{"gene":"NSMCE4A","run_date":"2026-06-10T05:19:52","timeline":{"discoveries":[{"year":2022,"finding":"Human SMC5/6 complex silences episomal DNA transcription via a three-step mechanism: (1) entrapment of episomal DNA dependent on SMC5/6 ATPase activity and a function specific to NSE4A (NSE4B paralog cannot substitute); (2) recruitment to PML nuclear bodies via SLF2; (3) silencing through NSE2 (SUMO ligase activity not required). The related cohesin and condensin complexes fail to bind or silence episomal DNA.","method":"Functional complementation assays distinguishing NSE4A vs NSE4B, ATPase mutant analysis, co-localization studies, episomal transcription reporter assays","journal":"Nature structural & molecular biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (ATPase mutagenesis, paralog substitution, PML body recruitment, functional silencing assays) in a single rigorous study","pmids":["36097294"],"is_preprint":false},{"year":2020,"finding":"NSMCE4A (kleisin subunit of SMC5/6) directly interacts with GPS1, a component of the COP9 signalosome (CSN), as identified by yeast two-hybrid screen and confirmed by co-immunoprecipitation. GPS1 and SMC5/6 components co-localize during interphase and mitosis. Depletion of GPS1 or inhibition of CSN deneddylation activity increased SMC5/6 levels at sites of laser-induced DNA damage, indicating that the CSN complex influences SMC5/6 function during DNA damage response.","method":"Yeast two-hybrid screen, co-immunoprecipitation, co-localization by immunofluorescence, GPS1 depletion and CSN inhibition with laser-induced DNA damage assay","journal":"BMC molecular and cell biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP plus functional readout (SMC5/6 accumulation at damage sites), single lab, two orthogonal methods","pmids":["32384871"],"is_preprint":false},{"year":2025,"finding":"NSMCE4A was identified as a novel interaction partner of TOP3A (topoisomerase 3A) in human cells, as revealed by tandem affinity purification coupled with mass spectrometry.","method":"Tandem affinity purification coupled with mass spectrometry (TAP-MS)","journal":"Molecular & cellular proteomics : MCP","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single AP-MS experiment, no functional validation of the interaction reported","pmids":["41043513"],"is_preprint":false}],"current_model":"NSMCE4A is the kleisin subunit of the SMC5/6 complex that performs a unique and paralog-specific function in entrapping episomal DNA (dependent on SMC5/6 ATPase activity) as the first step of a three-step transcriptional silencing mechanism; it also links the SMC5/6 complex to the COP9 signalosome via direct interaction with GPS1, modulating SMC5/6 accumulation at DNA damage sites, and has been identified as a novel interaction partner of TOP3A."},"narrative":{"mechanistic_narrative":"NSMCE4A is the kleisin subunit of the human SMC5/6 complex and performs a paralog-specific function in transcriptional silencing of episomal DNA [PMID:36097294]. Within a three-step silencing mechanism, NSMCE4A mediates the initial entrapment of episomal DNA in a manner dependent on SMC5/6 ATPase activity, an activity the NSE4B paralog cannot substitute; subsequent steps involve SLF2-dependent recruitment to PML nuclear bodies and silencing through NSE2, distinguishing SMC5/6 from the related cohesin and condensin complexes which neither bind nor silence episomal DNA [PMID:36097294]. NSMCE4A also directly interacts with GPS1, a component of the COP9 signalosome (CSN), and CSN deneddylation activity restrains SMC5/6 accumulation at sites of laser-induced DNA damage, linking the complex to the DNA damage response [PMID:32384871].","teleology":[{"year":2020,"claim":"Establishing how the SMC5/6 complex is regulated during the DNA damage response, this work identified the NSMCE4A kleisin as a direct link between SMC5/6 and the COP9 signalosome.","evidence":"Yeast two-hybrid screen and reciprocal co-immunoprecipitation, co-localization, and GPS1 depletion/CSN inhibition with laser-induced DNA damage in human cells","pmids":["32384871"],"confidence":"Medium","gaps":["Whether the NSMCE4A-GPS1 interaction is direct in vitro or bridged by other CSN/SMC5/6 subunits is not resolved","The neddylation target whose deneddylation modulates SMC5/6 at damage sites is not identified","No structural basis for the interaction"]},{"year":2022,"claim":"Resolving the molecular basis of episomal DNA silencing by SMC5/6, this study assigned NSMCE4A a unique, non-redundant role in ATPase-dependent DNA entrapment within a defined three-step mechanism.","evidence":"Functional complementation