{"gene":"MCMBP","run_date":"2026-06-10T02:59:50","timeline":{"discoveries":[{"year":2010,"finding":"MCM-BP accumulates in nuclei in late S phase and can disassemble the MCM2-7 complex; immunodepletion of MCM-BP in Xenopus egg extracts inhibits replication-dependent MCM dissociation without affecting pre-RC formation or DNA replication, while excess MCM-BP promotes disassembly of MCM2-7 and recombinant MCM-BP releases MCM2-7 from isolated late-S-phase chromatin (activity abolished when replication is blocked). MCM-BP silencing in human cells also delays MCM dissociation in late S phase.","method":"Xenopus egg extract immunodepletion, immunopurification of MCM2-7, recombinant protein incubation with isolated chromatin, human cell siRNA knockdown","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — multiple orthogonal methods (immunodepletion, recombinant protein reconstitution, human cell knockdown) in a single study, replicated across species","pmids":["21196493"],"is_preprint":false},{"year":2010,"finding":"In Xenopus egg extracts, MCM-BP exists in a stable complex with MCM7 but is NOT associated with the full MCM2-7 hexameric complex.","method":"Co-immunoprecipitation from Xenopus egg extracts","journal":"Genes & development","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP in a well-controlled study, single organism/condition","pmids":["21196493"],"is_preprint":false},{"year":2011,"finding":"S. pombe Mcb1 (MCM-BP ortholog) interacts robustly with Mcm3-7 but not Mcm2 by co-immunoprecipitation; overproduction of Mcb1 disrupts association of Mcm2 with other MCM proteins, inhibits DNA replication, causes DNA damage, and activates checkpoint kinase Chk1.","method":"Co-immunoprecipitation, overexpression analysis, cell cycle and checkpoint assays in fission yeast","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP plus functional overexpression phenotype in single lab, fission yeast ortholog","pmids":["21813639"],"is_preprint":false},{"year":2011,"finding":"In fission yeast, the MCM(Mcb1) complex (variant MCM complex with MCM-BP replacing Mcm2) was purified; loss of MCM(Mcb1) function via temperature-sensitive alleles leads to DNA damage accumulation, checkpoint activation, and cell cycle arrest, and evidence for a role in meiosis was obtained.","method":"Protein complex purification, temperature-sensitive allele generation, DNA damage/checkpoint assays in fission yeast","journal":"FEBS letters","confidence":"Medium","confidence_rationale":"Tier 1–2 / Moderate — biochemical purification plus genetic temperature-sensitive alleles in single lab","pmids":["22036784"],"is_preprint":false},{"year":2012,"finding":"Human MCM-BP interacts with individual MCM proteins 2–7 when co-expressed in insect cells; glycerol gradient sedimentation shows MCM-BP interacts most strongly with MCM4 and MCM7; large MCM-BP–MCM complexes form specifically at mid-to-late S phase in human cells.","method":"Insect cell co-expression, glycerol gradient sedimentation, co-immunoprecipitation from human cells","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal biochemical methods in single lab","pmids":["22540012"],"is_preprint":false},{"year":2012,"finding":"Human MCM-BP interacts with Dbf4, the regulatory subunit of DDK kinase, verified by yeast 2-hybrid, insect cell co-expression, and co-immunoprecipitation of endogenous proteins; in vitro kinase assays showed MCM-BP is not a DDK substrate but inhibits DDK phosphorylation of MCM4,6,7 within MCM4,6,7 or MCM2-7 complexes, with little effect on DDK phosphorylation of MCM2.","method":"Yeast 2-hybrid, insect cell co-expression, co-immunoprecipitation of endogenous proteins, in vitro kinase assay","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — three orthogonal interaction methods plus in vitro kinase assay with defined substrate specificity, single lab","pmids":["22540012"],"is_preprint":false},{"year":2012,"finding":"Depletion of MCM-BP by shRNA in human cells results in highly abnormal nuclear morphology, centrosome amplification, transient G2 checkpoint activation, slowed G2 progression, increased RPA foci (replication stress), and increased cellular MCM protein levels. Abnormal nuclear morphology was rescued by shRNA-resistant MCM-BP and was not seen with depletion of other MCM proteins.","method":"Stable shRNA knockdown in human cells, rescue experiment with shRNA-resistant construct, flow cytometry, immunofluorescence","journal":"Journal of cell science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — KD with rescue, multiple phenotypic readouts, single lab","pmids":["22250201"],"is_preprint":false},{"year":2013,"finding":"Fission yeast Mcb1 continuously interacts with MCM proteins throughout the cell cycle in vivo and can interact with any individual MCM subunit in vitro; temperature-sensitive mcb1 mutants are suppressed by multicopy mcm5+ and show reduced Mcm7 loading onto replication origins, delayed S-phase progression, and redistribution of MCM subunits to the cytoplasm via active nuclear export. CDK modulation (Cig2 repression or Rum1 overproduction) suppressed mcb1(ts) mutants, implicating Mcb1 in pre-RC formation.","method":"Co-immunoprecipitation, in