{"schema":"https://ver.cy/schemas/card/1.0.0","id":"vr.tr.chromatin-remodeling","code":"thing-q5113739","url":"https://ver.cy/models/thing/q5113739/","name":"chromatin remodeling","alternateNames":["epigenetic maintenance of chromatin in transcription-competent conformation","DNA repair-dependent chromatin remodeling","co-transcriptional chromatin reassembly","heterochromatin organization","nucleosome organization","chromatin remodeling at centromere"],"kind":"thing","status":"published","version":"0.1.0-research.1","language":"en","classifiers":{"family":"Thing Registry","category":"Activities and processes","entryKind":"thing","plane":"ACT","domain":["ACT.PRC"],"industry":[],"navPath":"","tags":[],"facets":{}},"whatItIs":"Chromatin remodeling is the alteration of chromatin organization that changes access to DNA, referring most specifically to ATP-dependent repositioning, restructuring, assembly or removal of nucleosomes, although broader usage includes histone modifications and other changes to chromatin.","purpose":"Enable an agent to recognize chromatin remodeling events, assess evidence for local and global structural changes to chromatin throughout the cell division cycle, and evaluate the suitability of measurements or perturbations.","scope":{"in":["Remodeling episodes are identified by genomic substrate, biological context and observation interval.","ATP-dependent remodeling includes nucleosome sliding, spacing, restructuring, eviction and histone exchange.","Mechanistic descriptions include remodeler identity, recruitment, catalytic activity and substrate dependence where applicable.","Evidence includes changes in nucleosome organization, higher-order chromatin structure and associated DNA accessibility.","Evidence distinguishes demonstrated structural remodeling from correlated chromatin changes.","Perturbation and recovery evidence can inform assessments of remodeling mechanisms.","Global structural changes involved in chromosome segregation fall within the supplied sense."],"out":["Remodeler proteins and complexes as independently catalogued molecular entities are outside this process model.","Histone modification and DNA methylation reactions without evidence of chromatin structural change do not by themselves establish remodeling.","Transcription, DNA replication and DNA repair as complete processes are outside this model.","Static chromosome looping and compartment organization without a structural change are not remodeling events.","Passive nucleosome fluctuations must not be treated as evidence of enzyme-driven remodeling.","Diseases and treatments associated with remodeler dysfunction as complete clinical models are outside this model."],"boundaries":[]},"distinguishingFeatures":["An instance describes a structural transition in chromatin at the nucleosome or higher-order level; an accessible or compact chromatin state alone is insufficient.","Remodeler binding establishes association with a substrate but does not by itself establish catalytic remodeling.","Histone acetylation or methylation alone does not establish repositioning, eviction, or exchange of nucleosomes.","ATP-dependent attribution requires evidence connecting catalytic energy use to substrate change, rather than ATPase activity alone.","Remodeling may expose DNA, occlude DNA, regularize nucleosome spacing or change global chromatin organization for chromosome segregation; increased transcription is not a defining test."],"structure":{"bundles":[{"id":"process-boundary-and-instance","name":"Process boundary and instance","description":"Defines what counts as a remodeling event and locates the substrate on which it occurs.","layers":[{"id":"operational-definition","name":"Operational definition","description":"Separates a nucleosome transition from a general chromatin label.","findings":[{"id":"declared-remodeling-meaning","name":"Declared remodeling meaning","description":"Record whether the source means ATP-dependent nucleosome remodeling or a broader class of chromatin changes, and require a stated physical transition for an instance.","questions":[{"text":"Does this study define remodeling through ATP-dependent nucleosome reorganization or use a broader meaning?","id":"declared-remodeling-meaning-q01","kind":"definition"},{"text":"What observed transition distinguishes this instance from histone modification, passive breathing, or a static accessibility state?","id":"declared-remodeling-meaning-q02","kind":"boundary"}]}]},{"id":"substrate-and-context","name":"Substrate and context","description":"Identifies the DNA, nucleosomes, and biological setting under observation.","findings":[{"id":"anchored-remodeling-episode","name":"Anchored remodeling episode","description":"Record genomic coordinates or construct sequence, starting chromatin organization, biological system, and the interval over which change is assessed.","questions":[{"text":"Which genome assembly and interval, or defined DNA construct, identifies the remodeled substrate?","id":"anchored-remodeling-episode-q01","kind":"provenance"},{"text":"What starting nucleosome organization, cell state, and observation interval define this episode?","id":"anchored-remodeling-episode-q02","kind":"measurement"}]}]}]},{"id":"machinery-and-targeting","name":"Machinery and targeting","description":"Connects a chromatin substrate to the remodeler and the conditions that enable its activity.","layers":[{"id":"catalytic-machinery","name":"Catalytic