Inherited CDA-I disease: anemia-associated mutations disrupt CDIN1-Codanin1 complex

  1. Martin Stojaspal
  2. Tomáš Brom
  3. Ivona Nečasová
  4. Tomáš Janovič
  5. Pavel Veverka
  6. Naina Verma
  7. Lukáš Uhrík
  8. Lenka Hernychova
  9. Ctirad Hofr

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Abstract

Congenital dyserythropoietic anemia type I (CDA-I) is a rare hereditary disease marked by ineffective erythropoiesis, a characteristic spongy heterochromatin structure in erythroblasts, and mutations in the genes CDAN1 and CDIN1, which encode the proteins Codanin1 and CDIN1. Codanin1 regulates histone shuttling via the chaperone ASF1, yet the role of CDIN1 in CDA-I pathology remains unclear. Notably, CDIN1 is known to interact directly with the C-terminus of Codanin1. Although mutations in both genes are critical to the disease phenotype, their molecular-level effects have not been fully elucidated. Here, we present a comprehensive structural and functional analysis of the CDIN1-Codanin1 C-terminus complex. Using complementary biophysical techniques, we show that CDIN1 and Codanin1 C-terminus form a high-affinity heterodimeric complex with equimolar stoichiometry. We further delineate the essential interacting regions of CDIN1 and Codanin1. We demonstrate that CDA-I-associated mutations in either protein disrupt CDIN1-Codanin1 interaction, suggesting a potential molecular mechanism underlying the disease.

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    Reply to the reviewers

    1. General Statements

    • This manuscript represents a full revision incorporating all reviewer recommendations; the additional follow-up experiments and expanded analyses will be presented in dedicated subsequent manuscripts.
    • Congenital dyserythropoietic anemia type I (CDA-I) is a rare hereditary disease characterized by ineffective erythropoiesis and mutations in Codanin1 and CDIN1.
    • Our study reveals the structural and functional dynamics of the CDIN1-Codanin1 complex, shedding light on the molecular mechanisms of protein-protein interactions implicated in CDA-I pathology.
    • The main goal of our study was to examine the interaction between CDIN1 and the C‑terminal binding domain of Codanin1 using complementary biophysical approaches.
    • We quantified binding and identified interacting regions of Codanin1 and CDIN1.
    • We found that CDA-I-associated mutations in interacting regions disturb CDIN1‑Codanin1 complex.
    • We proposed a hypothetical molecular model of CDIN1-Codanin1 role in CDA-I hallmarks development.
    • Our initial studies on BioRxiv (2023) have been cited by leading publications in the field (Jeong, Frater et al. 2025, Sedor and Shao 2025, Nature Communications) and prompted further research on this topic.

    2. Point-by-point description of the revisions

    *Here we provide a point-by-point reply describing the revisions already carried out and included in the transferred manuscript. *

    Reply to the reviewers

    Reviewer #1 – Evidence, reproducibility and clarity

    This is a rigorous biophysical characterization of a protein-protein interaction relevant to CDA-1 disease. The two proteins were purified in an E. coli host but CD and DLS was performed to ensure that the purified protein is well folded. An impressive native protein EMSA was used to show a 1:1 complex. While common for protein-nucleic acid complexes, EMSAs are much more challenging with protein complexes. A higher-running complex, likely a heterotetramer was implied at higher protein concentrations. These results were supported with SEC-MALS analysis and analytic ultracentrifugation analysis. Thermophoresis and ITC were used to report a nanomolar affinity of the proteins for each other. SEC-SAXS supported the conclusions about stoichiometry and composition inferred from the earlier methods and suggested that the dimerization interface comes from CDIN1. Next HDX-MS was used to identify putative interface residues, which were then mutated in each of the proteins and assessed for binding using coimmunoprecipitation. This study uses at least 10 orthogonal biophysical and/or biochemical methodologies to characterize an important protein-protein interaction and the analysis is clear and so is the writing. I couldn't (reading it once) find any grammatical or other errors in the text or figures. This manuscript is top-quality and suitable for publication.

    __Reviewer #1 – Significance __

    Such detailed structural and mechanistic studies are greatly lacking in many clinical conditions for which mutations are known (unless they cause cancer, neurodegenerative disease, and so on). We need more such studies on disease topics! This study will be of interest to the hematologic diseases community.

    1. Response – ____Significance

    We thank Reviewer #1 for the thoughtful and encouraging evaluation of our work. We are particularly grateful for recognizing the significance of studying protein-protein interaction in the context of CDA-I disease, as well as the rigor and clarity of our biophysical and biochemical characterization.

    We appreciate the reviewer's acknowledgment of the challenges associated with native protein EMSAs. We are pleased that our use of multiple orthogonal techniques was recognized as a strength of the study. We are gratified that the comprehensiveness and coherence of our data and the manuscript's clarity were well received.

    We thank the reviewer for noting the broader impact of our findings on the hematologic disease community. As highlighted, there is a pressing need for a mechanistic understanding of non-oncologic, non-neurodegenerative diseases, and our studies address this gap.

