Chromatinbinding

Chromatin binding refers to the interaction of proteins, peptides, or other molecules with chromatin, the DNA-protein complex that forms chromosomes in the nucleus. Binding can occur directly to DNA or indirectly through histone tails or other chromatin-associated proteins. Chromatin-binding events influence gene expression, DNA replication, repair, and higher-order chromatin organization by altering accessibility and recruiting enzymatic activities.

Binding modes are diverse. Some proteins bind DNA directly, recognizing specific sequences or structural features and thereby guiding transcription, replication, or repair processes. Others engage chromatin indirectly through histone tails or nucleosome surfaces, often via electrostatic interactions with the DNA backbone. A prominent class of chromatin binders are histone reader domains that interpret post-translational modifications: bromodomains recognize acetylated lysines, chromodomains and Tudor domains recognize methylated lysines, and PHD fingers can read various histone marks. Proteins such as HP1 recognize H3K9 methylation and contribute to heterochromatin formation. Binding can occur on nucleosomes or to linker DNA, and binding affinity is modulated by chromatin state, ionic conditions, and post-translational modifications.

The functional consequences of chromatin binding include recruitment of transcription factors and chromatin-modifying enzymes, stabilization of active or repressive chromatin states, or remodeling and repositioning of nucleosomes. This binding underpins processes such as transcription initiation, elongation, DNA repair, and chromatin remodeling. Techniques to study chromatin binding include chromatin immunoprecipitation (ChIP), ChIP-seq, CUT&RUN, and various in vitro binding assays.

Misregulation of chromatin binding can contribute to diseases such as cancer and developmental disorders, reflecting its central role in genome regulation.