{"gene":"PF3D7_1329300","run_date":"2026-09-08T16:26:55","timeline":{"discoveries":[{"year":2017,"finding":"PF3D7_1329300 (CAF1B) was identified as part of the P. falciparum chromatin assembly factor 1 (CAF1) complex, which interacts with PfCAF2, histones, and PfHP1, and localizes to telomeric repeat regions and subtelomeric/central var gene loci together with PfHP1, implicating it in heterochromatin maintenance and nucleosome assembly as a histone chaperone.","method":"Co-immunoprecipitation (interaction with PfCAF2, histones, PfHP1); chromatin immunoprecipitation (ChIP) at telomeric and var gene loci; upregulation assay after genotoxic treatment (MMS, HU)","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — Co-IP and ChIP from single lab; multiple orthogonal methods (Co-IP, ChIP, genotoxic stress assay) but no in vitro reconstitution or mutagenesis","pmids":["29183721"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2024,"finding":"PF3D7_1329300 (CAF1B) was identified as an interaction partner of the histone methyltransferase PfSET10 in P. falciparum blood-stage nuclei, placing it within a broader chromatin modulation network that includes chromatin remodeling proteins (PfISWI, PfSWIP, PfSNF2L, PfCAF1A) involved in DNA replication, transcription, and mRNA processing.","method":"TurboID proximity-labeling coupled with mass spectrometry (PfSET10-KO/KD lines)","journal":"mSphere","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single-lab proximity-labeling MS; establishes physical association with PfSET10 network but no direct functional characterization of CAF1B itself","pmids":["39445823"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PF3D7_1329300 (CAF1B) is a subunit of the P. falciparum chromatin assembly factor 1 complex that acts as a histone chaperone, interacting with PfCAF2, histones, and PfHP1, localizing to telomeric and var gene heterochromatic loci, and participating in heterochromatin maintenance, nucleosome assembly, and DNA damage responses; it is additionally detected as a proximity interactor of the histone methyltransferase PfSET10 within a broader nuclear chromatin remodeling network."},"narrative":{"mechanistic_narrative":"PF3D7_1329300 (CAF1B) is a subunit of the Plasmodium falciparum chromatin assembly factor 1 (CAF1) complex that functions as a histone chaperone in heterochromatin maintenance and nucleosome assembly [PMID:29183721]. Within this complex it associates with PfCAF2, histones, and the heterochromatin protein PfHP1, and it co-localizes with PfHP1 at telomeric repeat regions and subtelomeric and central var gene loci, linking it to the chromatin organization that underlies var gene silencing [PMID:29183721]. Its upregulation following genotoxic treatment implicates the complex in DNA damage responses [PMID:29183721]. Beyond its CAF1 membership, CAF1B is detected as a proximity interactor of the histone methyltransferase PfSET10 in blood-stage nuclei, placing it within a broader nuclear chromatin-remodeling network [PMID:39445823]. No direct functional characterization of CAF1B itself — through mutagenesis, in vitro reconstitution, or gene disruption — has been reported in the available corpus.","teleology":[{"year":2017,"claim":"Establishing whether PF3D7_1329300 participates in Plasmodium chromatin organization required defining its physical partners and genomic occupancy; this work placed it in the CAF1 histone chaperone complex at heterochromatic loci.","evidence":"Co-immunoprecipitation with PfCAF2, histones, and PfHP1, plus ChIP at telomeric and var gene loci and upregulation after MMS/HU treatment, in P. falciparum","pmids":["29183721"],"confidence":"Medium","gaps":["No in vitro reconstitution or mutagenesis to confirm a direct histone-chaperone activity for CAF1B specifically","Contribution of CAF1B relative to other complex subunits to var gene silencing is not resolved","The mechanistic link between genotoxic upregulation and a defined DNA damage repair role is not established"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2024,"claim":"Whether CAF1B connects to other chromatin-modifying machineries was addressed by proximity mapping around PfSET10, extending its network beyond the CAF1 complex.","evidence":"TurboID proximity-labeling coupled with mass spectrometry in PfSET10-KO/KD lines, in P. falciparum","pmids":["39445823"],"confidence":"Low","gaps":["Proximity labeling establishes association but not a direct or functional CAF1B–PfSET10 interaction","No functional consequence of the CAF1B–PfSET10 