    We are honored by the reviewer's endorsement of our manuscript as "top-quality and suitable for publication". We value the reviewer's highly supportive and motivating feedback.

    __Reviewer #2 – 1. Evidence, reproducibility and clarity __

    This manuscript presents structural and biochemical characterization of the interaction between CDIN1 and the C-terminal domain of Codanin1, shedding light on a complex implicated in Congenital Dyserythropoietic Anemia Type I (CDA-I). While the authors provide valuable structural insights and identify disease-associated mutations that impair CDIN1-Codanin1 binding, I think several important concerns should be addressed to strengthen both the mechanistic claims and their functional relevance.

    Contradiction Between Stoichiometry Models:

    The authors propose that CDIN1 and Codanin1Cterm primarily form a heterodimer in vitro. However, this appears to contradict previous reports indicating a tetra-heteromeric arrangement. Additionally, while CDIN1 homodimerize seems confusing to me, do the authors suggest it is stable without Codanin1? This seems contrary to findings that CDIN1 is unstable in the absence of Codanin1 (Sedor, S.F., Shao, S. nature comm 2025, Swickley, G., Bloch, Y., Malka, L. et al 2020 BMC Mol and Cell Biol). These inconsistencies raise concerns about whether the observed stoichiometries are physiologically relevant or artifacts of in vitro reconstitution, especially since full-length Codanin1 was not studied.

    2.1 Response ____– Consistent stoichiometry of Codanin1Cterm

    We thank Reviewer #2 for raising critical points regarding the stoichiometry and physiological relevance of the CDIN1-Codanin1 interaction. The following response clarifies the rationale and interpretation in relation to previous findings.

    Stoichiometry of CDIN1-Codanin1Cterm complex:

    Recent Cryo-EM studies of full-length Codanin1 (Jeong, Frater et al. 2025, Sedor and Shao 2025) suggest independent internal dimerization domains (452-798 and 841-1000 amino acid residue) driving homodimer formation, with each Codanin1 monomer binding one CDIN1 via the C-terminal region (1005-1227 amino acid residue), resulting in a tetra-heteromeric complex. Therefore, the complete assembly appears as a dimer of heterodimers in the full-length context.

    In our study, Codanin1 was truncated to retain only the CDIN1-binding C-terminus (1005-1227 amino acid residues), eliminating the homodimerization ability of Codanin1. Hence, in the case of truncated Codanin1Cterm, the minimal complex we observe is a 1:1 heterodimer of CDIN1-Codanin1Cterm, which is fully consistent with the equimolar stoichiometry of CDIN1-Codanin1 complex seen in the full-length structure.

    Stability and oligomeric state of CDIN1 in the absence of Codanin1:

    We concur with the reviewer that Sedor et al. (2025) and Swickley et al. (2020) reported decreased CDIN1 levels in cells lacking Codanin1, implying in vivo dependence of CDIN1 on Codanin1 partner for stability (Swickley, Bloch et al. 2020, Sedor and Shao 2025). The purified CDIN1 is monodisperse (Supplementary Figure 2D), exhibits thermal stability with a melting temperature of 48 °C (Supplementary Figure 2E), and displays proper folding as indicated by CD measurements (Supplementary Figure 2B). Additionally, SAXS profiles of CDIN1 correspond to AlphaFold predictions (Fig. 2B). Together, our findings indicate that the recombinant CDIN1 forms a stable conformation in vitro without Codanin1. To the best of our knowledge, no previous research has directly identified the endogenous oligomeric states of CDIN1 within cellular content.

    We fully acknowledge that future analysis of the full-length Codanin1-CDIN1 assembly in a cellular context will be necessary for understanding physiological stoichiometries. As outlined in the General statements, our study focuses on the C-terminus of Codanin1 to describe the binding interface and complex biophysical properties of the CDIN-Codanin1Cterm complex.

    __Reviewer #2 – ____2. Unvalidated Functional Claims: __

    The manuscript identifies several CDA-I-associated mutations that disrupt CDIN1-Codanin1 interaction. However, the authors do not test how these mutations affect the biological function of the complex, particularly its role in ASF1 sequestration or histone trafficking. Given the central importance of this axis in their disease model, functional validation (e.g., ASF1 localization, histone deposition assays) is necessary to support these mechanistic conclusions.

    2.2 Response – ____Hypothetical model as discussion merit

    We thank the reviewer for the comment regarding the functional implications of CDA-I-associated mutations and their potential impact on ASF1 sequestration and histone trafficking hypothesized within the Discussion. We fully agree that understanding the downstream biological consequences of disrupted CDIN1-Codanin1 interaction is critical for elucidating the full molecular basis of CDA-I pathogenesis.

    In the Future research directions of the Discussion, we have acknowledged and emphasized the need for follow-up studies using erythroblast cell lines to determine whether specific disease-associated mutations disrupt CDIN1-Codanin1 binding, leading to functional defects relevant to erythropoiesis and nuclear architecture typical for CDA-I disease.