vitro binding, temperature-sensitive allele genetic analysis, multicopy suppressor screen, chromatin immunoprecipitation (Mcm7 loading), fluorescence microscopy for localization","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — multiple orthogonal methods (in vitro binding, in vivo Co-IP, genetic epistasis, ChIP, localization) in single focused study on fission yeast ortholog","pmids":["23322785"],"is_preprint":false},{"year":2014,"finding":"Both MCMBP knockdown and overexpression in breast and colorectal cell lines leads to emergence of a subpopulation of cells with abnormal nuclear morphology, attributed to aberrant sister chromatid cohesion events.","method":"siRNA knockdown, overexpression in human cell lines, nuclear morphology analysis","journal":"Neoplasia (New York, N.Y.)","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, single method per condition, no mechanistic pathway placement beyond morphology phenotype","pmids":["25246271"],"is_preprint":false},{"year":2022,"finding":"MCMBP associates with MCM3 and is critical for assembly of the MCM2-7 hexamer using nascent MCM3; acute depletion of MCMBP reduces MCM2-7 hexamer levels, reduces replication licensing, and causes p53-dependent G1 arrest or DNA damage accumulation and loss of viability in p53-null cells.","method":"Acute protein depletion (auxin-inducible degron), co-immunoprecipitation, flow cytometry, DNA damage markers, cell viability assays in human cells","journal":"eLife","confidence":"High","confidence_rationale":"Tier 2 / Strong — acute depletion system plus Co-IP plus multiple orthogonal phenotypic readouts in human cells; multiple genetic backgrounds tested","pmids":["35438632"],"is_preprint":false},{"year":2025,"finding":"CRL4DCAF12 ubiquitin ligase facilitates the degradation of MCMBP in the nucleus; during MCM biogenesis, MCMBP facilitates assembly and nuclear transport of nascent MCM3-7 subcomplexes, but must be removed (via CRL4DCAF12-mediated degradation) to allow MCM2 incorporation into the MCM3-7 subcomplex. Absence of CRL4DCAF12 reduces chromatin-bound nascent MCMs and causes accelerated replication forks and replication stress.","method":"CRL4DCAF12 knockout/depletion, MCMBP protein stability assays, chromatin fractionation, replication fork speed measurement, co-immunoprecipitation in human cells","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (genetic KO, protein degradation assays, chromatin fractionation, replication fork assays) establishing a defined molecular mechanism in a peer-reviewed study","pmids":["41145411"],"is_preprint":false},{"year":2024,"finding":"Selective deletion of MCMBP in neural progenitor radial glial cells accelerates replication fork speed, causes DNA damage, micronuclei formation, p53 activation, and microcephaly; concurrent Trp53 and Mcmbp deletion further increases fork speed and causes RGC detachment. MCM3 was found to coordinate DNA and centrosome duplication, mediating RGC attachment.","method":"Conditional knockout in mouse neural progenitors, DNA fiber assay (fork speed), immunofluorescence, p53 pathway analysis","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — conditional KO with multiple readouts in mouse model; preprint, not yet peer-reviewed","pmids":[],"is_preprint":true}],"current_model":"MCMBP (MCM-BP) is a chaperone and regulator of the MCM2-7 replicative helicase: it associates preferentially with MCM3 (and MCM3-7 subcomplexes) to facilitate assembly and nuclear transport of nascent MCM2-7 hexamers, inhibits DDK (Dbf4-dependent kinase) phosphorylation of MCM4,6,7, accumulates on chromatin in late S phase to promote unloading/disassembly of MCM2-7 after replication, and is itself degraded by the CRL4DCAF12 ubiquitin ligase once MCM2 has been incorporated into the MCM3-7 subcomplex, thereby controlling the balance between nascent and parental MCM pools and maintaining genome stability."},"narrative":{"mechanistic_narrative":"MCMBP (MCM-BP) is a dedicated chaperone and regulator of the MCM2-7 replicative helicase that governs the assembly, nuclear delivery, and turnover of MCM subcomplexes to maintain replication licensing fidelity and genome stability [PMID:35438632, PMID:21196493]. It associates preferentially with MCM3 and MCM3-7 subcomplexes — interacting with individual MCM subunits but not the intact MCM2-7 hexamer — and uses nascent MCM3 to template hexamer assembly, such that acute MCMBP depletion lowers MCM2-7 levels, reduces licensing, and triggers p53-dependent G1 arrest or, in p53-null cells, DNA damage and loss of viability [PMID:35438632, PMID:21196493, PMID:22540012]. During biogenesis MCMBP facilitates assembly and nuclear transport of MCM3-7 subcomplexes and is then removed by the CRL4DCAF12 ubiquitin ligase to permit MCM2 incorporation; loss of this ligase reduces chromatin-bound nascent MCMs and produces accelerated forks and replication stress [PMID:41145411]. In addition to its biogenesis role, MCMBP accumulates in nuclei in late S phase and promotes the replication-dependent disassembly of MCM2-7 from chromatin, and it inhibits DDK (via direct binding to its Dbf4 subunit) phosphorylation of MCM4,6,7 without