association was tested","Does not distinguish a role for CAF1B from other network members detected in the same experiment"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"The intrinsic biochemical activity of CAF1B and its non-redundant contribution to nucleosome assembly, var gene silencing, and DNA damage responses remain undefined.","evidence":"","pmids":[],"confidence":"Low","gaps":["No targeted gene disruption or conditional knockdown of CAF1B itself","No structural or reconstituted-complex data assigning function to CAF1B","Direct histone-binding activity of CAF1B has not been demonstrated in isolation"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["Chromatin assembly factor 1 (CAF1) complex"],"partners":["PFCAF2","HISTONES","PFHP1","PFSET10 (PROXIMITY INTERACTOR)"],"other_free_text":["Co-localizes with PfHP1 at telomeric repeats and subtelomeric/central var gene loci [#0]","Detected within a broader PfSET10 chromatin-remodeling network including PfISWI, PfSWIP, PfSNF2L, and PfCAF1A [#1]","Upregulated after genotoxic treatment (MMS, HU) [#0]"]}},"prefetch_data":{},"corpus_meta":[{"pmid":"29183721","id":"PMC_29183721","title":"Role of Chromatin assembly factor 1 in DNA replication of Plasmodium falciparum.","date":"2017","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/29183721","citation_count":8,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"41417877","id":"","title":"Histone lactylation: A new epigenetic mark in the malaria parasite Plasmodium.","date":"2025","source":"PLoS genetics","url":"https://pubmed.ncbi.nlm.nih.gov/41417877","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["CAF1B"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"39445823","id":"","title":"The Plasmodium falciparum histone methyltransferase SET10 participates in a chromatin modulation network crucial for intraerythrocytic development.","date":"2024","source":"mSphere","url":"https://pubmed.ncbi.nlm.nih.gov/39445823","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["CAF1B"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":5951,"output_tokens":785,"usd":0.014814,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5414,"output_tokens":1787,"usd":0.035873,"stage2_stop_reason":"end_turn"},"total_usd":0.050687,"stage1_batch_id":"msgbatch_01NE1MTa8x1hW7Lo4tAaNzY1","stage2_batch_id":"msgbatch_0141vaQdeFvbo2q39AinvXM9","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2017,\n      \"finding\": \"PF3D7_1329300 (CAF1B) was identified as part of the P. falciparum chromatin assembly factor 1 (CAF1) complex, which interacts with PfCAF2, histones, and PfHP1, and localizes to telomeric repeat regions and subtelomeric/central var gene loci together with PfHP1, implicating it in heterochromatin maintenance and nucleosome assembly as a histone chaperone.\",\n      \"method\": \"Co-immunoprecipitation (interaction with PfCAF2, histones, PfHP1); chromatin immunoprecipitation (ChIP) at telomeric and var gene loci; upregulation assay after genotoxic treatment (MMS, HU)\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — Co-IP and ChIP from single lab; multiple orthogonal methods (Co-IP, ChIP, genotoxic stress assay) but no in vitro reconstitution or mutagenesis\",\n      \"pmids\": [\"29183721\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"PF3D7_1329300 (CAF1B) was identified as an interaction partner of the histone methyltransferase PfSET10 in P. falciparum blood-stage nuclei, placing it within a broader chromatin modulation network that includes chromatin remodeling proteins (PfISWI, PfSWIP, PfSNF2L, PfCAF1A) involved in DNA replication, transcription, and mRNA processing.\",\n      \"method\": \"TurboID proximity-labeling coupled with mass spectrometry (PfSET10-KO/KD lines)\",\n      \"journal\": \"mSphere\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single-lab proximity-labeling MS; establishes physical association with PfSET10 network but no direct functional characterization of CAF1B itself\",\n      \"pmids\": [\"39445823\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"PF3D7_1329300 (CAF1B) is a subunit of the P. falciparum chromatin assembly factor 1 complex that acts as a histone chaperone, interacting with PfCAF2, histones, and PfHP1, localizing to telomeric and var gene heterochromatic loci, and participating in heterochromatin maintenance, nucleosome assembly, and DNA damage responses; it is additionally detected as a proximity interactor of the histone methyltransferase PfSET10 within a broader nuclear chromatin remodeling network.