A complex comprising C15ORF41 and Codanin-1: the products of two genes mutated in congenital dyserythropoietic anaemia type I (CDA-I)

Mechanism of ASF1 Inhibition by CDAN1

Codanin-1 (CDAN1) is an essential and ubiquitous protein named after congenital dyserythropoietic anemia type I (CDA-I), an autosomal recessive disease that manifests from mutations in the CDAN1 or CDIN1 (CDAN1 interacting nuclease 1) gene. CDAN1 interacts with CDIN1 and the paralogous histone H3-H4 chaperones ASF1A (Anti-Silencing Function 1A) and ASF1B, but its function remains unclear. Here, we biochemically and structurally analyze CDAN1 complexes. We find that CDAN1 dimerizes and assembles into cytosolic complexes with CDIN1 and multiple copies of ASF1A/B. Single-particle cryogenic electron microscopy (cryo-EM) structures of CDAN1 complexes identify interactions with ASF1 mediated by two CDAN1 B-domains commonly found in ASF1 binding partners and two helices that mimic histone H3 binding. We additionally observe that one CDAN1 can recruit two ASF1 molecules and that ASF1A and ASF1B have different requirements for CDAN1 engagement. Our findings explain how CDAN1 sequesters and inhibits the chaperone function of ASF1A/B and provide new molecular-level insights into this enigmatic complex.

Molecular complex detection in protein interaction networks through reinforcement learning

BACKGROUND

Proteins often assemble into higher-order complexes to perform their biological functions. Such protein-protein interactions (PPI) are often experimentally measured for pairs of proteins and summarized in a weighted PPI network, to which community detection algorithms can be applied to define the various higher-order protein complexes. Current methods include unsupervised and supervised approaches, often assuming that protein complexes manifest only as dense subgraphs. Utilizing supervised approaches, the focus is not on how to find them in a network, but only on learning which subgraphs correspond to complexes, currently solved using heuristics. However, learning to walk trajectories on a network to identify protein complexes leads naturally to a reinforcement learning (RL) approach, a strategy not extensively explored for community detection. Here, we develop and evaluate a reinforcement learning pipeline for community detection on weighted protein-protein interaction networks to detect new protein complexes. The algorithm is trained to calculate the value of different subgraphs encountered while walking on the network to reconstruct known complexes. A distributed prediction algorithm then scales the RL pipeline to search for novel protein complexes on large PPI networks.

RESULTS

The reinforcement learning pipeline is applied to a human PPI network consisting of 8k proteins and 60k PPI, which results in 1,157 protein complexes. The method demonstrated competitive accuracy with improved speed compared to previous algorithms. We highlight protein complexes such as C4orf19, C18orf21, and KIAA1522 which are currently minimally characterized. Additionally, the results suggest TMC04 be a putative additional subunit of the KICSTOR complex and confirm the involvement of C15orf41 in a higher-order complex with HIRA, CDAN1, ASF1A, and by 3D structural modeling.

CONCLUSIONS

Reinforcement learning offers several distinct advantages for community detection, including scalability and knowledge of the walk trajectories defining those communities. Applied to currently available human protein interaction networks, this method had comparable accuracy with other algorithms and notable savings in computational time, and in turn, led to clear predictions of protein function and interactions for several uncharacterized human proteins.

The congenital dyserythropoieitic anemias: genetics and pathophysiology

PURPOSE OF REVIEW

The congenital dyserythropoietic anemias (CDA) are hereditary disorders characterized by ineffective erythropoiesis. This review evaluates newly developed CDA disease models, the latest advances in understanding the pathogenesis of the CDAs, and recently identified CDA genes.