machinery","description":"Records the ATPase, complex composition, and evidence of catalytic competence.","findings":[{"id":"complex-specific-assignment","name":"Complex-specific assignment","description":"Identify the actual ATPase and associated subunits tested, preserving species and preparation details rather than transferring a family-level label directly to an event.","questions":[{"text":"Which ATPase and complex composition were measured or manipulated in this system?","id":"complex-specific-assignment-q01","kind":"provenance"},{"text":"What establishes that the detected complex is catalytically competent on the relevant nucleosome substrate?","id":"complex-specific-assignment-q02","kind":"measurement"}]}]},{"id":"recruitment-and-engagement","name":"Recruitment and engagement","description":"Distinguishes arrival at chromatin from productive substrate interaction.","findings":[{"id":"targeting-requirements","name":"Targeting requirements","description":"Record candidate recruitment cues, including bound factors, histone features, and DNA context, separately from evidence that recruitment produces remodeling.","questions":[{"text":"Which factor, histone feature, or DNA context is proposed to recruit or retain the remodeler?","id":"targeting-requirements-q01","kind":"definition"},{"text":"Does disrupting that cue alter remodeler occupancy, nucleosome reorganization, or both?","id":"targeting-requirements-q02","kind":"action"}]}]}]},{"id":"nucleosome-transformation","name":"Nucleosome transformation","description":"Describes the physical change to DNA-histone organization.","layers":[{"id":"position-and-spacing","name":"Position and spacing","description":"Captures nucleosome movement and organization within arrays.","findings":[{"id":"sliding-and-array-reorganization","name":"Sliding and array reorganization","description":"Record dyad displacement and changes in spacing separately. Individual ACF complexes have been studied through nucleosome remodeling dynamics using single-molecule FRET. [Primary study](https://www.nature.com/articles/nature08627)","questions":[{"text":"How far and in which coordinate direction did the nucleosome move relative to its initial position?","id":"sliding-and-array-reorganization-q01","kind":"measurement"},{"text":"Did neighboring nucleosomes become more regularly spaced, and what evidence distinguishes repositioning from loss?","id":"sliding-and-array-reorganization-q02","kind":"measurement"}]}]},{"id":"occupancy-and-composition","name":"Occupancy and composition","description":"Distinguishes nucleosome removal from changes in histone content.","findings":[{"id":"eviction-versus-histone-exchange","name":"Eviction versus histone exchange","description":"Record histone loss and replacement direction independently of repositioning; INO80 research connects remodeling with both sliding and histone editing. [Primary study](https://www.nature.com/articles/s41586-018-0029-y)","questions":[{"text":"Was an entire nucleosome lost, a histone component exchanged, or only the measured footprint changed?","id":"eviction-versus-histone-exchange-q01","kind":"boundary"},{"text":"Which histones or variants were present before and after, and how was replacement distinguished from net loss?","id":"eviction-versus-histone-exchange-q02","kind":"measurement"}]}]}]},{"id":"energy-coupling-and-dynamics","name":"Energy coupling and dynamics","description":"Assesses how catalytic activity produces a time-dependent nucleosome transition.","layers":[{"id":"atp-dependent-coupling","name":"ATP-dependent coupling","description":"Tests whether ATPase activity is coupled to the recorded physical outcome.","findings":[{"id":"productive-catalysis","name":"Productive catalysis","description":"Record evidence linking nucleotide state to nucleosomal DNA movement. Structural work on Snf2 provides a specific mechanistic example, not a universal kinetic rule for all remodelers. [Primary study](https://www.nature.com/articles/s41586-019-1029-2)","questions":[{"text":"Which ATP depletion, nucleotide substitution, or catalytic mutant controls test dependence of the observed transition on ATP hydrolysis?","id":"productive-catalysis-q01","kind":"action"},{"text":"Were ATP turnover and nucleosome reorganization both measured, or is productive coupling inferred?","id":"productive-catalysis-q02","kind":"measurement"}]}]},{"id":"intermediates-and-persistence","name":"Intermediates and persistence","description":"Tracks transient DNA movements, completed products, and subsequent recovery.","findings":[{"id":"resolved-transition-trajectory","name":"Resolved transition trajectory","description":"Preserve the temporal resolution of observations: entry-side and exit-side DNA movement can be separated during remodeling, so a single endpoint may conceal intermediate states. [Primary study](https://www.nature.com/articles/s41467-019-09657-1)","questions":[{"text":"Does the measurement resolve intermediate DNA movements, completed repositioning, or only a population endpoint?","id":"resolved-transition-trajectory-q01","kind":"measurement"},{"text":"How long does the resulting nucleosome organization persist after remodeler activity or the recruiting stimulus is removed?","id":"resolved-transition-trajectory-q02","kind":"measurement"}]}]}]},{"id":"evidence-and-causal-attribution","name":"Evidence and causal attribution","description":"Evaluates what each assay