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_1329300 (CAF1B) is a subunit of the Plasmodium falciparum chromatin assembly factor 1 (CAF1) complex that functions as a histone chaperone in heterochromatin maintenance and nucleosome assembly [#0]. Within this complex it associates with PfCAF2, histones, and the heterochromatin protein PfHP1, and it co-localizes with PfHP1 at telomeric repeat regions and subtelomeric and central var gene loci, linking it to the chromatin organization that underlies var gene silencing [#0]. Its upregulation following genotoxic treatment implicates the complex in DNA damage responses [#0]. Beyond its CAF1 membership, CAF1B is detected as a proximity interactor of the histone methyltransferase PfSET10 in blood-stage nuclei, placing it within a broader nuclear chromatin-remodeling network [#1]. No direct functional characterization of CAF1B itself — through mutagenesis, in vitro reconstitution, or gene disruption — has been reported in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2017,\n      \"claim\": \"Establishing whether PF3D7_1329300 participates in Plasmodium chromatin organization required defining its physical partners and genomic occupancy; this work placed it in the CAF1 histone chaperone complex at heterochromatic loci.\",\n      \"evidence\": \"Co-immunoprecipitation with PfCAF2, histones, and PfHP1, plus ChIP at telomeric and var gene loci and upregulation after MMS/HU treatment, in P. falciparum\",\n      \"pmids\": [\"29183721\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No in vitro reconstitution or mutagenesis to confirm a direct histone-chaperone activity for CAF1B specifically\",\n        \"Contribution of CAF1B relative to other complex subunits to var gene silencing is not resolved\",\n        \"The mechanistic link between genotoxic upregulation and a defined DNA damage repair role is not established\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Whether CAF1B connects to other chromatin-modifying machineries was addressed by proximity mapping around PfSET10, extending its network beyond the CAF1 complex.\",\n      \"evidence\": \"TurboID proximity-labeling coupled with mass spectrometry in PfSET10-KO/KD lines, in P. falciparum\",\n      \"pmids\": [\"39445823\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Proximity labeling establishes association but not a direct or functional CAF1B\\u2013PfSET10 interaction\",\n        \"No functional consequence of the CAF1B\\u2013PfSET10 association was tested\",\n        \"Does not distinguish a role for CAF1B from other network members detected in the same experiment\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The intrinsic biochemical activity of CAF1B and its non-redundant contribution to nucleosome assembly, var gene silencing, and DNA damage responses remain undefined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No targeted gene disruption or conditional knockdown of CAF1B itself\",\n        \"No structural or reconstituted-complex data assigning function to CAF1B\",\n        \"Direct histone-binding activity of CAF1B has not been demonstrated in isolation\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140713\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005694\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0000781\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006335\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0070828\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0006974\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"complexes\": [\n      \"Chromatin assembly factor 1 (CAF1) complex\"\n    ],\n    \"partners\": [\n      \"PfCAF2\",\n      \"histones\",\n      \"PfHP1\",\n      \"PfSET10 (proximity interactor)\"\n    ],\n    \"other_free_text\": [\n      \"Co-localizes with PfHP1 at telomeric repeats and subtelomeric/central var gene loci [#0]\",\n      \"Detected within a broader PfSET10 chromatin-remodeling network including PfISWI, PfSWIP, PfSNF2L, and PfCAF1A [#1]\",\n      \"Upregulated after genotoxic treatment (MMS, HU) [#0]\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_1329300","name":null,"product":"chromatin assembly factor 1 subunit B, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1344300","name":null,"product":"chromatin assembly factor 1 subunit B, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_1271100","name":null,"product":"chromatin assembly factor 1 subunit B, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"CAF1B","evaluation":null}