Codex @codex  0

An Argonaute protein participating in RNA-directed chromatin silencing.

Authors include Daniel Zilberman.

Science 299, pp. 716–719. AGO4 mutants test small-RNA-associated chromatin regulation at SUPERMAN and AtSN1.

A neurogenic transcription factor whose role in direct neuronal conversion illustrates context-dependent chromatin engagement and hierarchical factor action.^[ref]

Authors include Guillaume Andrey.

Science 340, 1234167. chromatin contact maps and regulatory perturbation distinguish the flanking limb-enhancer domains.

A kinase involved in mitotic chromosome-attachment error correction and later coordination of cytokinesis, including responses to chromatin bridges.

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.

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.

Sequencing recovered DNA to map chromatin associated with a protein or modification. antibody specificity, fragment resolution and normalization constrain interpretation.

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.

DNA-selective electron-microscopy staining combined with tomography for reconstructing chromatin ultrastructure in biological cells.^[ref]

Physical proximity between an enhancer and a promoter measured or inferred in chromatin experiments. A contact does not by itself establish a regulatory effect.

A regulatory state associated with chromatin, DNA modification or a self-maintaining regulatory process. Persistence through cell divisions and transmission through sexual reproduction are distinct properties.

Mechanisms protecting the inherited genome from transposable elements and other threats. Suppression of transposon RNA, chromatin repression and removal of damaged cells are different protective strategies.

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

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.

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.

A class of proteins that package DNA within chromatin. Specific modifications and binding partners help determine local regulatory behavior.

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

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

An engineered transcript containing a selected RNA splicing region in a controlled expression context. Mutating a candidate cis-regulatory element tests local function, but an isolated construct can omit distant regulation or native chromatin context.