itself being a DDK substrate [PMID:21196493, PMID:22540012]. Loss of MCMBP function causes abnormal nuclear morphology, centrosome amplification, replication stress, and DNA-damage checkpoint activation across human cells and yeast orthologs [PMID:22250201, PMID:21813639, PMID:23322785], establishing it as a balance point between nascent and parental MCM pools.","teleology":[{"year":2010,"claim":"Established that MCM-BP is a late-S-phase factor that actively disassembles the MCM2-7 helicase from chromatin, defining a regulated unloading step distinct from licensing.","evidence":"Xenopus egg extract immunodepletion, recombinant protein on isolated chromatin, and human cell siRNA knockdown","pmids":["21196493"],"confidence":"High","gaps":["Did not define how MCM-BP recognizes replicated versus unreplicated chromatin","Mechanism of helicase disassembly not resolved at the molecular level"]},{"year":2010,"claim":"Showed MCM-BP forms a stable complex with MCM7 but not the intact MCM2-7 hexamer, indicating it engages MCM subunits in a subcomplex rather than the assembled helicase.","evidence":"Reciprocal co-immunoprecipitation from Xenopus egg extracts","pmids":["21196493"],"confidence":"Medium","gaps":["Single organism/condition","Did not establish whether the MCM7 interaction reflects assembly or disassembly intermediates"]},{"year":2011,"claim":"Defined the binding selectivity of the ortholog for Mcm3-7 (excluding Mcm2) and showed that excess MCM-BP disrupts Mcm2 association, links the protein to replication and checkpoint control.","evidence":"Co-IP and overexpression with checkpoint/cell-cycle assays in fission yeast; protein complex purification with temperature-sensitive alleles","pmids":["21813639","22036784"],"confidence":"Medium","gaps":["Whether the Mcm2-excluding subcomplex is an assembly or disassembly intermediate not resolved","Meiotic role only preliminarily characterized"]},{"year":2012,"claim":"Identified a direct mechanism by which MCM-BP restrains helicase activation: it binds DDK's Dbf4 subunit and inhibits DDK phosphorylation of MCM4,6,7 without being a substrate itself.","evidence":"Yeast 2-hybrid, insect-cell co-expression, endogenous co-IP, and in vitro kinase assays","pmids":["22540012"],"confidence":"High","gaps":["Whether DDK inhibition occurs on chromatin in vivo not established","Functional consequence of MCM2 escaping inhibition unclear"]},{"year":2012,"claim":"Demonstrated that loss of MCM-BP produces genome-instability phenotypes — abnormal nuclei, centrosome amplification, and replication stress — specific to MCM-BP rather than other MCM subunits.","evidence":"shRNA knockdown with shRNA-resistant rescue, flow cytometry, and immunofluorescence in human cells","pmids":["22250201"],"confidence":"Medium","gaps":["Did not separate replication-licensing defects from disassembly defects as the cause of phenotypes","Centrosome amplification mechanism unexplained"]},{"year":2013,"claim":"Placed the ortholog upstream in pre-RC formation, showing it interacts with MCMs throughout the cycle, supports Mcm7 origin loading, and controls MCM nuclear retention.","evidence":"Co-IP, in vitro binding, temperature-sensitive genetics, multicopy suppressor screen, ChIP, and localization microscopy in fission yeast","pmids":["23322785"],"confidence":"High","gaps":["Reconciliation of pre-RC (assembly) and disassembly roles not fully resolved","Direct nuclear-import mechanism not defined"]},{"year":2014,"claim":"Linked MCMBP dosage perturbation to abnormal nuclear morphology via aberrant sister chromatid cohesion in cancer cell lines.","evidence":"siRNA knockdown and overexpression with nuclear morphology analysis in breast and colorectal cells","pmids":["25246271"],"confidence":"Low","gaps":["Single method per condition with no mechanistic placement beyond morphology","Cohesion link not validated biochemically"]},{"year":2022,"claim":"Resolved MCMBP's core function as an MCM3-anchored hexamer-assembly chaperone, showing acute loss collapses MCM2-7 levels and licensing with p53-dependent outcomes.","evidence":"Auxin-inducible degron depletion, co-IP, flow cytometry, DNA-damage markers, and viability assays in human cells","pmids":["35438632"],"confidence":"High","gaps":["Structural basis of MCM3 recognition not defined","Relationship between assembly role and the earlier disassembly role not unified"]},{"year":2025,"claim":"Defined MCMBP turnover control: CRL4DCAF12 degrades MCMBP to allow MCM2 incorporation into the MCM3-7 subcomplex, tying ligase loss to accelerated forks and replication stress.","evidence":"CRL4DCAF12 knockout/depletion, MCMBP stability assays, chromatin fractionation, and fork-speed measurement in human cells","pmids":["41145411"],"confidence":"High","gaps":["Degron and recognition determinants on MCMBP not mapped","How removal timing is coupled to MCM2 availability unresolved"]},{"year":2024,"claim":"Extended MCMBP function to an in vivo developmental context, linking its loss to fork acceleration, p53 activation, and microcephaly in neural progenitors.","evidence":"Conditional knockout in mouse neural progenitors, DNA fiber assay, immunofluorescence, p53 analysis (preprint)","pmids":[],"confidence":"Medium","gaps":["Preprint, not yet peer-reviewed","Direct molecular cause of fork acceleration not established","Whether centrosome/RGC attachment defects are MCM3-specific or MCMBP-dependent unclear"]},{"year":null,"claim":"How the assembly-chaperone and chromatin-disassembly activities are mechanistically partitioned, and the structural basis for MCMBP's subunit-selective binding, remain unresolved.","evidence":"","pmids":[],"confidence":"High","gaps":["No structure of MCMBP bound to MCM subunits","No reconstitution distinguishing assembly versus disassembly modes","Recruitment determinants to late-S chromatin undefined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0044183","term_label":"protein folding chaperone","supporting_discovery_ids":[9,0,10]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[5,0]},{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[1,4,2]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0,10]},{"term_id":"GO:0000228","term_label":"nuclear chromosome","supporting_discovery_ids":[0,10]}],"pathway":[{"term_id":"R-HSA-69306","term_label":"DNA Replication","supporting_discovery_ids":[9,0,10]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[6,9]}],"complexes":["MCM2-7 helicase","MCM(Mcb1) variant MCM complex"],"partners":["MCM3","MCM7","MCM4","DBF4","MCM2","DCAF12"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9BTE3","full_name":"Mini-chromosome maintenance complex-binding protein","aliases":[],"length_aa":642,"mass_kda":73.0,"function":"Associated component of the MCM complex that acts as a regulator of DNA replication. Binds to the MCM complex during late S phase and promotes the disassembly of the MCM complex from chromatin, thereby acting as a key regulator of pre-replication complex (pre-RC) unloading from replicated DNA. Can dissociate the MCM complex without addition of ATP; probably acts by destabilizing interactions of each individual subunits of the MCM complex. Required for sister chromatid cohesion","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/Q9BTE3/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/MCMBP","classification":"Common Essential","n_dependent_lines":837,"n_total_lines":1208,"dependency_fraction":0.6928807947019867},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"FKBP5","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/MCMBP","total_profiled":1310},"omim":[{"mim_id":"610909","title":"MINICHROMOSOME MAINTENANCE COMPLEX-BINDING PROTEIN; MCMBP","url":"https://www.omim.org/entry/610909"},{"mim_id":"602696","title":"MINICHROMOSOME MAINTENANCE COMPLEX COMPONENT 5; MCM5","url":"https://www.omim.org/entry/602696"},{"mim_id":"602693","title":"MINICHROMOSOME MAINTENANCE COMPLEX COMPONENT 3; MCM3","url":"https://www.omim.org/entry/602693"},{"mim_id":"602638","title":"MINICHROMOSOME MAINTENANCE COMPLEX COMPONENT 4; MCM4","url":"https://www.omim.org/entry/602638"},{"mim_id":"601806","title":"MINICHROMOSOME MAINTENANCE COMPLEX COMPONENT 6; MCM6","url":"https://www.omim.org/entry/601806"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Cell Junctions","reliability":"Additional"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/MCMBP"},"hgnc":{"alias_symbol":["FLJ13081","MCM-BP"],"prev_symbol":["C10orf119"]},"alphafold":{"accession":"Q9BTE3","domains":[{"cath_id":"2.40.50.140","chopping":"11-79_124-152_231-265_301-313","consensus_level":"high","plddt":89.0655,"start":11,"end":313},{"cath_id":"3.40.50.300","chopping":"350-545","consensus_level":"high","plddt":92.0702,"start":350,"end":545},{"cath_id":"-","chopping":"561-642","consensus_level":"medium","plddt":83.7572,"start":561,"end":642}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9BTE3","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9BTE3-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9BTE3-F1-predicted_aligned_error_v6.png","plddt_mean":81.31},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=MCMBP","jax_strain_url":"https://www.jax.org/strain/search?query=MCMBP"},"sequence":{"accession":"Q9BTE3","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9BTE3.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9BTE3/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9BTE3"}},"corpus_meta":[{"pmid":"21196493","id":"PMC_21196493","title":"MCM-BP regulates unloading of the MCM2-7 helicase in late S phase.","date":"2010","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/21196493","citation_count":53,"is_preprint":false},{"pmid":"23451133","id":"PMC_23451133","title":"MCM-BP is required for repression of life-cycle specific genes transcribed by RNA polymerase I in the mammalian infectious form of Trypanosoma brucei.","date":"2013","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/23451133","citation_count":35,"is_preprint":false},{"pmid":"35438632","id":"PMC_35438632","title":"MCMBP promotes the assembly of the MCM2-7 hetero-hexamer to ensure robust DNA replication in human cells.","date":"2022","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/35438632","citation_count":25,"is_preprint":false},{"pmid":"30407533","id":"PMC_30407533","title":"Genome-wide function of MCM-BP in Trypanosoma brucei