RECENT FINDINGS

Mice exhibiting features of CDAI were recently generated, demonstrating that Codanin-1 (encoded by Cdan1) is essential for primitive erythropoiesis. Additionally, Codanin-1 was found to physically interact with CDIN1, suggesting that mutations in CDAN1 and CDIN1 result in CDAI via a common mechanism. Recent advances in CDAII (which results from SEC23B mutations) have also been made. SEC23B was found to functionally overlap with its paralogous protein, SEC23A, likely explaining the absence of CDAII in SEC23B-deficient mice. In contrast, mice with erythroid-specific deletion of 3 or 4 of the Sec23 alleles exhibited features of CDAII. Increased SEC23A expression rescued the CDAII erythroid defect, suggesting a novel therapeutic strategy for the disease. Additional recent advances included the identification of new CDA genes, RACGAP1 and VPS4A, in CDAIII and a syndromic CDA type, respectively.

SUMMARY

Establishing cellular and animal models of CDA is expected to result in improved understanding of the pathogenesis of these disorders, which may ultimately lead to the development of new therapies.

Recapitulation of erythropoiesis in congenital dyserythropoietic anaemia type I (CDA-I) identifies defects in differentiation and nucleolar abnormalities

The investigation of inherited disorders of erythropoiesis has elucidated many of the principles underlying the production of normal red blood cells and how this is perturbed in human disease. Congenital Dyserythropoietic Anaemia type 1 (CDA-I) is a rare form of anaemia caused by mutations in two genes of unknown function: CDAN1 and CDIN1 (previously called C15orf41), whilst in some cases, the underlying genetic abnormality is completely unknown. Consequently, the pathways affected in CDA-I remain to be discovered. To enable detailed analysis of this rare disorder we have validated a culture system which recapitulates all of the cardinal haematological features of CDA-I, including the formation of the pathognomonic 'spongy' heterochromatin seen by electron microscopy. Using a variety of cell and molecular biological approaches we discovered that erythroid cells in this condition show a delay during terminal erythroid differentiation, associated with increased proliferation and widespread changes in chromatin accessibility. We also show that the proteins encoded by CDAN1 and CDIN1 are enriched in nucleoli which are structurally and functionally abnormal in CDA-I. Together these findings provide important pointers to the pathways affected in CDA-I which for the first time can now be pursued in the tractable culture system utilised here.

Cdan1 Is Essential for Primitive Erythropoiesis

Congenital dyserythropoietic anemia type I (CDA I) is an autosomal recessive disease characterized by moderate to severe macrocytic anemia and pathognomonic morphologic abnormalities of the erythroid precursors, including spongy heterochromatin. The disease is mainly caused by mutations in CDAN1 (encoding for Codanin-1). No patients with homozygous null type mutations have been described, and mouse null mutants die during early embryogenesis prior to the initiation of erythropoiesis. The cellular functions of Codanin-1 and the erythroid specificity of the phenotype remain elusive. To investigate the role of Codanin-1 in erythropoiesis, we crossed mice carrying the Cdan1 floxed allele (Cdan^fl/fl) with mice expressing Cre-recombinase under regulation of the erythropoietin receptor promoter (ErGFPcre). The resulting Cdan^ΔEry transgenic embryos died at mid-gestation (E12.5–E13.5) from severe anemia, with very low numbers of circulating erythroblast. Transmission electron microscopy studies of primitive erythroblasts (E9.5) revealed the pathognomonic spongy heterochromatin. The morphology of Cdan^ΔEry primitive erythroblasts demonstrated progressive development of dyserythropoiesis. Annexin V staining showed increases in both early and late-apoptotic erythroblasts compared to controls. Flow cytometry studies using the erythroid-specific cell-surface markers CD71 and Ter119 demonstrated that Cdan^ΔEry erythroid progenitors do not undergo the semi-synchronous maturation characteristic of primitive erythroblasts. Gene expression studies aimed to evaluate the effect of Cdan1 depletion on erythropoiesis revealed a delay of ζ to α globin switch compared to controls. We also found increased expression of Gata2, Pu.1, and Runx1, which are known to inhibit terminal erythroid differentiation. Consistent with this data, our zebrafish model showed increased gata2 expression upon cdan1 knockdown. In summary, we demonstrated for the first time that Cdan1 is required for primitive erythropoiesis, while providing two experimental models for studying the role of Codanin-1 in erythropoiesis and in the pathogenesis of CDA type I.