establishes and whether remodeling explains downstream changes.","layers":[{"id":"assay-interpretation","name":"Assay interpretation","description":"Connects each claimed outcome to its readout, calibration, and alternative explanations.","findings":[{"id":"orthogonal-remodeling-evidence","name":"Orthogonal remodeling evidence","description":"Record whether the assay measures accessibility, protected DNA, histone abundance, variant identity, or molecular movement; use complementary evidence where one readout cannot discriminate outcomes.","questions":[{"text":"What does each assay directly measure, and which step converts its signal into a claim about nucleosome remodeling?","id":"orthogonal-remodeling-evidence-q01","kind":"measurement"},{"text":"Could altered factor binding, digestion bias, cell composition, or histone abundance explain the signal without the proposed remodeling mechanism?","id":"orthogonal-remodeling-evidence-q02","kind":"boundary"},{"text":"Which complementary measurement would distinguish the remaining physical explanations?","id":"orthogonal-remodeling-evidence-q03","kind":"action"}]}]},{"id":"perturbations-and-consequences","name":"Perturbations and consequences","description":"Tests causal links between machinery, nucleosome transitions, and biological responses.","findings":[{"id":"causal-order-and-rescue","name":"Causal order and rescue","description":"Treat accessibility and transcriptional responses as outcomes to test, recording temporal order, perturbation specificity, and whether rescue restores the physical remodeling phenotype.","questions":[{"text":"Does nucleosome reorganization precede the accessibility, transcription, replication, or repair response being attributed to it?","id":"causal-order-and-rescue-q01","kind":"measurement"},{"text":"Does rescue with functional remodeler restore the nucleosome phenotype, and what happens with a catalytically impaired version?","id":"causal-order-and-rescue-q02","kind":"action"},{"text":"Could complex destabilization, compensatory remodeling, or secondary cell-state changes account for the perturbation result?","id":"causal-order-and-rescue-q03","kind":"boundary"}]}]}]},{"id":"evidence-and-external-alignment","name":"Evidence and external alignment","description":"What the world already says about this thing, gathered so the model can be checked against it.","layers":[{"id":"reported-evidence","name":"Reported evidence","description":"Findings from the breadth pass, kept separate from the structural claims.","findings":[{"id":"evidence-confidence-notes","name":"Check these first","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these check these first hold for the sense of chromatin remodeling this model covers, and on what evidence?","id":"evidence-confidence-notes-q01","kind":"provenance"}]},{"id":"evidence-kinds","name":"Kinds and varieties","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these kinds and varieties hold for the sense of chromatin remodeling this model covers, and on what evidence?","id":"evidence-kinds-q01","kind":"provenance"}]},{"id":"evidence-identifiers","name":"Identifiers and schemes","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these identifiers and schemes hold for the sense of chromatin remodeling this model covers, and on what evidence?","id":"evidence-identifiers-q01","kind":"provenance"}]},{"id":"evidence-real-world-use","name":"Real-world use","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these real-world use hold for the sense of chromatin remodeling this model covers, and on what evidence?","id":"evidence-real-world-use-q01","kind":"provenance"}]},{"id":"evidence-measurements","name":"Typical measurements","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these typical measurements hold for the sense of chromatin remodeling this model covers, and on what evidence?","id":"evidence-measurements-q01","kind":"provenance"}]},{"id":"evidence-failure-modes-and-hazards","name":"Failure modes and hazards","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these failure modes and hazards hold for the sense of chromatin remodeling this model covers, and on what evidence?","id":"evidence-failure-modes-and-hazards-q01","kind":"provenance"}]},{"id":"evidence-neighbours","name":"Neighbouring kinds and how to tell them apart","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these neighbouring kinds and how to tell them apart hold for the sense of chromatin remodeling this model covers, and on what evidence?","id":"evidence-neighbours-q01","kind":"provenance"}]}]}]}]},"agentConduct":{"may":["Explain chromatin remodeling and its roles from peer-reviewed sources.","Distinguish ATP-dependent remodeling from broader chromatin modification."],"mustNot":["Overstate links between remodeling and disease or treatment.","Present early research as clinical fact.","Promote unproven epigenetic products or tests."],"requiresHuman":["Interpreting a patient's genetic or epigenetic results."]