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A protein domain that can recognize particular methylated histone states, with specificity depending on the particular protein.

A plant chromomethylase important for CHG methylation and its coupling to H3K9 methylation.

Recognition of chromatin state helps couple DNA methylation to histone methylation, reinforcing a locally repressive environment. This is an interaction between two kinds of molecular mark, rather than conversion of one mark into the other. ^[ref]

A dinoflagellate belongs to a eukaryotic lineage notable for unusual nuclear chromosome organization. Many species have persistently condensed DNA with low bulk histone abundance, while retained histones and alternative nucleoproteins caution against a universal histone-free description.

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 DNA-binding protein associates physically with DNA. Some recognize selected base patterns, while others preferentially recognize DNA shape, ends or damage. Transcription factors regulate expression, histones organize packaging and repair factors inspect damaged substrates. These roles illustrate why binding alone does not establish a specific regulatory outcome. Sequence selectivity, affinity and cellular occupancy are distinct measurable properties. ^[ref]

H3K27 methylation is addition of one or more methyl groups to the side chain of lysine 27 in histone H3. Mono-, di- and trimethylated states are different chemical states; a measurement of one is not automatically a measurement of the others. H3K27 trimethylation is particularly associated with Polycomb-mediated gene silencing. ^[ref]

A mechanistic test distinguishes correlation from catalysis. A purified complex can be supplied with histones and a methyl donor to test transfer, while changing a catalytic region tests whether that activity depends on an intact enzyme. In a cell, the distribution of the mark also depends on recruitment, removal and replacement of histones, not only on total enzyme abundance.

A plant histone deacetylase participating in chromatin silencing, including nucleolar dominance.

Removal of acetyl groups can alter histone interactions and recruitment of chromatin-associated factors. Its association with silencing should be interpreted at the specified loci and developmental stage rather than as a universal consequence of every histone deacetylation event. ^[ref]

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.

Addition of acetyl groups to histones. Its functional effects depend on the site, associated readers and local chromatin context.

A histone acetyltransferase catalyses acetyl-group transfer to histone residues. The resulting changes in charge and reader-protein recruitment can influence chromatin accessibility; the effect depends on the modified site and regulatory context.

An enzyme that removes acetyl groups from histones. Its local recruitment can oppose histone acetylation and favor repressive chromatin.

An enzyme that removes particular histone methyl marks.

Different demethylases act on different residues and methylation states, so removal of H3K4 methylation and removal of H3K27 trimethylation are distinct activities. Regulated removal makes a chromatin mark reversible without requiring replacement of the underlying DNA sequence. ^[ref]

A core histone carrying several sites of regulatory modification, including the lysine modified in H3K9 methylation.

Histone methylation adds methyl groups to selected residues of histones. The position and number of methyl groups affect which binding partners recognize the mark. H3K4 methylation, H3K9 methylation and H3K27 trimethylation therefore cannot be treated as one interchangeable signal. Their distributions can be associated with different transcriptional states, and direct causation requires more than correlation between a mark and gene expression. ^[ref]

An enzyme that adds methyl groups to specified histone residues. Its presence alone does not specify repression, because distinct modified sites can have different regulatory roles.

A covalent modification of a histone. Its genomic distribution and associated regulatory state do not by themselves specify chromatin accessibility or causation.

The core histone assembly containing two copies each of H2A, H2B, H3 and H4 around which nucleosomal DNA wraps.

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.

A distinct histone sequence with properties or localization differing from another histone of the same broad class. CENP-A provides a specialized centromeric example.

Jason D. Buenrostro coauthored research on dNA-binding protein.^[ref]

A DNA-binding protein associates physically with DNA. Some recognize selected base patterns, while others preferentially recognize DNA shape, ends or damage. Transcription factors regulate expression, histones organize packaging and repair factors inspect damaged substrates. These roles illustrate why binding alone does not establish a specific regulatory outcome. Sequence selectivity, affinity and cellular occupancy are distinct measurable properties.