized in the further experimentation, or were the data obtained from the input material prior to the separation of the different peaks? If the latter, how might this have affected the results? Do the forms inter-convert spontaneously?

2. Given the strong structural predication about the roles of residues L359 and F380 (Fig. 2f), these should be mutated to determine effects on histone binding.

3. Could it be that the apparent lack of histone deposition by the delta-WHD mutant complex occurs because this mutant complex is unstable when added to the Xenopus extract?

Reviewer #2 (Public Review):

Summary:
The authors describe the structure-functional relationship of domains in S. pombe CAF-1, which promotes DNA replication-coupled deposition of histone H3-H4 dimer. The authors nicely showed that the ED domain with an intrinsically disordered structure binds to histone H3-H4, that the KER domain binds to DNA, and that, in addition to a PIP box, the KER domain also contributes to the PCNA binding. The ED and KER domains as well as the WHD domain are essential for nucleosome assembly in vitro. The ED, KER domains, and the PIP box are important for the maintenance of heterochromatin.

Strengths:
The combination of structural analysis using NMR and Alphafold2 modeling with biophysical and biochemical analysis provided strong evidence on the role of the different domain structures of the large subunit of SpCAF-1, spPCF-1 in the binding to histone H3-H4, DNA as well as PCNA. The conclusion was further supported by genetic analysis of the various pcf1 mutants. The large amounts of data provided in the paper support the authors' conclusion very well.

Reviewer #3 (Public Review):

Summary:
The study conducted by Ouasti et al. is an elegant investigation of fission yeast CAF-1, employing a diverse array of technologies to dissect its functions and their interdependence. These functions play a critical role in specifying interactions vital for DNA replication, heterochromatin maintenance, and DNA damage repair, and their dynamics involve multiple interactions. The authors have extensively utilized various in vitro and in vivo tools to validate their model and emphasize the dynamic nature of this complex.

Strengths:
Their work is supported by robust experimental data from multiple techniques, including NMR and SAXS, which validate their molecular model. They conducted in vitro interactions using EMSA and isothermal microcalorimetry, in vitro histone deposition using Xenopus high-speed egg extract, and systematically generated and tested various genetic mutants for functionality in in vivo assays. They successfully delineated domain-specific functions using in vitro assays and could validate their roles to large extent using genetic mutants. One significant revelation from this study is the unfolded nature of the acidic domain, observed to fold when binding to histones. Additionally, the authors also elucidated the role of the long KER helix in mediating DNA binding and enhancing the association of CAF-1 with PCNA. The paper effectively addresses its primary objective and is strong.

Weaknesses:
A few relatively minor unresolved aspects persist, which, if clarified or experimentally addressed by the authors, could further bolster the study.

1. The precise function of the WHD domain remains elusive. Its deletion does not result in DNA damage accumulation or defects in heterochromatin maintenance. This raises questions about the biological significance of this domain and whether it is dispensable. While in vitro assays revealed defects in chromatin assembly using this mutant (Figure 5), confirming these phenotypes through in vivo assays would provide additional assurance that the lack of function is not simply due to the in vitro system lacking PTMs or other regulatory factors.

2. The observation of increased Pcf2-gfp foci in pcf1-ED* cells, particularly in mono-nucleated (G2-phase) and bi-nucleated cells with septum marks (S-phase), might suggest the presence of replication stress. This could imply incomplete replication in specific regions, leading to the persistence of Caf1-ED*-PCNA factories throughout the cell cycle. To further confirm this, detecting accumulated single-stranded DNA (ssDNA) regions outside of S-phase using RPA as an ssDNA marker could be informative.

3. Moreover, considering the authors' strong assertion of histone binding defects in ED* through in vitro assays (Figure 2d and S2a), these claims could be further substantiated, especially considering that some degree of histone deposition might still persist in vivo in the ED* mutant (Figure 7d, viable though growth defective double ED*+hip1D mutants). For example, the approach, akin to the one employed in Fig. 6a (FLAG-IPs of various Pcf1-FLAG-tagged mutants), could also enable a comparison of the association of different mutants with histones and PCNA, providing a more thorough validation of their findings.

4. It would be valuable for the authors to speculate on the necessity of having disordered regions in CAF1. Specifically, exploring the overall distribution of these domains within disordered/unfolded structures could provide insightful perspectives. Additionally, it's intriguing to note that the significant disparities observed among mutants (ED*, PIP*, and KER*) in in vitro assays seem to become more generic in vivo, except for the indispensability of the WHD-domain. Could these disordered regions potentially play a crucial role in the phase separation of replication factories? Considering these questions could offer valuable insights into the underlying mechanisms at play.

Author Response

We thank the three reviewers and the reviewing editor for their positive evaluation of our manuscript. We particularly appreciate that they unanimously consider our work as “important contributions to the understanding of how the CAF-1 complex works”, “The large amounts of data provided in the paper support the authors' conclusion very well” and “The paper effectively addresses its primary objective and is strong”.

We also thank them for a careful reading and useful comments to improve the manuscript. We will build on this input to provide an improved version of the manuscript that will hope to submit soon to eLife along with our point by point answer.