ChIPmentation-based mapping of histone modifications in aging: Experimental design and analytical considerations.

Histone modifications: mechanisms, metabolic regulation, and therapeutic targeting in cancer

This review comprehensively summarizes the multifaceted roles of major histone modifications, including acetylation, methylation, ubiquitination, phosphorylation, and emerging metabolism-linked acylations, in governing critical DNA-templated processes such as replication, transcription, and the DNA damage response.

Single-residue variation in the nucleosome core reveals a regulatory hub for phenotypic innovation

Nucleosomes organize genomes and regulate DNA access, yet accumulating evidence suggests that their constituent histones may have functions beyond canonical chromatin regulation, but the breadth of such regulatory diversity remains unclear. Here, we used the six-residue loop 2 (L2) of H2A and H2A.Z to map, at single-re...

Histone deacetylases: From acetylation homeostasis to oncogenic and neurodegenerative disorders.

Enhanced chromatin compaction is associated with de novo expression of a nuclear microprotein, global loss of H3 acetylation and local transcriptional changes in retinal rod photoreceptors

We have limited understanding of how aging alters gene expression and remodels cellular architecture in post-mitotic neurons. The inverted nuclear organization of mouse rod photoreceptors provides a unique model to gain mechanistic insights into age-associated decline in neuronal function. We have generated and integra...

ChromID: A Protocol for Mapping Protein Chromatin Interactions in Living Cells

A proximity-labeling protocol for identifying the chromatin-dependent protein interactome associated with specific chromatin marks, termed ChromID, which preserves native chromatin organization and captures transient chromatin-associated interactions that are often lost during conventional affinity purification workflo...

DPF3a couples H3K36me2-dependent chromatin remodeling to genome architecture during myogenesis

The findings uncover a non-canonical mechanism whereby a chromatin remodeler regulates transcription primarily through three-dimensional genome organization rather than local accessibility control, and establish histone modification-guided chromatin remodeling as a key principle in gene regulation.