    However, as we respectfully note in General Statements, the main aim of the present study was to provide a rigorous biophysical characterization of the CDIN1-Codanin1Cterm interaction. Proposed cellular experiments, though relevant, are beyond the conceptual scope of the presented studies.

    Reviewer #2 – ____3. Speculative and Potentially Contradictory Model:

    The proposed model suggests that CDIN1 competes with ASF1 for Codanin1 binding, thereby indirectly promoting histone delivery to the nucleus. However, emerging data indicate that Codanin1, CDIN1, and ASF1 can form a stable ternary complex, calling into question this competitive binding hypothesis (Sedor, S.F., Shao, S. nature comm 2025). The authors do not acknowledge or discuss these findings, and the model in its current form may therefore be oversimplified or inaccurate.

    2.3 Response – ____Hypothetical model fully aligned with current knowledge

    We fully acknowledged and discussed in the current manuscript the recent findings demonstrating that Codanin1, CDIN1, and ASF1 can form a ternary complex (Sedor, S.F., Shao, S. Nature Comm. 2025; Jeong, T. K. et al. Nature Comm. 2025). Our revised model was updated accordingly to reflect the collaborative binding of Codanin1, CDIN1, and ASF1, and is presented in alignment with published data.

    While earlier versions of our work published on the BioRxiv server (May 26, 2023) proposed a competitive hypothesis, the current manuscript incorporates recent literature and prior reviewer feedback to offer a refined model. We believe that the updated hypothesis suggests a plausible mechanism for how CDIN1 modulates Codanin1 function, which will be further tested in future cellular studies.

    Reviewer #2 – 4. Significance:

    Overall, the study adds to our structural understanding of CDIN1 and Codanin1 interactions, but the functional interpretations are currently speculative, and in some cases in conflict with existing literature. The manuscript would benefit significantly from addressing these discrepancies, incorporating relevant data on ASF1, and clarifying whether the observed assemblies reflect physiological complexes.

    __2.4 Response – Significance __

    We thank Reviewer #2 for the constructive feedback. As noted in General Statements, our current manuscript is primarily dedicated to defining the molecular architecture and interactions of the CDIN1–Codanin1Cterm core interface. We agree that follow-up ASF1‑dependent functional assays will be critical to fully validate observed assemblies, but these experiments lie outside the scope of the present study and are ongoing in our laboratory.

    To address the reviewer's concern about possible speculative interpretation, we have:

    • Used cautious language in Results and Discussion to prevent overstatement (e.g., page 31, line 754, “leads” exchanged to “may contribute” in legend of Fig. 4).
    • Described in the Discussion how our results enhance and add understanding to the body of published structural data of CDIN1–Codanin1Cterm.
    • Updated our hypothetical model in Fig. 4 to be fully in line with published data.
    • Clearly stated that the working hypothesis is connected with a subset of CDA-I mutations (p. 31, l. 758-759, “The proposed model represents a working hypothesis relating to a subset of CDA-I mutations and is not currently substantiated by experimental evidence at the cellular level.”)
    • Stated in Future research directions of Discussion that functional validation, including ASF1, will motivate future critical studies, p. 32, l. 771-773: “The ability of Codanin1 to interact with both CDIN1 and ASF1 motivates further investigation of how CDIN1 and ASF1 affect the function of full-length Codanin1, which even recent cryo-EM data has not addressed yet.”
    • Highlighted the necessity of complementary in vivo studies in erythroblast cell lines to determine if CDA-I-related mutations in CDIN1-Codanin1 interaction region cause typical CDA-I phenotypes, aiming to clarify the molecular mechanisms of inherited CDA-I anemia. We state in Future research directions in Discussion, p. 32, l. 774-780: “…follow-up research utilizing erythroblast model cell lines must be conducted to determine if specific mutations that disrupt CDIN1-Codanin1 binding also affect ASF1 localization and cause a phenotype typical of CDA-I. In future work, additional Codanin1 mutations, including those outside the C-terminal region, should be evaluated to determine how the mutations affect ASF1’s nuclear concentration and subcellular localization. The proposed research directions will provide additional deeper insights into the underlying mechanisms of the molecular origin of inherited anemia CDA-I.” We believe that the revisions objectively clarify the significance and the limits of the current work and set the stage for the detailed functional studies to follow.

    __Reviewer #3 – Evidence, reproducibility and clarity: __

    Congenital Dyserythropoietic Anemia Type I (CDA I) is an autosomal recessive disorder characterized by ineffective erythropoiesis and distinctive nuclear morphology ("Swiss cheese" heterochromatin) in erythroblasts. CDA I is caused by mutations in CDAN1 and CDIN1. Codanin1, encoded by CDAN1, is part of the cytosolic ASF1-H3.1-H4-Importin-4 complex, which regulates histone trafficking to the nucleus. CDIN1 has been shown to bind the C-terminal domain of Codanin-1, but until now, pathogenic mutations had not been directly linked to the disruption of this interaction.