distinguishing NSE4A vs NSE4B, ATPase mutant analysis, PML body co-localization, and episomal transcription reporter assays in human cells","pmids":["36097294"],"confidence":"High","gaps":["The structural feature of NSE4A that NSE4B lacks for episomal DNA entrapment is undefined","How episomal DNA is recognized versus chromosomal DNA is not established","Mechanism by which NSE2 enacts silencing downstream of entrapment is unresolved"]},{"year":2025,"claim":"Expanding the interactome of the SMC5/6 kleisin, NSMCE4A was identified as a partner of the topoisomerase TOP3A.","evidence":"Tandem affinity purification coupled with mass spectrometry in human cells","pmids":["41043513"],"confidence":"Low","gaps":["Single AP-MS experiment with no functional validation or reciprocal confirmation","Whether the interaction is direct or part of a larger assembly is unknown","No cellular consequence of the NSMCE4A-TOP3A interaction is reported"]},{"year":null,"claim":"How NSMCE4A coordinates its DNA-entrapment activity with the broader SMC5/6 functions in DNA repair and genome maintenance remains to be defined.","evidence":"","pmids":[],"confidence":"Low","gaps":["No structural model of NSMCE4A within the assembled SMC5/6 complex in the corpus","Functional significance of the TOP3A interaction uncharacterized","Substrate or DNA-feature specificity of NSMCE4A-mediated entrapment unresolved"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[0]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0,1]}],"pathway":[{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[0]}],"complexes":["SMC5/6 complex"],"partners":["GPS1","TOP3A","SLF2","NSE2"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9NXX6","full_name":"Non-structural maintenance of chromosomes element 4 homolog A","aliases":[],"length_aa":385,"mass_kda":44.3,"function":"Component of the SMC5-SMC6 complex, a complex involved in DNA double-strand breaks by homologous recombination. The complex may promote sister chromatid homologous recombination by recruiting the SMC1-SMC3 cohesin complex to double-strand breaks. The complex is required for telomere maintenance via recombination in ALT (alternative lengthening of telomeres) cell lines and mediates sumoylation of shelterin complex (telosome) components which is proposed to lead to shelterin complex disassembly in ALT-associated PML bodies (APBs). Is involved in positive regulation of response to DNA damage stimulus","subcellular_location":"Nucleus; Chromosome, telomere","url":"https://www.uniprot.org/uniprotkb/Q9NXX6/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/NSMCE4A","classification":"Not Classified","n_dependent_lines":434,"n_total_lines":1208,"dependency_fraction":0.35927152317880795},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/NSMCE4A","total_profiled":1310},"omim":[{"mim_id":"617263","title":"NSE1 HOMOLOG, SMC5-SMC6 COMPLEX COMPONENT; NSMCE1","url":"https://www.omim.org/entry/617263"},{"mim_id":"617246","title":"NSE2 (MMS21) HOMOLOG, SMC5-SMC6 COMPLEX SUMO LIGASE; NSMCE2","url":"https://www.omim.org/entry/617246"},{"mim_id":"612987","title":"NSE4 HOMOLOG A, SMC5-SMC6 COMPLEX COMPONENT; NSMCE4A","url":"https://www.omim.org/entry/612987"},{"mim_id":"609145","title":"NEUROFASCIN; NFASC","url":"https://www.omim.org/entry/609145"},{"mim_id":"608243","title":"NSE3 HOMOLOG, SMC5-SMC6 COMPLEX COMPONENT; NSMCE3","url":"https://www.omim.org/entry/608243"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Nucleoplasm","reliability":"Enhanced"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/NSMCE4A"},"hgnc":{"alias_symbol":["FLJ20003","bA500G22.3","NSE4A"],"prev_symbol":["C10orf86"]},"alphafold":{"accession":"Q9NXX6","domains":[{"cath_id":"-","chopping":"75-156","consensus_level":"high","plddt":88.0398,"start":75,"end":156},{"cath_id":"-","chopping":"161-195","consensus_level":"high","plddt":69.1891,"start":161,"end":195},{"cath_id":"1.10.10.580","chopping":"261-337_351-378","consensus_level":"high","plddt":85.6264,"start":261,"end":378}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NXX6","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NXX6-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NXX6-F1-predicted_aligned_error_v6.png","plddt_mean":69.94},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=NSMCE4A","jax_strain_url":"https://www.jax.org/strain/search?query=NSMCE4A"},"sequence":{"accession":"Q9NXX6","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9NXX6.