DNA replication and transcription.","date":"2019","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/30407533","citation_count":19,"is_preprint":false},{"pmid":"21813639","id":"PMC_21813639","title":"Schizosaccharomyces pombe minichromosome maintenance-binding protein (MCM-BP) antagonizes MCM helicase.","date":"2011","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/21813639","citation_count":19,"is_preprint":false},{"pmid":"22250201","id":"PMC_22250201","title":"The MCM-associated protein MCM-BP is important for human nuclear morphology.","date":"2012","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/22250201","citation_count":17,"is_preprint":false},{"pmid":"23322785","id":"PMC_23322785","title":"The fission yeast minichromosome maintenance (MCM)-binding protein (MCM-BP), Mcb1, regulates MCM function during prereplicative complex formation in DNA replication.","date":"2013","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/23322785","citation_count":16,"is_preprint":false},{"pmid":"22540012","id":"PMC_22540012","title":"Interactions of the human MCM-BP protein with MCM complex components and Dbf4.","date":"2012","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/22540012","citation_count":14,"is_preprint":false},{"pmid":"25246271","id":"PMC_25246271","title":"Deregulation of the replisome factor MCMBP prompts oncogenesis in colorectal carcinomas through chromosomal instability.","date":"2014","source":"Neoplasia (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/25246271","citation_count":12,"is_preprint":false},{"pmid":"22036784","id":"PMC_22036784","title":"Purification and functional inactivation of the fission yeast MCM(MCM-BP) complex.","date":"2011","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/22036784","citation_count":11,"is_preprint":false},{"pmid":"41145411","id":"PMC_41145411","title":"CRL4DCAF12 regulation of MCMBP ensures optimal licensing of DNA replication.","date":"2025","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/41145411","citation_count":1,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.11.26.625391","title":"CRL4  <sup>DCAF12</sup>  regulation of MCMBP ensures optimal licensing of DNA replication","date":"2024-11-28","source":"bioRxiv","url":"https://doi.org/10.1101/2024.11.26.625391","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.11.05.622174","title":"DNA replication fork speed Acts as a Pacer in Cortical Neurogenesis","date":"2024-11-05","source":"bioRxiv","url":"https://doi.org/10.1101/2024.11.05.622174","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":7636,"output_tokens":3048,"usd":0.034314,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10518,"output_tokens":3479,"usd":0.069782,"stage2_stop_reason":"end_turn"},"total_usd":0.104096,"stage1_batch_id":"msgbatch_01BbTCMyrRPyhtEq6b1MdwCN","stage2_batch_id":"msgbatch_011dEed5bbxYvTAaQWKJevxu","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2010,\n      \"finding\": \"MCM-BP accumulates in nuclei in late S phase and can disassemble the MCM2-7 complex; immunodepletion of MCM-BP in Xenopus egg extracts inhibits replication-dependent MCM dissociation without affecting pre-RC formation or DNA replication, while excess MCM-BP promotes disassembly of MCM2-7 and recombinant MCM-BP releases MCM2-7 from isolated late-S-phase chromatin (activity abolished when replication is blocked). MCM-BP silencing in human cells also delays MCM dissociation in late S phase.\",\n      \"method\": \"Xenopus egg extract immunodepletion, immunopurification of MCM2-7, recombinant protein incubation with isolated chromatin, human cell siRNA knockdown\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — multiple orthogonal methods (immunodepletion, recombinant protein reconstitution, human cell knockdown) in a single study, replicated across species\",\n      \"pmids\": [\"21196493\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"In Xenopus egg extracts, MCM-BP exists in a stable complex with MCM7 but is NOT associated with the full MCM2-7 hexameric complex.\",\n      \"method\": \"Co-immunoprecipitation from Xenopus egg extracts\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP in a well-controlled study, single organism/condition\",\n      \"pmids\": [\"21196493\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"S. pombe Mcb1 (MCM-BP ortholog) interacts robustly with Mcm3-7 but not Mcm2 by co-immunoprecipitation; overproduction of Mcb1 disrupts association of Mcm2 with other MCM proteins, inhibits DNA replication, causes DNA damage, and activates checkpoint kinase Chk1.\",\n      \"method\": \"Co-immunoprecipitation, overexpression analysis, cell cycle and checkpoint assays in fission yeast\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP plus functional overexpression phenotype in single lab, fission yeast ortholog\",\n      \"pmids\": [\"21813639\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"In fission yeast, the MCM(Mcb1) complex (variant MCM complex with MCM-BP replacing Mcm2) was purified; loss of MCM(Mcb1) function via temperature-sensitive alleles leads to DNA damage accumulation, checkpoint activation, and cell cycle arrest, and evidence for a role in meiosis was obtained.