    In this study, the authors used biophysical techniques to characterize the interaction between Codanin-1's C-terminal region (residues 1005-1227) and CDIN1, demonstrating high-affinity, equimolar binding. HDX-MS identified interaction hotspots, and disease-associated mutations in these regions disrupted complex formation. The authors propose that such disruption prevents ASF1 sequestration in the cytoplasm, thereby reducing nuclear histone levels and contributing to the chromatin abnormalities seen in CDA I.

    Major Comments:

    1. Use of Codanin-1 Fragment:

    Most experiments were conducted using only the C-terminal 223 amino acids of Codanin-1. While this region is known to bind CDIN1, it is unclear whether its conformation is maintained in the context of the full-length protein. This could affect binding properties and structural interpretations. The authors should discuss how structural differences between the isolated C-terminus and the full-length Codanin-1 may influence the conclusions.

    Response of authors ____#3

    3.1 Response: Use of Codanin-1 Fragment as biding part to CDIN1

    We thank the reviewer for the important observation regarding the use of the C-terminal fragment of Codanin1. As noted in the manuscript (e.g., p. 30, line 721 and p. 32, line 761), we fully acknowledge that the truncation of Codanin1 may influence its conformational dynamics or contextual folding relative to the full-length protein.

    However, several lines of evidence suggest that the C-terminal 223 amino acid residues—responsible for CDIN1 binding—are structurally autonomous and have minimal intramolecular contacts with upstream regions. Published cryo-EM and biochemical data (Jeong, Frater et al. 2025, Sedor and Shao 2025), in conjunction with AlphaFold structural predictions (Fig. 2D) and our co-immunoprecipitation assays (Fig. 3F), consistently support a model wherein the CDIN1-binding region is flexible and spatially isolated from the core structural domains of Codanin1. Additionally, results from our co-immunoprecipitation assay (Fig. 3F) indicate that full-length Codanin1 and truncated Codanin1Cterm interact with CDIN1 similarly, further supporting the isolated manner of the C-terminal fragment. The available data together imply that the C-terminal fragment used in our study retains its native conformation and binding properties when expressed independently.

    While our findings are confined to the interaction domain and do not reflect full-length Codanin1’s architecture, we believe the use of the C-terminal minimal fragment of Codanin1 enables precise dissection of the CDIN1-binding interface and yields mechanistic insights without introducing significant structural artifacts.

    We agree with the reviewer that future work incorporating full-length Codanin1, especially in a cellular context, will be instrumental to fully characterize higher-order assembly and regulatory functions.

    __Reviewer #3 – 2. ____Graphical Abstract and Domain Independence: __

    The graphical abstract presents the Codanin-1 C-terminus as an independent domain, but no direct evidence is provided to support its structural autonomy in vivo.

    The authors should clarify whether the C-terminal region functions as a distinct domain in the context of the full-length protein.

    __3.2 Response –____ Independent C-terminal domain __

    We thank the reviewer for bringing up the question of the independence of the C-terminal domain. Although direct in vivo proof of C-terminal autonomy is not yet available, published cryo-EM structures of full-length Codanin1, our biophysical characterization, and AlphaFold models all consistently indicate that the C-terminal 223 amino acid residues of Codanin1 form a structurally independent binding module. In the graphical abstract, we illustrated the C‑terminal domain as a loosely connected part of Codanin1 to highlight its independence and to emphasize the specific focus of our studies.

    To articulate limitations of our studies focused on the C-terminal part of Codanin1, we stated in the Functional implications of CDA-I-related mutations in the Discussion, p. 30, l. 721-724: “However, our measurements do not exclude the possible role of the disordered regions in full-length Codanin1. For example, CDIN1 could potentially stabilize full-length Codanin1 by rearranging the disordered regions into a more condensed structure, thereby augmenting the structural stability of Codanin1.”

    Reviewer #3 – 3.____Pathogenic Mutations Beyond the Binding Site:

    The study highlights a triplet mutation that impairs CDIN1 binding. However, most CDA I‑associated mutations in CDAN1 are dispersed across the entire protein and may not affect CDIN1 interaction directly.

    The authors should discuss alternative mechanisms by which mutations in other regions of Codanin-1 might cause disease.

    3.3 Response – Pathogenic mutations outside the binding site – alternative mechanisms

    We appreciate the reviewer noting that most CDA-I-associated CDAN1 mutations are outside the CDIN1-Codanin1 binding site and suggesting alternative mechanisms. In the revised Discussion, we added a paragraph on alternative pathogenic models, p. 29, l. 702-713:

    "Our study centers on the CDIN1-binding C-terminus, however, most CDA-I-associated CDAN1 mutations lie elsewhere and probably act through alternative mechanisms. Mutations such as P672L and F868I in the LOBE2 (452-798 amino acid residue) and F868I in the coiled-coil (841-1000 amino acid residue) domains may disturb Codanin1 homodimerization and higher-order complex assembly, directly affecting ASF1 sequestration (Jeong, T. K. et al. Nature Comm. 2025). Other mutant variants may also interfere with ASF1 sequestration, nuclear targeting, or chromatin-remodeling functions, while destabilizing mutations may induce misfolding and proteasomal degradation. Moreover, CDA-I-associated mutations, such as R714W and R1042W, might compromise the interaction between Codanin1 and ASF1 (Ask, Jasencakova et al. 2012). Collectively, the complementary alternative pathogenic mechanisms associated with Codanin1 mutations in distal regions and mutations in CDIN1‑binding C-terminus of Codanin1 may contribute to erythroid dysfunction in CDA-I."