},"ethics":{"considerations":["Hype about epigenetics can mislead patients.","Research on human cells requires consent and ethical review."],"affectedParties":["Patients","Researchers","Students"]},"owners":{"steward":"Nobody owns the process; researchers hold their data.","roles":[],"masterSystems":[]},"relations":[{"target":"Q15322272","type":"parent","note":"registry parent class"}],"interaction":{"identity":{"applicability":"required","items":["Vercy registry: vr.tr.chromatin-remodeling","Wikidata: Q5113739 (https://www.wikidata.org/wiki/Q5113739)"]},"properties":{"applicability":"not-applicable","items":["Usage boundary: ATP-dependent nucleosome remodeling; broader chromatin reorganization; unresolved","Genomic substrate: Genome assembly and interval, or defined experimental DNA construct","Biological context: Organism, cell type, cell-cycle phase, stimulus, or reconstituted system","Remodeler assignment: Named ATPase and complex composition; candidate; unknown","Remodeling outcome: Sliding; spacing; eviction; histone exchange; altered wrapping; mixed; unresolved","Nucleosome displacement: Base pairs relative to an initial dyad position and explicit coordinate orientation","Nucleosome occupancy: Occupied fraction when calibrated; otherwise assay-specific normalized signal","Internucleosomal spacing: Base pairs between neighboring dyads, with distribution","Histone composition transition: Initial and resulting histone or variant identities, with exchange direction","Accessibility change: Assay-specific effect size relative to a stated control","Transition kinetics: Seconds or minutes; events per unit time when directly resolved","Mechanistic evidence status: Directly observed; perturbation-supported; association-only; conflicting; unresolved"]},"recognition":{"applicability":"not-applicable","items":[]},"capabilities":{"applicability":"required","items":["Classify a reported chromatin change by physical outcome and strength of mechanistic evidence.","Compare nucleosome states at the same locus across time, conditions, or remodeler perturbations.","Select complementary measurements to distinguish sliding, eviction, exchange, and altered wrapping.","Design controlled tests of remodeler recruitment, ATPase dependence, and substrate requirements.","Assess whether accessibility or transcription changes can reasonably be attributed to the measured remodeling event.","Record competing mechanisms and identify the next experiment needed to discriminate between them."]},"hazards":{"applicability":"required","items":["Disrupted chromatin remodeling can impair gene regulation and genome maintenance.","Perturbations of remodeling machinery can affect many genes and compromise cell viability or differentiation.","Treating indirect assay signals as proof of remodeling can produce incorrect mechanistic conclusions and misdirect subsequent research."]},"interfaces":{"applicability":"required","items":["The Gene Ontology biological process classification, maintained by the Gene Ontology Consortium, includes chromatin remodeling for annotating gene product functions."]},"context":{"applicability":"required","items":["Chromatin remodeling is studied in eukaryotic cells to understand how nucleosome organization affects access to DNA.","It is relevant to research on transcription, DNA replication, DNA repair, development and chromosome organization.","Experimental interpretation requires distinguishing direct evidence of nucleosome changes from associated changes in gene expression or histone marks."]}},"sources":[{"title":"Wikidata item Q5113739: chromatin remodeling","url":"https://www.wikidata.org/wiki/Q5113739","note":"identity and sense of the item"},{"title":"Wikipedia: Chromatin remodeling","url":"https://en.wikipedia.org/wiki/Chromatin_remodeling","note":"general description of the item"}],"openQuestions":["Should the registry formally restrict chromatin remodeling to ATP-dependent nucleosome remodeling, or retain a broader meaning with explicit mechanism qualifiers?","For a particular locus, what evidence can distinguish active histone exchange from replication-associated deposition or transcription-associated turnover?","Which remodeling trajectories measured on purified nucleosomes also occur in native chromatin with competing factors and heterogeneous substrates?","What temporal and spatial resolution is needed to distinguish nucleosome motion within individual cells from changes in population composition?","Under which substrate and cellular conditions does a given remodeler produce exposure, occlusion, eviction, or regular spacing, and how predictable are those outcomes?"],"resources":{"spec":"/models/things/publications/thing-q5113739/spec.json"},"provenance":{"origin":"thing registry research (pass 2)","builtFrom":["models/things/publications/thing-q5113739/spec.json"],"providers":["Codex"],"researchStatus":"unreviewed","generatedAt":"2026-09-12T08:41:12Z","builder":"tools/build_cards.py@1.0.0"},"completeness":{"sections":{"classifiers":"filled","whatItIs":"filled","purpose":"filled","distinguishingFeatures":"filled","structure":"filled","agentConduct":"filled","ethics":"filled","owners":"filled","relations":"filled","interaction.identity":"filled","interaction.properties":"not-applicable","interaction.recognition":"not-applicable","interaction.capabilities":"filled","interaction.hazards":"filled","interaction.interfaces":"filled","interaction.context":"filled","sources":"filled"},"notes":{"_gate":"Published through the thing publication gate 1.0 on 2026-10-07T12:16:33+00:00: completeness 1.00; sense: Wikidata description; 2 live sources; review by codex: pass","interaction.properties":"Plane ACT: no invented physical properties.","interaction.recognition":"Chromatin remodeling is a molecular process without a directly recognizable visual appearance and requires experimental evidence for identification."},"score":1.0}}