chromatin remodeling

Declared remodeling meaning

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.

1. Does this study define remodeling through ATP-dependent nucleosome reorganization or use a broader meaning? definition
2. What observed transition distinguishes this instance from histone modification, passive breathing, or a static accessibility state? boundary

Anchored remodeling episode

Record genomic coordinates or construct sequence, starting chromatin organization, biological system, and the interval over which change is assessed.

1. Which genome assembly and interval, or defined DNA construct, identifies the remodeled substrate? provenance
2. What starting nucleosome organization, cell state, and observation interval define this episode? measurement

Complex-specific assignment

Identify the actual ATPase and associated subunits tested, preserving species and preparation details rather than transferring a family-level label directly to an event.

1. Which ATPase and complex composition were measured or manipulated in this system? provenance
2. What establishes that the detected complex is catalytically competent on the relevant nucleosome substrate? measurement

Targeting requirements

Record candidate recruitment cues, including bound factors, histone features, and DNA context, separately from evidence that recruitment produces remodeling.

1. Which factor, histone feature, or DNA context is proposed to recruit or retain the remodeler? definition
2. Does disrupting that cue alter remodeler occupancy, nucleosome reorganization, or both? action

Sliding and array reorganization

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)

1. How far and in which coordinate direction did the nucleosome move relative to its initial position? measurement
2. Did neighboring nucleosomes become more regularly spaced, and what evidence distinguishes repositioning from loss? measurement

Eviction versus histone exchange

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)

1. Was an entire nucleosome lost, a histone component exchanged, or only the measured footprint changed? boundary
2. Which histones or variants were present before and after, and how was replacement distinguished from net loss? measurement

Productive catalysis

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)

1. Which ATP depletion, nucleotide substitution, or catalytic mutant controls test dependence of the observed transition on ATP hydrolysis? action
2. Were ATP turnover and nucleosome reorganization both measured, or is productive coupling inferred? measurement

Resolved transition trajectory

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)

1. Does the measurement resolve intermediate DNA movements, completed repositioning, or only a population endpoint? measurement
2. How long does the resulting nucleosome organization persist after remodeler activity or the recruiting stimulus is removed? measurement

Orthogonal remodeling evidence

Record whether the assay measures accessibility, protected DNA, histone abundance, variant identity, or molecular movement; use complementary evidence where one readout cannot discriminate outcomes.

1. What does each assay directly measure, and which step converts its signal into a claim about nucleosome remodeling? measurement
2. Could altered factor binding, digestion bias, cell composition, or histone abundance explain the signal without the proposed remodeling mechanism? boundary
3. Which complementary measurement would distinguish the remaining physical explanations? action

Causal order and rescue

Treat accessibility and transcriptional responses as outcomes to test, recording temporal order, perturbation specificity, and whether rescue restores the physical remodeling phenotype.

1. Does nucleosome reorganization precede the accessibility, transcription, replication, or repair response being attributed to it? measurement
2. Does rescue with functional remodeler restore the nucleosome phenotype, and what happens with a catalytically impaired version? action
3. Could complex destabilization, compensatory remodeling, or secondary cell-state changes account for the perturbation result? boundary

Check these first

Recalled without web access and unsourced; every item is a lead to verify.

1. Which of these check these first hold for the sense of chromatin remodeling this model covers, and on what evidence? provenance

Kinds and varieties

Recalled without web access and unsourced; every item is a lead to verify.

1. Which of these kinds and varieties hold for the sense of chromatin remodeling this model covers, and on what evidence? provenance

Identifiers and schemes

Recalled without web access and unsourced; every item is a lead to verify.

1. Which of these identifiers and schemes hold for the sense of chromatin remodeling this model covers, and on what evidence? provenance

Real-world use

Recalled without web access and unsourced; every item is a lead to verify.

1. Which of these real-world use hold for the sense of chromatin remodeling this model covers, and on what evidence? provenance

Typical measurements

Recalled without web access and unsourced; every item is a lead to verify.

1. Which of these typical measurements hold for the sense of chromatin remodeling this model covers, and on what evidence? provenance

Failure modes and hazards

Recalled without web access and unsourced; every item is a lead to verify.

1. Which of these failure modes and hazards hold for the sense of chromatin remodeling this model covers, and on what evidence? provenance

Neighbouring kinds and how to tell them apart

Recalled without web access and unsourced; every item is a lead to verify.

1. 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? provenance