    Reviewer #3 – 4. ____Contradictory Functional Models:

    Ask et al. (EMBO J, 2012) reported that Codanin-1 depletion increases nuclear ASF1 and accelerates DNA replication. This contrasts with the current hypothesis that disruption of the Codanin-1/CDIN1 complex reduces nuclear ASF1.

    The authors should attempt to reconcile this apparent contradiction, possibly by proposing a context-specific or dual-function model for Codanin-1 in histone trafficking.

    3.4 Response – ____Clarified explanation of hypothetical functional model

    We thank the reviewer for raising this point, which improved the clarity of our work. There is no real discrepancy between Ask et al. and our findings; both agree that Codanin1 restrains ASF1 in the cytoplasm. Ask et al. examined the complete loss of Codanin1, which abolishes cytoplasmic ASF1 sequestration and thus leads to maximal nuclear accumulation. We suggest the CDA-I-associated mutations selectively disrupt the CDIN1-Codanin1 interface, releasing ASF1 from the cytoplasm into the nucleus.

    To enhance clarity, we now state in the legend of Figure 4 describing the hypothesis (p. 31, l. 752-753): "…CDA-I-associated mutations prevent CDIN1-Codanin1 complex formation, thus prevent ASF1 sequestration to cytoplasm; ASF1 remains accumulated in nucleus."

    Reviewer #3 – 5. ____Conclusions and Claims:

    The proposed model of CDA I pathogenesis (Fig. 4) is plausible but not yet fully supported by the available data. The authors suggest that disruption of the Codanin-1/CDIN1 interaction leads to nuclear histone depletion, but this has not been experimentally confirmed.

    Claims about the general pathogenesis of CDA I should be clearly qualified as hypothetical and applicable to a subset of mutations. The presence and localization of ASF1 in the nucleus following disruption of the Codanin-1/CDIN1 complex should be tested experimentally.

    3.5 Response – __Tempered ____conclusions and claims: __

    We thank the reviewer for underscoring the need to temper our conclusions and to distinguish hypotheses from available results. We fully agree that our Fig. 4 model—linking disruption of the Codanin1-CDIN1 interface to nuclear histone imbalance—remains a working hypothesis, currently supported by indirect biochemical and structural data.

    Accordingly, we have:

    • Revised the text to explicitly state that this model is hypothetical and pertains to a subset of CDA-I-associated CDAN1 mutations. Specifically, we
    1. Added to the last paragraph of the section Functional implications of CDA-I-related mutations in Discussion (p. 31, l. 744-749): “In considering functional implications of our findings within available data, it is essential to qualify that mechanistic claims regarding the general pathogenesis of CDA-I remain hypothetical and are restricted to a specific subset of mutations. Furthermore, direct experimental validation, such as immunolocalization or live-cell imaging, to assess ASF1’s nuclear presence and distribution following disruption of the CDIN1-Codanin1 complex is required to substantiate the proposed model.”
    2. Included in the legend of Fig. 4: ”The proposed model represents a working hypothesis relating to a subset of CDA-I mutations and is not currently substantiated by experimental evidence at the cellular level.”
    • Replaced any associated definitive language (e.g., “leads to”) with qualified phrasing (e.g., “may contribute to”) in the legend of Fig. 4.
    • Clarified in the Discussion that direct measurement of nuclear ASF1 redistribution and histone levels following interface disruption has not yet been performed. Specifically, we added to the section Functional implications of CDA-I-related mutations in Discussion (p. 30, l. 734-735): “It should be noted, however, that direct quantification of nuclear ASF1 redistribution and histone levels after CDIN1-Codanin1 disruption has not yet been conducted.” Although experimental verification of nuclear ASF1 localization upon CDIN1-Codanin1 complex disruption falls beyond the current manuscript’s scope, we acknowledge its importance and have emphasized the need for such studies in future work within the Future research directions of the Discussion. Specifically, we concluded by stating (p. 32, l. 774-776): “Finally, follow‑up research utilizing erythroblast model cell lines must be conducted to determine if specific mutations that disrupt CDIN1-Codanin1 binding, also affect ASF1 localization and cause a phenotype typical of CDA-I.”

    __Reviewer #3 – 6.____Broader Mutation Analysis and ASF1 Localization: __

    To strengthen the link between Codanin-1/CDIN1 disruption and disease pathogenesis, it would be important to test the effects of additional CDAN1 mutations, including those outside the C-terminal region. Similarly, the impact on ASF1 nuclear concentration and localization should be directly assessed. These experiments would significantly bolster the central hypothesis. If feasible, they should be pursued or at least acknowledged as important future directions.