\",\n      \"method\": \"Protein complex purification, temperature-sensitive allele generation, DNA damage/checkpoint assays in fission yeast\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — biochemical purification plus genetic temperature-sensitive alleles in single lab\",\n      \"pmids\": [\"22036784\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Human MCM-BP interacts with individual MCM proteins 2–7 when co-expressed in insect cells; glycerol gradient sedimentation shows MCM-BP interacts most strongly with MCM4 and MCM7; large MCM-BP–MCM complexes form specifically at mid-to-late S phase in human cells.\",\n      \"method\": \"Insect cell co-expression, glycerol gradient sedimentation, co-immunoprecipitation from human cells\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal biochemical methods in single lab\",\n      \"pmids\": [\"22540012\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Human MCM-BP interacts with Dbf4, the regulatory subunit of DDK kinase, verified by yeast 2-hybrid, insect cell co-expression, and co-immunoprecipitation of endogenous proteins; in vitro kinase assays showed MCM-BP is not a DDK substrate but inhibits DDK phosphorylation of MCM4,6,7 within MCM4,6,7 or MCM2-7 complexes, with little effect on DDK phosphorylation of MCM2.\",\n      \"method\": \"Yeast 2-hybrid, insect cell co-expression, co-immunoprecipitation of endogenous proteins, in vitro kinase assay\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — three orthogonal interaction methods plus in vitro kinase assay with defined substrate specificity, single lab\",\n      \"pmids\": [\"22540012\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Depletion of MCM-BP by shRNA in human cells results in highly abnormal nuclear morphology, centrosome amplification, transient G2 checkpoint activation, slowed G2 progression, increased RPA foci (replication stress), and increased cellular MCM protein levels. Abnormal nuclear morphology was rescued by shRNA-resistant MCM-BP and was not seen with depletion of other MCM proteins.\",\n      \"method\": \"Stable shRNA knockdown in human cells, rescue experiment with shRNA-resistant construct, flow cytometry, immunofluorescence\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KD with rescue, multiple phenotypic readouts, single lab\",\n      \"pmids\": [\"22250201\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Fission yeast Mcb1 continuously interacts with MCM proteins throughout the cell cycle in vivo and can interact with any individual MCM subunit in vitro; temperature-sensitive mcb1 mutants are suppressed by multicopy mcm5+ and show reduced Mcm7 loading onto replication origins, delayed S-phase progression, and redistribution of MCM subunits to the cytoplasm via active nuclear export. CDK modulation (Cig2 repression or Rum1 overproduction) suppressed mcb1(ts) mutants, implicating Mcb1 in pre-RC formation.\",\n      \"method\": \"Co-immunoprecipitation, in vitro binding, temperature-sensitive allele genetic analysis, multicopy suppressor screen, chromatin immunoprecipitation (Mcm7 loading), fluorescence microscopy for localization\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — multiple orthogonal methods (in vitro binding, in vivo Co-IP, genetic epistasis, ChIP, localization) in single focused study on fission yeast ortholog\",\n      \"pmids\": [\"23322785\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Both MCMBP knockdown and overexpression in breast and colorectal cell lines leads to emergence of a subpopulation of cells with abnormal nuclear morphology, attributed to aberrant sister chromatid cohesion events.\",\n      \"method\": \"siRNA knockdown, overexpression in human cell lines, nuclear morphology analysis\",\n      \"journal\": \"Neoplasia (New York, N.Y.)\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single method per condition, no mechanistic pathway placement beyond morphology phenotype\",\n      \"pmids\": [\"25246271\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"MCMBP associates with MCM3 and is critical for assembly of the MCM2-7 hexamer using nascent MCM3; acute depletion of MCMBP reduces MCM2-7 hexamer levels, reduces replication licensing, and causes p53-dependent G1 arrest or DNA damage accumulation and loss of viability in p53-null cells.\",\n      \"method\": \"Acute protein depletion (auxin-inducible degron), co-immunoprecipitation, flow cytometry, DNA damage markers, cell viability assays in human cells\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — acute depletion system plus Co-IP plus multiple orthogonal phenotypic readouts in human cells; multiple genetic backgrounds tested\",\n      \"pmids\": [\"35438632\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"CRL4DCAF12 ubiquitin ligase facilitates the degradation of MCMBP in the nucleus; during MCM biogenesis, MCMBP facilitates assembly and nuclear transport of nascent MCM3-7 subcomplexes, but must be removed (via CRL4DCAF12-mediated degradation) to allow MCM2 incorporation into the MCM3-7 subcomplex. Absence of CRL4DCAF12 reduces chromatin-bound nascent MCMs and causes accelerated replication forks and replication stress.