The complex of DNA and associated proteins that organises nuclear genetic material and helps regulate its accessibility.
Transcriptional repression mediated by Polycomb-group proteins and associated chromatin states. Developmental regulators can be kept inactive until appropriate activation.
The spatial arrangement and dynamic interactions of chromatin. Hi-C, imaging and accessibility assays measure different aspects; no one readout establishes a universal three-dimensional structure.
A bacterial DNA-recognition pair marks an integrated operator array with a fluorescent repressor. It enables live tracking of a chosen genetic locus, while the array and bound protein can perturb that locus.
A nuclear volume preferentially occupied by a chromosome. Territories can contact and intermingle at their boundaries rather than forming sealed compartments.
A genomic interaction pattern in which regions with related properties preferentially associate. Large-scale compartments and cohesin-dependent loop domains can respond differently to perturbation.
An organization in which separated genomic regions are brought into enhanced proximity. Contact enrichment and a fixed loop in every biological cell are different claims.
A mechanism in which a molecular complex progressively enlarges a DNA loop. Its predictions can be tested through contact maps and acute perturbation of architectural factors.
A genomic interval with preferential internal contact frequency under a specified analysis. Its boundaries and physical realization can vary between biological cells and conditions.
Crosslinking, fragmentation and ligation methods that infer genomic proximity from recovered junctions. Contact frequency is not automatically an absolute spatial distance or proof of direct functional interaction.
A genome-wide chromosome-contact assay. Coverage, fragment recovery and bin size affect interpretable resolution; the matrix describes sampled contacts rather than a single universal chromosome structure.
A succession of nucleosomes connected by linker DNA. Regular arrays reconstituted under selected conditions need not represent one universal cellular fibre architecture.
The propensity of a chromatin region to be reached by a specified probe or enzyme under stated conditions. Accessibility, transcription-factor occupancy and regulatory function are related but distinct.
Sequencing-based mapping of DNA cleavage by DNase, used to identify accessible regions and hypersensitive sites. Sequence preferences and digestion conditions require controls.
Profiling accessible DNA through transposase-mediated adapter insertion and sequencing. Enzyme bias, sample preparation and biological cell composition affect the observed accessibility landscape.
A dinoflagellate histone-like protein in the HU-related families is distinct from a canonical eukaryotic core histone. Its distribution is lineage dependent; the label must not be used to imply restoration of a conventional nucleosomal genome.
A dinoflagellate viral nucleoprotein is a member of the DVNP family of basic nuclear proteins found in dinoflagellates and related large DNA viruses. Comparative abundance and yeast perturbation experiments support interactions with DNA packaging, without fully reconstructing the evolutionary transition.
Liquid-crystalline chromosome organization describes ordered dense DNA packing with orientational organization distinct from a conventional nucleosome array. Microscopic order does not by itself identify the proteins or interactions required to maintain it.
A region or activity limiting propagation of a chromatin state. A functional boundary is demonstrated by perturbing it and measuring the resulting domain behavior, rather than merely observing an endpoint.
A relatively inaccessible, frequently repressive form of chromatin. Different forms have distinct marks and mechanisms; H3K9 methylation is a major example rather than a universal definition.
Methylation of lysine 9 of histone H3. Different methylation states can recruit specific reader proteins and contribute to heterochromatin regulation.
Extension of a repressive chromatin domain beyond its initial nucleation site. Reader–writer positive feedback can propagate local marks, while histone turnover, opposing activities and chromatin boundaries constrain the domain.
Alteration of nucleosome organization, positioning or composition by associated machinery. Increased accessibility does not by itself identify the direct molecular target of a drug.
An ATP-dependent chromatin remodelling complex uses ATP-dependent activity to alter nucleosome positioning, composition or organization. It changes access to DNA without needing to change the DNA sequence.
Addition of acetyl groups to histones. Its functional effects depend on the site, associated readers and local chromatin context.
A repeating chromatin unit in which DNA wraps around a histone core. Position, turnover and modification affect accessibility of the associated DNA.
Movement of histones from one DNA substrate or complex to another. In competition experiments, loss of histones from a labelled complex need not release free DNA if another DNA-binding protein remains attached.
Resistance of a histone–DNA particle to loss or rearrangement of its components under specified conditions. Competitor-induced histone transfer can reveal destabilization even while a DNA-binding protein remains attached.
Transient local unwrapping and rewrapping of nucleosomal DNA. This changes the accessibility of DNA and histone surfaces without requiring complete and irreversible loss of the histone octamer.
DNA connecting adjacent nucleosome cores. Its length and accessibility affect nucleosome-array organization.
The core histone assembly containing two copies each of H2A, H2B, H3 and H4 around which nucleosomal DNA wraps.
Mapping DNA fragments protected during controlled micrococcal-nuclease digestion. Digestion titration and fragment validation help distinguish nucleosome occupancy from sequence bias and other protected complexes.
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