    3.6 Response – Broader mutation analysis and ASF1 localization in future directions

    We thank Reviewer #3 for emphasizing the value of a broader mutation survey and direct ASF1 localization studies. As noted above, our current manuscript is centered on delineating the molecular architecture of the CDIN1-Codanin1Cterm core interface; comprehensive mutational analyses outside the C-terminal binding region and ASF1-dependent functional assays will be critical to extend these findings but fall beyond the scope of the present work and will be the objective of our following studies. To address the reviewer’s concern, we have:

    • Expanded the Future Directions section to specify that additional CDA-I-linked CDAN1 variants, including non-C-terminal mutations, and quantitative assessments of ASF1 nuclear localization will be the subject of ongoing and planned investigations. Specifically, we added (p. 32, l. 776-778):” In future work, additional Codanin1 mutations, including those outside the C-terminal region, should be evaluated to determine how the mutations affect ASF1’s nuclear concentration and subcellular localization.”

    • Emphasized the need for complementary in vivo validation in erythroblast models to confirm whether the disturbance of CDIN1-Codanin1 binding recapitulates CDA-I phenotypes. We acknowledged the need for cell-line studies in future work within the Future research directions of Discussion (p. 32, l. 774-776): “Finally, follow-up research utilizing erythroblast model cell lines must be conducted to determine if specific mutations that disrupt CDIN1-Codanin1 binding, also affect ASF1 localization and cause a phenotype typical of CDA-I.” We believe these changes more precisely delimit the scope and significance of the current study while laying out a clear roadmap for the essential follow-up experiments.

    Reviewer #3 – 7. ____Rigor and Presentation and Cross-commenting

    __Minor Comments: __

    • Methods and Reproducibility:

    The experimental methods are well described, and the results appear reproducible.

    • Presentation:

    The text and figures are clear and well organized.

    Referee Cross-commenting

    I agree with reviewer 1 that the paper presents detailed structure study of Codanin-1 and CDIN1 protein. However, as reviewer 2 claims functional studies are missing and therefore the hypothesis regarding the pahtogenesis of CDAI is speculaltive especially with no studies regarding ASF1.

    3____.7 Response ____–____ Rigor and Presentation and Cross-commenting:

    We thank the reviewers for their positive appraisal of our results' reproducibility, presentation, and method descriptions. We also appreciate the cross-comment that, while our structural analysis of the CDIN1-Codanin1 complex is thorough, functional validation, particularly regarding ASF1, remains to be addressed.

    As outlined above, we have revised the manuscript to:

    • Emphasize that pathogenic hypotheses drawn from structural data are provisional (refer to Responses 2.2, 2.3, and 3.5).
    • Include follow-up studies for ASF1 localization assays and broader mutation profiling in our Future Directions (refer to Responses 2.4, 3.5, 3.6).
    • Integrate cautious language throughout to clearly delineate verified findings from model-based speculation (refer to Responses 2.4, 3.5, 3.6). The implemented adjustments ensure that the current work is positioned as a detailed structural and interaction foundation, upon which the essential functional studies will build. We believe that all extensions and clarifications fully satisfy the reviewers’ collective recommendations.

    __Reviewer #3 –____ Significance: __

    Nature and Significance of the Advance:

    This study extends prior work (e.g., Swickley et al., BMC Mol Cell Biol 2020; Shroff et al., Biochem J 2020) on Codanin-1/CDIN1 interaction by applying high-resolution biophysical techniques to identify mutations that disrupt this complex. It provides a plausible cellular mechanism by which specific mutations may lead to CDA I through impaired histone trafficking.

    Nevertheless, key question remains: How do mutations outside the Codanin-1 C-terminus contribute to the pathology?

    3.8 Response – Significance:

    • We thank Reviewer #3 for this important point. Although our work specifically dissects the C-terminal CDIN1-binding domain of Codanin1, we fully acknowledge that CDA-I-associated mutations throughout Codanin1 may operate via additional mechanisms. To address the additional mechanisms, we have added a new paragraph describing other possible pathogenic models to the Discussion (please refer to Response 3.3).

    • We also fully acknowledged the need for systematic functional assays of non-C-terminal mutations and their impact on ASF1 localization (please refer to Response 3.6).

    • We revised the text to clarify how mutations beyond the C-terminus may contribute to CDA-I pathogenesis and present the significance of our current structural analyses, biophysical characterizations, and molecular insights as a foundation for future research (please refer to Response 3.6). __Audience: __

    • Molecular and cellular biologists investigating nuclear-cytoplasmic trafficking mechanisms

    • Hematologists and geneticists studying rare red cell disorders

    • Clinicians managing CDA I patients and researchers exploring targeted therapies __Reviewer Expertise: __

    Pediatric hematologist with over 20 years of research experience in CDA I, including the initial identification of CDAN1 and the elucidation of Codanin-1's role in embryonic erythropoiesis. Not a specialist in the biophysical techniques used in this study.

