{"id":"8cc28988-0c76-59a1-a52f-5ae97b2abed3","stable_key":"08ce9896-9d1c-5bbf-b705-5bfe771091d5:b7-histone-rare-report","predicate":"reported_rarely_on","statement":"The 2011 study reported natural biotinylation of less than 0.001% of human H3/H4 and argued for rare modification rather than a universal assay artifact.","claim_class":"observational","status":"source_derived_draft","evidence_grade":"ungraded","direction":"context_dependent","is_public":true,"mechanism_event_id":"7f16b18d-6c8f-5110-8f1b-bc2888ae483b","mechanism_event_label":"Later work defended a very rare mark while questioning whether that tiny amount explains biological effects.","subject":{"id":"37a8e96b-f95b-5ba7-a0bc-8ed3cfaf5fd8","slug":"biotin","display_name":"Biotin","entity_type_key":"small_molecule"},"object":{"id":"22263bc3-0a00-59b7-9371-5a420da05660","slug":"human-histone-biotin-detection","display_name":"Detection of biotin on human histones","entity_type_key":"cellular_process"},"evidence_count":1,"mechanism_event":{"id":"7f16b18d-6c8f-5110-8f1b-bc2888ae483b","stable_key":"08ce9896-9d1c-5bbf-b705-5bfe771091d5:b7-histone-rare-report-event","event_type":"observed_intervention","label":"Later work defended a very rare mark while questioning whether that tiny amount explains biological effects.","description":"The 2011 study reported natural biotinylation of less than 0.001% of human H3/H4 and argued for rare modification rather than a universal assay artifact.","status":"provisional","compartment":null,"participants":[{"entity":{"id":"9d6fd008-3b67-5e29-824f-e636b16c8b98","slug":"histone-h4","display_name":"Human histone H4 protein family","entity_type_key":"protein_family"},"role":"candidate modified protein","stoichiometry":null,"state_label":"","sequence_order":0,"notes":""},{"entity":{"id":"2a21d46e-59ef-505a-8c2d-7bcd088dde28","slug":"histone-h3","display_name":"Histone H3","entity_type_key":"protein_family"},"role":"candidate modified protein","stoichiometry":null,"state_label":"","sequence_order":1,"notes":""},{"entity":{"id":"518c7af6-7e78-59ed-a9cb-3de53c9a39c8","slug":"hlcs","display_name":"Human holocarboxylase synthetase / HLCS","entity_type_key":"protein"},"role":"proposed chromatin role","stoichiometry":null,"state_label":"","sequence_order":2,"notes":""},{"entity":{"id":"37a8e96b-f95b-5ba7-a0bc-8ed3cfaf5fd8","slug":"biotin","display_name":"Biotin","entity_type_key":"small_molecule"},"role":"subject","stoichiometry":null,"state_label":"","sequence_order":3,"notes":""},{"entity":{"id":"22263bc3-0a00-59b7-9371-5a420da05660","slug":"human-histone-biotin-detection","display_name":"Detection of biotin on human histones","entity_type_key":"cellular_process"},"role":"target","stoichiometry":null,"state_label":"","sequence_order":4,"notes":""}]},"contexts":[{"dimension":"evidence_span","value_text":"{\"source_cache\": \"artifacts/biotin-research/21930408.abstract.txt\", \"locator\": \"Exact primary indexed abstract; zero-based, end-exclusive Unicode character offsets\", \"file_sha256\": \"51af2341c7be0cb58c57e09784ebb8daabdd98cc93f04be52bb7b04b496e0b91\", \"start_char\": 0, \"end_char\": 1318, \"text_sha256\": \"51af2341c7be0cb58c57e09784ebb8daabdd98cc93f04be52bb7b04b496e0b91\"}","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"experimental_model","value_text":"Multiple antibody, radiotracer and cell-line comparisons of human histone biotinylation","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"exposure","value_text":"Assay comparisons responding to artifact criticism","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"limitations","value_text":"Authors estimated extremely low abundance and proposed HLCS chromatin scaffolding as a working model; nutritional epigenetic benefit was not demonstrated.","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"nutrient_topic","value_text":"Biotin research collection; topical membership is not evidence of a direct dietary effect.","comparator":null,"unit":null,"notes":"","entity":{"slug":"biotin","display_name":"Biotin","entity_type_key":"small_molecule"}},{"dimension":"organism","value_text":"Homo sapiens","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"plain_language","value_text":"Later work defended a very rare mark while questioning whether that tiny amount explains biological effects.","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"primary_references","value_text":"[b7-p21930408] Biotinylation is a natural, albeit rare, modification of human histones. (2011). https://pubmed.ncbi.nlm.nih.gov/21930408/ DOI: 10.1016/j.ymgme.2011.08.030","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"tissue_or_cell_type","value_text":"Human histones H3/H4 in cultured cells","comparator":null,"unit":null,"notes":"","entity":null}],"evidence":[{"id":"7424ade2-25b5-514f-8e5a-83f3573e6758","evidence_kind":"source_excerpt","locator":"Lines 1183-1194","start_line":1183,"end_line":1194,"excerpt":"### b7-histone-rare-report\nThe 2011 study reported natural biotinylation of less than 0.001% of human H3/H4 and argued for rare modification rather than a universal assay artifact.