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9NXX6/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NXX6"}},"corpus_meta":[{"pmid":"31036599","id":"PMC_31036599","title":"The SMC5/6 Complex Subunit NSE4A Is Involved in DNA Damage Repair and Seed Development.","date":"2019","source":"The Plant cell","url":"https://pubmed.ncbi.nlm.nih.gov/31036599","citation_count":32,"is_preprint":false},{"pmid":"36097294","id":"PMC_36097294","title":"Smc5/6 silences episomal transcription by a three-step function.","date":"2022","source":"Nature structural & molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/36097294","citation_count":30,"is_preprint":false},{"pmid":"31281324","id":"PMC_31281324","title":"Ultrastructure and Dynamics of Synaptonemal Complex Components During Meiotic Pairing and Synapsis of Standard (A) and Accessory (B) Rye Chromosomes.","date":"2019","source":"Frontiers in plant science","url":"https://pubmed.ncbi.nlm.nih.gov/31281324","citation_count":21,"is_preprint":false},{"pmid":"33875724","id":"PMC_33875724","title":"Induced pluripotent stem cells from subjects with Lesch-Nyhan disease.","date":"2021","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/33875724","citation_count":15,"is_preprint":false},{"pmid":"39315143","id":"PMC_39315143","title":"Developing diagnostic biomarkers for Alzheimer's disease based on histone lactylation-related gene.","date":"2024","source":"Heliyon","url":"https://pubmed.ncbi.nlm.nih.gov/39315143","citation_count":12,"is_preprint":false},{"pmid":"32384871","id":"PMC_32384871","title":"Interaction between NSMCE4A and GPS1 links the SMC5/6 complex to the COP9 signalosome.","date":"2020","source":"BMC molecular and cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/32384871","citation_count":8,"is_preprint":false},{"pmid":"39336750","id":"PMC_39336750","title":"Positive Selection Drives the Evolution of the Structural Maintenance of Chromosomes (SMC) Complexes.","date":"2024","source":"Genes","url":"https://pubmed.ncbi.nlm.nih.gov/39336750","citation_count":4,"is_preprint":false},{"pmid":"41043513","id":"PMC_41043513","title":"Proteomic Analysis of Human Topoisomerases Reveals Their Distinct and Diverse Cellular Functions.","date":"2025","source":"Molecular & cellular proteomics : MCP","url":"https://pubmed.ncbi.nlm.nih.gov/41043513","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":5955,"output_tokens":907,"usd":0.015735,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":7371,"output_tokens":1657,"usd":0.03914,"stage2_stop_reason":"end_turn"},"total_usd":0.054875,"stage1_batch_id":"msgbatch_013a8chtv3AWyTqv4z4sEF4C","stage2_batch_id":"msgbatch_01AHsuW63vinsvuTgzmQ3n62","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2022,\n      \"finding\": \"Human SMC5/6 complex silences episomal DNA transcription via a three-step mechanism: (1) entrapment of episomal DNA dependent on SMC5/6 ATPase activity and a function specific to NSE4A (NSE4B paralog cannot substitute); (2) recruitment to PML nuclear bodies via SLF2; (3) silencing through NSE2 (SUMO ligase activity not required). The related cohesin and condensin complexes fail to bind or silence episomal DNA.\",\n      \"method\": \"Functional complementation assays distinguishing NSE4A vs NSE4B, ATPase mutant analysis, co-localization studies, episomal transcription reporter assays\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (ATPase mutagenesis, paralog substitution, PML body recruitment, functional silencing assays) in a single rigorous study\",\n      \"pmids\": [\"36097294\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"NSMCE4A (kleisin subunit of SMC5/6) directly interacts with GPS1, a component of the COP9 signalosome (CSN), as identified by yeast two-hybrid screen and confirmed by co-immunoprecipitation. GPS1 and SMC5/6 components co-localize during interphase and mitosis. Depletion of GPS1 or inhibition of CSN deneddylation activity increased SMC5/6 levels at sites of laser-induced DNA damage, indicating that the CSN complex influences SMC5/6 function during DNA damage response.\",\n      \"method\": \"Yeast two-hybrid screen, co-immunoprecipitation, co-localization by immunofluorescence, GPS1 depletion and CSN inhibition with laser-induced DNA damage assay\",\n      \"journal\": \"BMC molecular and cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP plus functional readout (SMC5/6 accumulation at damage sites), single lab, two orthogonal methods\",\n      \"pmids\": [\"32384871\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"NSMCE4A was identified as a novel interaction partner of TOP3A (topoisomerase 3A) in human cells, as revealed by tandem affinity purification coupled with mass spectrometry.