    References

    Ask, K., Z. Jasencakova, P. Menard, Y. Feng, G. Almouzni and A. Groth (2012). "Codanin-1, mutated in the anaemic disease CDAI, regulates Asf1 function in S-phase histone supply." The EMBO Journal 31(8): 2013–2023.

    Jeong, T.-K., R. C. M. Frater, J. Yoon, A. Groth and J.-J. Song (2025). "CODANIN-1 sequesters ASF1 by using a histone H3 mimic helix to regulate the histone supply." Nature Communications 16(1): 2181.

    Sedor, S. F. and S. Shao (2025). "Mechanism of ASF1 engagement by CDAN1." Nature Communications 16(1): 2599.

    Swickley, G., Y. Bloch, L. Malka, A. Meiri, S. Noy-Lotan, A. Yanai, H. Tamary and B. Motro (2020). "Characterization of the interactions between Codanin-1 and C15Orf41, two proteins implicated in congenital dyserythropoietic anemia type I disease." Molecular and Cell Biology 21(1).

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    Referee #3

    Evidence, reproducibility and clarity

    Congenital Dyserythropoietic Anemia type I (CDA I) is an autosomal recessive disorder characterized by ineffective erythropoiesis and distinctive nuclear morphology ("Swiss cheese" heterochromatin) in erythroblasts. CDA I is caused by mutations in CDAN1 and CDIN1. Codanin-1, encoded by CDAN1, is part of the cytosolic ASF1-H3.1-H4-Importin-4 complex, which regulates histone trafficking to the nucleus. CDIN1 has been shown to bind the C-terminal domain of Codanin-1, but until now, pathogenic mutations had not been directly linked to the disruption of this interaction. In this study, the authors used biophysical techniques to characterize the interaction between Codanin-1's C-terminal region (residues 1005-1227) and CDIN1, demonstrating high-affinity, equimolar binding. HDX-MS identified interaction hotspots, and disease-associated mutations in these regions disrupted complex formation. The authors propose that such disruption prevents ASF1 sequestration in the cytoplasm, thereby reducing nuclear histone levels and contributing to the chromatin abnormalities seen in CDA I.

    Major Comments:

    1. Use of Codanin-1 Fragment: Most experiments were conducted using only the C-terminal 223 amino acids of Codanin-1. While this region is known to bind CDIN1, it is unclear whether its conformation is maintained in the context of the full-length protein. This could affect binding properties and structural interpretations. The authors should discuss how structural differences between the isolated C-terminus and the full-length Codanin-1 may influence the conclusions.
    2. Graphical Abstract and Domain Independence: The graphical abstract presents the Codanin-1 C-terminus as an independent domain, but no direct evidence is provided to support its structural autonomy in vivo. The authors should clarify whether the C-terminal region functions as a distinct domain in the context of the full-length protein.
    3. Pathogenic Mutations Beyond the Binding Site: The study highlights a triplet mutation that impairs CDIN1 binding. However, most CDA I-associated mutations in CDAN1 are dispersed across the entire protein and may not affect CDIN1 interaction directly. The authors should discuss alternative mechanisms by which mutations in other regions of Codanin-1 might cause disease.
    4. Contradictory Functional Models: Ask et al. (EMBO J, 2012) reported that Codanin-1 depletion increases nuclear ASF1 and accelerates DNA replication. This contrasts with the current hypothesis that disruption of the Codanin-1/CDIN1 complex reduces nuclear ASF1. The authors should attempt to reconcile this apparent contradiction, possibly by proposing a context-specific or dual-function model for Codanin-1 in histone trafficking.
    5. Conclusions and Claims: The proposed model of CDA I pathogenesis (Fig. 4) is plausible but not yet fully supported by the available data. The authors suggest that disruption of the Codanin-1/CDIN1 interaction leads to nuclear histone depletion, but this has not been experimentally confirmed. Claims about the general pathogenesis of CDA I should be clearly qualified as hypothetical and applicable to a subset of mutations. The presence and localization of ASF1 in the nucleus following disruption of the Codanin-1/CDIN1 complex should be tested experimentally.
    6. Broader Mutation Analysis and ASF1 Localization: To strengthen the link between Codanin-1/CDIN1 disruption and disease pathogenesis, it would be important to test the effects of additional CDAN1 mutations, including those outside the C-terminal region. Similarly, the impact on ASF1 nuclear concentration and localization should be directly assessed. These experiments would significantly bolster the central hypothesis. If feasible, they should be pursued or at least acknowledged as important future directions.

    Minor Comments:

    • Methods and Reproducibility: The experimental methods are well described, and the results appear reproducible.
    • Presentation: The text and figures are clear and well organized.

    Referee Cross-commenting

    I agree with reviewer 1 that the paper present detailed strucutre study of Codann-1 and CDIN1 protein. However, as reviewer 2 claims functional studies are missing and therefore the hypothesis regarding the pahtogenesis of CDAI is speculaltive especially with no studies regarding ASF1.