\",\n      \"method\": \"CRL4DCAF12 knockout/depletion, MCMBP protein stability assays, chromatin fractionation, replication fork speed measurement, co-immunoprecipitation in human cells\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (genetic KO, protein degradation assays, chromatin fractionation, replication fork assays) establishing a defined molecular mechanism in a peer-reviewed study\",\n      \"pmids\": [\"41145411\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Selective deletion of MCMBP in neural progenitor radial glial cells accelerates replication fork speed, causes DNA damage, micronuclei formation, p53 activation, and microcephaly; concurrent Trp53 and Mcmbp deletion further increases fork speed and causes RGC detachment. MCM3 was found to coordinate DNA and centrosome duplication, mediating RGC attachment.\",\n      \"method\": \"Conditional knockout in mouse neural progenitors, DNA fiber assay (fork speed), immunofluorescence, p53 pathway analysis\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — conditional KO with multiple readouts in mouse model; preprint, not yet peer-reviewed\",\n      \"pmids\": [],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"MCMBP (MCM-BP) is a chaperone and regulator of the MCM2-7 replicative helicase: it associates preferentially with MCM3 (and MCM3-7 subcomplexes) to facilitate assembly and nuclear transport of nascent MCM2-7 hexamers, inhibits DDK (Dbf4-dependent kinase) phosphorylation of MCM4,6,7, accumulates on chromatin in late S phase to promote unloading/disassembly of MCM2-7 after replication, and is itself degraded by the CRL4DCAF12 ubiquitin ligase once MCM2 has been incorporated into the MCM3-7 subcomplex, thereby controlling the balance between nascent and parental MCM pools and maintaining genome stability.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"MCMBP (MCM-BP) is a dedicated chaperone and regulator of the MCM2-7 replicative helicase that governs the assembly, nuclear delivery, and turnover of MCM subcomplexes to maintain replication licensing fidelity and genome stability [#9, #0]. It associates preferentially with MCM3 and MCM3-7 subcomplexes — interacting with individual MCM subunits but not the intact MCM2-7 hexamer — and uses nascent MCM3 to template hexamer assembly, such that acute MCMBP depletion lowers MCM2-7 levels, reduces licensing, and triggers p53-dependent G1 arrest or, in p53-null cells, DNA damage and loss of viability [#9, #1, #4]. During biogenesis MCMBP facilitates assembly and nuclear transport of MCM3-7 subcomplexes and is then removed by the CRL4DCAF12 ubiquitin ligase to permit MCM2 incorporation; loss of this ligase reduces chromatin-bound nascent MCMs and produces accelerated forks and replication stress [#10]. In addition to its biogenesis role, MCMBP accumulates in nuclei in late S phase and promotes the replication-dependent disassembly of MCM2-7 from chromatin, and it inhibits DDK (via direct binding to its Dbf4 subunit) phosphorylation of MCM4,6,7 without itself being a DDK substrate [#0, #5]. Loss of MCMBP function causes abnormal nuclear morphology, centrosome amplification, replication stress, and DNA-damage checkpoint activation across human cells and yeast orthologs [#6, #2, #7], establishing it as a balance point between nascent and parental MCM pools.\"\n,\n  \"teleology\": [\n    {\n      \"year\": 2010,\n      \"claim\": \"Established that MCM-BP is a late-S-phase factor that actively disassembles the MCM2-7 helicase from chromatin, defining a regulated unloading step distinct from licensing.\",\n      \"evidence\": \"Xenopus egg extract immunodepletion, recombinant protein on isolated chromatin, and human cell siRNA knockdown\",\n      \"pmids\": [\"21196493\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define how MCM-BP recognizes replicated versus unreplicated chromatin\", \"Mechanism of helicase disassembly not resolved at the molecular level\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Showed MCM-BP forms a stable complex with MCM7 but not the intact MCM2-7 hexamer, indicating it engages MCM subunits in a subcomplex rather than the assembled helicase.\",\n      \"evidence\": \"Reciprocal co-immunoprecipitation from Xenopus egg extracts\",\n      \"pmids\": [\"21196493\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single organism/condition\", \"Did not establish whether the MCM7 interaction reflects assembly or disassembly intermediates\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Defined the binding selectivity of the ortholog for Mcm3-7 (excluding Mcm2) and showed that excess MCM-BP disrupts Mcm2 association, links the protein to replication and checkpoint control.\",\n      \"evidence\": \"Co-IP and overexpression with checkpoint/cell-cycle assays in fission yeast; protein complex purification with temperature-sensitive alleles\",\n      \"pmids\": [\"21813639\", \"22036784\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether the Mcm2-excluding subcomplex is an assembly or disassembly intermediate not resolved\", \"Meiotic role only preliminarily characterized\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Identified a direct mechanism by which MCM-BP restrains helicase activation: it binds DDK's Dbf4 subunit and inhibits DDK phosphorylation of MCM4,6,7 without being a substrate itself.