\nCondition category: normal\nnutrient_topic: Biotin research collection; topical membership is not evidence of a direct dietary effect.\nplain_language: Later work defended a very rare mark while questioning whether that tiny amount explains biological effects.\norganism: Homo sapiens\ntissue_or_cell_type: Human histones H3/H4 in cultured cells\nexperimental_model: Multiple antibody, radiotracer and cell-line comparisons of human histone biotinylation\nlimitations: Authors estimated extremely low abundance and proposed HLCS chromatin scaffolding as a working model; nutritional epigenetic benefit was not demonstrated.\nexposure: Assay comparisons responding to artifact criticism\nevidence_span: {\"source_cache\": \"artifacts/biotin-research/21930408.abstract.txt\", \"locator\": \"Exact primary indexed abstract; zero-based, end-exclusive Unicode character offsets\", \"file_sha256\": \"51af2341c7be0cb58c57e09784ebb8daabdd98cc93f04be52bb7b04b496e0b91\", \"start_char\": 0, \"end_char\": 1318, \"text_sha256\": \"51af2341c7be0cb58c57e09784ebb8daabdd98cc93f04be52bb7b04b496e0b91\"}\n[b7-p21930408] Biotinylation is a natural, albeit rare, modification of human histones. (2011). https://pubmed.ncbi.nlm.nih.gov/21930408/ DOI: 10.1016/j.ymgme.2011.08.030","model_system":"Multiple antibody, radiotracer and cell-line comparisons of human histone biotinylation","directness":"author_interpretation","verification_status":"source_derived_draft","notes":"Exact curation-document quotation, not publisher quotation. Study references: [b7-p21930408] Biotinylation is a natural, albeit rare, modification of human histones. (2011). https://pubmed.ncbi.nlm.nih.gov/21930408/ DOI: 10.1016/j.ymgme.2011.08.030","relationship":"supports","weight":1.0,"link_notes":"","source":{"id":"9608806b-adb6-5a35-b042-057147135642","stable_key":"import-08ce9896-9d1c-5bbf-b705-5bfe771091d5","title":"Biotin: carboxylases, recycling, deficiency and nutrient interactions (2026-09-17)","document_type":"imported_text","citation_label":"AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text.","file_path":"","sha256":"a05b23a45e0813ba2fcda0027e3f5d9d58b82858f8dd8598ffb7aca17e942a38","revision_id":"e0d0c2a2-e9e2-55dd-b467-41c22ba960d4","review_status":"unverified_draft","notes":""}}],"relations":[],"conflicts":[{"id":"ed200767-9fee-5883-86e7-8f39cc9c61fe","title":"Histone biotinylation: assay artifact, rare modification, or functional regulator?","kind":"qualification","status":"open","why":"The published studies explicitly dispute the interpretation and specificity of histone-biotin measurements. This is not a conflict between the numerical bounds: less than 0.001% is compatible with less than 0.03%. Peptide assays, antibody specificity, streptavidin binding and radiotracer sensitivity address different parts of the dispute.","resolution":"Retain the competing experiments and assay limitations. Do not describe histone biotinylation as an established abundant epigenetic switch or as evidence that supplements control genes. HLCS chromatin functions and causal roles of rare marks remain research questions.","created_at":"2026-09-17 16:34:00","record_type":"conflict","display_label":"Recorded conflict","record_url":"/conflicts/ed200767-9fee-5883-86e7-8f39cc9c61fe","sides":[{"conflict_id":"ed200767-9fee-5883-86e7-8f39cc9c61fe","ordinal":0,"label":"Early experiments proposed that biotin could also mark histones.","revision_id":"e0d0c2a2-e9e2-55dd-b467-41c22ba960d4","start_line":1157,"end_line":1168,"quote":"### b7-histone-h4-report\nThe 2004 study identified H4 K8/K12 as candidate biotinylation sites in peptide assays and reported K12-biotinylated H4 immunoreactivity in human nuclear extracts.\nCondition category: normal\nnutrient_topic: Biotin research collection; topical membership is not evidence of a direct dietary effect.\nplain_language: Early experiments proposed that biotin could also mark histones.\norganism: Homo sapiens\ntissue_or_cell_type: Synthetic H4 peptides and human cell extracts\nexperimental_model: Synthetic human histone H4 peptide biotinylation and human nuclear-extract immunodetection\nlimitations: Peptide reactions and immunoreactivity do not establish abundant endogenous histone biotinylation; later assay-method work explicitly challenges this interpretation.