    Significance

    Nature and Significance of the Advance:

    This study extends prior work (e.g., Swickley et al., BMC Mol Cell Biol 2020; Shroff et al., Biochem J 2020) on Codanin-1/CDIN1 interaction by applying high-resolution biophysical techniques to identify mutations that disrupt this complex. It provides a plausible cellular mechanism by which specific mutations may lead to CDA I through impaired histone trafficking. Nevertheless, key question remains: How do mutations outside the Codanin-1 C-terminus contribute to the pathology?

    Audience:

    Molecular and cellular biologists investigating nuclear-cytoplasmic trafficking mechanisms Hematologists and geneticists studying rare red cell disorders Clinicians managing CDA I patients and researchers exploring targeted therapies

    Reviewer Expertise:

    Pediatric hematologist with over 20 years of research experience in CDA I, including the initial identification of CDAN1 and the elucidation of Codanin-1's role in embryonic erythropoiesis. Not a specialist in the biophysical techniques used in this study

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    Referee #2

    Evidence, reproducibility and clarity

    This manuscript presents structural and biochemical characterization of the interaction between CDIN1 and the C-terminal domain of Codanin1, shedding light on a complex implicated in Congenital Dyserythropoietic Anemia Type I (CDA-I). While the authors provide valuable structural insights and identify disease-associated mutations that impair CDIN1-Codanin1 binding, I think several important concerns should be addressed to strengthen both the mechanistic claims and their functional relevance.

    Contradiction Between Stoichiometry Models:

    The authors propose that CDIN1 and Codanin1Cterm primarily form a heterodimer in vitro. However, this appears to contradict previous reports indicating a tetra-heteromeric arrangement. Additionally, while CDIN1 homodimerize seems confusing to me, do the authors suggest it is stable without Codanin1? This seems contrary to findings that CDIN1 is unstable in the absence of Codanin1(Sedor, S.F., Shao, S. nature comm 2025, Swickley, G., Bloch, Y., Malka, L. et al 2020 BMC Mol and Cell Biol). These inconsistencies raise concerns about whether the observed stoichiometries are physiologically relevant or artifacts of in vitro reconstitution, especially since full-length Codanin1 was not studied.

    Unvalidated Functional Claims:

    The manuscript identifies several CDA-I-associated mutations that disrupt CDIN1-Codanin1 interaction. However, the authors do not test how these mutations affect the biological function of the complex, particularly its role in ASF1 sequestration or histone trafficking. Given the central importance of this axis in their disease model, functional validation (e.g., ASF1 localization, histone deposition assays) is necessary to support these mechanistic conclusions.

    Speculative and Potentially Contradictory Model:

    The proposed model suggests that CDIN1 competes with ASF1 for Codanin1 binding, thereby indirectly promoting histone delivery to the nucleus. However, emerging data indicate that Codanin1, CDIN1, and ASF1 can form a stable ternary complex, calling into question this competitive binding hypothesis (Sedor, S.F., Shao, S. nature comm 2025). The authors do not acknowledge or discuss these findings, and the model in its current form may therefore be oversimplified or inaccurate.

    Significance

    Overall, the study adds to our structural understanding of CDIN1 and Codanin1 interactions, but the functional interpretations are currently speculative, and in some cases in conflict with existing literature. The manuscript would benefit significantly from addressing these discrepancies, incorporating relevant data on ASF1, and clarifying whether the observed assemblies reflect physiological complexes.

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    Referee #1

    Evidence, reproducibility and clarity

    This is a rigorous biophysical characterization of a protein-protein interaction relevant to CDA-1 disease. The two proteins were purified in an E. coli host but CD and DLS was performed to ensure that the purified protein is well folded. An impressive native protein EMSA was used to show a 1:1 complex. While common for protein-nucleic acid complexes, EMSAs are much more challenging with protein complexes. A higher-running complex, likely a heterotetramer was implied at higher protein concentrations. These results were supported with SEC-MALS analysis and analytic ultracentrifugation analysis. Thermophoresis and ITC were used to report a nanomolar affinity of the proteins for each other. SEC-SAXS supported the conclusions about stoichiometry and composition inferred from the earlier methods and suggested that the dimerization interface comes from CDIN1. Next HDX-MS was used to identify putative interface residues, which were then mutated in each of the proteins and assessed for binding using coimmunoprecipitation. This study uses at least 10 orthogonal biophysical and/or biochemical methodologies to characterize an important protein-protein interaction and the analysis is clear and so is the writing. I couldn't (reading it once) find any grammatical or other errors in the text or figures. This manuscript is top-quality and suitable for publication.

    Significance

    Such detailed structural and mechanistic studies are greatly lacking in many clinical conditions for which mutations are known (unless they cause cancer, neurodegenerative disease, and so on). We need more such studies on disease topics! This study will be of interest for the hematologic diseases community.

  5. Version published to 10.1101/2023.05.25.542057v3 on bioRxiv
  6. Version published to 10.1101/2023.05.25.542057v2 on bioRxiv
  7. Version published to 10.1101/2023.05.25.542057v1 on bioRxiv