\",\n      \"method\": \"Tandem affinity purification coupled with mass spectrometry (TAP-MS)\",\n      \"journal\": \"Molecular & cellular proteomics : MCP\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single AP-MS experiment, no functional validation of the interaction reported\",\n      \"pmids\": [\"41043513\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"NSMCE4A is the kleisin subunit of the SMC5/6 complex that performs a unique and paralog-specific function in entrapping episomal DNA (dependent on SMC5/6 ATPase activity) as the first step of a three-step transcriptional silencing mechanism; it also links the SMC5/6 complex to the COP9 signalosome via direct interaction with GPS1, modulating SMC5/6 accumulation at DNA damage sites, and has been identified as a novel interaction partner of TOP3A.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"NSMCE4A is the kleisin subunit of the human SMC5/6 complex and performs a paralog-specific function in transcriptional silencing of episomal DNA [#0]. Within a three-step silencing mechanism, NSMCE4A mediates the initial entrapment of episomal DNA in a manner dependent on SMC5/6 ATPase activity, an activity the NSE4B paralog cannot substitute; subsequent steps involve SLF2-dependent recruitment to PML nuclear bodies and silencing through NSE2, distinguishing SMC5/6 from the related cohesin and condensin complexes which neither bind nor silence episomal DNA [#0]. NSMCE4A also directly interacts with GPS1, a component of the COP9 signalosome (CSN), and CSN deneddylation activity restrains SMC5/6 accumulation at sites of laser-induced DNA damage, linking the complex to the DNA damage response [#1].\",\n  \"teleology\": [\n    {\n      \"year\": 2020,\n      \"claim\": \"Establishing how the SMC5/6 complex is regulated during the DNA damage response, this work identified the NSMCE4A kleisin as a direct link between SMC5/6 and the COP9 signalosome.\",\n      \"evidence\": \"Yeast two-hybrid screen and reciprocal co-immunoprecipitation, co-localization, and GPS1 depletion/CSN inhibition with laser-induced DNA damage in human cells\",\n      \"pmids\": [\"32384871\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"single lab, two orthogonal methods\",\n      \"gaps\": [\n        \"Whether the NSMCE4A-GPS1 interaction is direct in vitro or bridged by other CSN/SMC5/6 subunits is not resolved\",\n        \"The neddylation target whose deneddylation modulates SMC5/6 at damage sites is not identified\",\n        \"No structural basis for the interaction\"\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Resolving the molecular basis of episomal DNA silencing by SMC5/6, this study assigned NSMCE4A a unique, non-redundant role in ATPase-dependent DNA entrapment within a defined three-step mechanism.\",\n      \"evidence\": \"Functional complementation distinguishing NSE4A vs NSE4B, ATPase mutant analysis, PML body co-localization, and episomal transcription reporter assays in human cells\",\n      \"pmids\": [\"36097294\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"The structural feature of NSE4A that NSE4B lacks for episomal DNA entrapment is undefined\",\n        \"How episomal DNA is recognized versus chromosomal DNA is not established\",\n        \"Mechanism by which NSE2 enacts silencing downstream of entrapment is unresolved\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Expanding the interactome of the SMC5/6 kleisin, NSMCE4A was identified as a partner of the topoisomerase TOP3A.\",\n      \"evidence\": \"Tandem affinity purification coupled with mass spectrometry in human cells\",\n      \"pmids\": [\"41043513\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Single AP-MS experiment with no functional validation or reciprocal confirmation\",\n        \"Whether the interaction is direct or part of a larger assembly is unknown\",\n        \"No cellular consequence of the NSMCE4A-TOP3A interaction is reported\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How NSMCE4A coordinates its DNA-entrapment activity with the broader SMC5/6 functions in DNA repair and genome maintenance remains to be defined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No structural model of NSMCE4A within the assembled SMC5/6 complex in the corpus\",\n        \"Functional significance of the TOP3A interaction uncharacterized\",\n        \"Substrate or DNA-feature specificity of NSMCE4A-mediated entrapment unresolved\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"complexes\": [\"SMC5/6 complex\"],\n    \"partners\": [\"GPS1\", \"TOP3A\", \"SLF2\", \"NSE2\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":3,"faith_total":3,"faith_pct":100.0}}