\nexposure: Biotinidase incubation, residue substitutions and antibody/streptavidin detection\nevidence_span: {\"source_cache\": \"artifacts/biotin-research/15153116.abstract.txt\", \"locator\": \"Exact primary indexed abstract; zero-based, end-exclusive Unicode character offsets\", \"file_sha256\": \"a3297d283f8a3980a77f1ba1d53f326fb32ee3971c76bda71ef9ba235fb53965\", \"start_char\": 0, \"end_char\": 1762, \"text_sha256\": \"a3297d283f8a3980a77f1ba1d53f326fb32ee3971c76bda71ef9ba235fb53965\"}\n[b7-p15153116] K8 and K12 are biotinylated in human histone H4. (2004). https://pubmed.ncbi.nlm.nih.gov/15153116/ DOI: 10.1111/j.1432-1033.2004.04167.x","source_key":"import-08ce9896-9d1c-5bbf-b705-5bfe771091d5","source_title":"Biotin: carboxylases, recycling, deficiency and nutrient interactions (2026-09-17)","claim_ids":["89cb34eb-b10e-570c-add0-aaf5a3aa5eca"]},{"conflict_id":"ed200767-9fee-5883-86e7-8f39cc9c61fe","ordinal":1,"label":"A histone band can arise from the detection reagent rather than a biotin attachment.","revision_id":"e0d0c2a2-e9e2-55dd-b467-41c22ba960d4","start_line":1170,"end_line":1181,"quote":"### b7-histone-artifact\nThe 2008 assay study found biotin-independent streptavidin binding to histones and detected radiolabeled biotin on carboxylases but not histones.\nCondition category: normal\nnutrient_topic: Biotin research collection; topical membership is not evidence of a direct dietary effect.\nplain_language: A histone band can arise from the detection reagent rather than a biotin attachment.\norganism: Cultured cells as specified in the primary paper\ntissue_or_cell_type: Histones and carboxylases\nexperimental_model: Cell-culture biotin depletion, streptavidin controls and radiolabeled-biotin incorporation\nlimitations: Failure to detect is an upper bound, not proof of zero; the stated less-than-0.03% bound is compatible numerically with the later less-than-0.001% estimate.\nexposure: Assay-method comparison\nevidence_span: {\"source_cache\": \"artifacts/biotin-research/17920026.abstract.txt\", \"locator\": \"Exact primary indexed abstract; zero-based, end-exclusive Unicode character offsets\", \"file_sha256\": \"4b20857841bd32babc7962b138c4e56b6502a92d3bd6443e83fc0be32308e26d\", \"start_char\": 0, \"end_char\": 1357, \"text_sha256\": \"4b20857841bd32babc7962b138c4e56b6502a92d3bd6443e83fc0be32308e26d\"}\n[b7-p17920026] Artifactual detection of biotin on histones by streptavidin. (2008). https://pubmed.ncbi.nlm.nih.gov/17920026/ DOI: 10.1016/j.ab.2007.09.003","source_key":"import-08ce9896-9d1c-5bbf-b705-5bfe771091d5","source_title":"Biotin: carboxylases, recycling, deficiency and nutrient interactions (2026-09-17)","claim_ids":["b1d9f686-39ca-5fe4-9db7-f81d85daf4ae"]},{"conflict_id":"ed200767-9fee-5883-86e7-8f39cc9c61fe","ordinal":2,"label":"Later work defended a very rare mark while questioning whether that tiny amount explains biological effects.","revision_id":"e0d0c2a2-e9e2-55dd-b467-41c22ba960d4","start_line":1183,"end_line":1194,"quote":"### b7-histone-rare-report\nThe 2011 study reported natural biotinylation of less than 0.001% of human H3/H4 and argued for rare modification rather than a universal assay artifact.\nCondition category: normal\nnutrient_topic: Biotin research collection; topical membership is not evidence of a direct dietary effect.\nplain_language: Later work defended a very rare mark while questioning whether that tiny amount explains biological effects.\norganism: Homo sapiens\ntissue_or_cell_type: Human histones H3/H4 in cultured cells\nexperimental_model: Multiple antibody, radiotracer and cell-line comparisons of human histone biotinylation\nlimitations: Authors estimated extremely low abundance and proposed HLCS chromatin scaffolding as a working model; nutritional epigenetic benefit was not demonstrated.\nexposure: Assay comparisons responding to artifact criticism\nevidence_span: {\"source_cache\": \"artifacts/biotin-research/21930408.abstract.txt\", \"locator\": \"Exact primary indexed abstract; zero-based, end-exclusive Unicode character offsets\", \"file_sha256\": \"51af2341c7be0cb58c57e09784ebb8daabdd98cc93f04be52bb7b04b496e0b91\", \"start_char\": 0, \"end_char\": 1318, \"text_sha256\": \"51af2341c7be0cb58c57e09784ebb8daabdd98cc93f04be52bb7b04b496e0b91\"}\n[b7-p21930408] Biotinylation is a natural, albeit rare, modification of human histones. (2011). https://pubmed.ncbi.nlm.nih.gov/21930408/ DOI: 10.1016/j.ymgme.2011.08.030","source_key":"import-08ce9896-9d1c-5bbf-b705-5bfe771091d5","source_title":"Biotin: carboxylases, recycling, deficiency and nutrient interactions (2026-09-17)","claim_ids":["8cc28988-0c76-59a1-a52f-5ae97b2abed3"]}]}],"corrections":[],"research":null}