\",\n      \"evidence\": \"Yeast 2-hybrid, insect-cell co-expression, endogenous co-IP, and in vitro kinase assays\",\n      \"pmids\": [\"22540012\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether DDK inhibition occurs on chromatin in vivo not established\", \"Functional consequence of MCM2 escaping inhibition unclear\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Demonstrated that loss of MCM-BP produces genome-instability phenotypes — abnormal nuclei, centrosome amplification, and replication stress — specific to MCM-BP rather than other MCM subunits.\",\n      \"evidence\": \"shRNA knockdown with shRNA-resistant rescue, flow cytometry, and immunofluorescence in human cells\",\n      \"pmids\": [\"22250201\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Did not separate replication-licensing defects from disassembly defects as the cause of phenotypes\", \"Centrosome amplification mechanism unexplained\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Placed the ortholog upstream in pre-RC formation, showing it interacts with MCMs throughout the cycle, supports Mcm7 origin loading, and controls MCM nuclear retention.\",\n      \"evidence\": \"Co-IP, in vitro binding, temperature-sensitive genetics, multicopy suppressor screen, ChIP, and localization microscopy in fission yeast\",\n      \"pmids\": [\"23322785\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Reconciliation of pre-RC (assembly) and disassembly roles not fully resolved\", \"Direct nuclear-import mechanism not defined\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Linked MCMBP dosage perturbation to abnormal nuclear morphology via aberrant sister chromatid cohesion in cancer cell lines.\",\n      \"evidence\": \"siRNA knockdown and overexpression with nuclear morphology analysis in breast and colorectal cells\",\n      \"pmids\": [\"25246271\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single method per condition with no mechanistic placement beyond morphology\", \"Cohesion link not validated biochemically\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Resolved MCMBP's core function as an MCM3-anchored hexamer-assembly chaperone, showing acute loss collapses MCM2-7 levels and licensing with p53-dependent outcomes.\",\n      \"evidence\": \"Auxin-inducible degron depletion, co-IP, flow cytometry, DNA-damage markers, and viability assays in human cells\",\n      \"pmids\": [\"35438632\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of MCM3 recognition not defined\", \"Relationship between assembly role and the earlier disassembly role not unified\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Defined MCMBP turnover control: CRL4DCAF12 degrades MCMBP to allow MCM2 incorporation into the MCM3-7 subcomplex, tying ligase loss to accelerated forks and replication stress.\",\n      \"evidence\": \"CRL4DCAF12 knockout/depletion, MCMBP stability assays, chromatin fractionation, and fork-speed measurement in human cells\",\n      \"pmids\": [\"41145411\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Degron and recognition determinants on MCMBP not mapped\", \"How removal timing is coupled to MCM2 availability unresolved\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Extended MCMBP function to an in vivo developmental context, linking its loss to fork acceleration, p53 activation, and microcephaly in neural progenitors.\",\n      \"evidence\": \"Conditional knockout in mouse neural progenitors, DNA fiber assay, immunofluorescence, p53 analysis (preprint)\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Preprint, not yet peer-reviewed\", \"Direct molecular cause of fork acceleration not established\", \"Whether centrosome/RGC attachment defects are MCM3-specific or MCMBP-dependent unclear\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How the assembly-chaperone and chromatin-disassembly activities are mechanistically partitioned, and the structural basis for MCMBP's subunit-selective binding, remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No structure of MCMBP bound to MCM subunits\", \"No reconstitution distinguishing assembly versus disassembly modes\", \"Recruitment determinants to late-S chromatin undefined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0044183\", \"supporting_discovery_ids\": [9, 0, 10]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [5, 0]},\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [1, 4, 2]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 10]},\n      {\"term_id\": \"GO:0000228\", \"supporting_discovery_ids\": [0, 10]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-69306\", \"supporting_discovery_ids\": [9, 0, 10]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [6, 9]}\n    ],\n    \"complexes\": [\"MCM2-7 helicase\", \"MCM(Mcb1) variant MCM complex\"],\n    \"partners\": [\"MCM3\", \"MCM7\", \"MCM4\", \"DBF4\", \"MCM2\", \"DCAF12\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}