Chromatin tracing at the rut locus in the Drosophila melanogaster adult brain

Integrative spatial profiling of 3D genome organization and gene expression in tissue

SUMMARY Three-dimensional genome organization shapes transcriptional regulation, yet measuring its spatial coordination in situ within intact tissues remains challenging. We present Spatial Hi-C-RNA, a multimodal platform that simultaneously maps genome-wide chromatin contacts and transcriptomes from the same tissue section at near single-cell resolution. Across mouse brain, developing embryos, and human melanoma, Spatial Hi-C-RNA generated multimodal maps that aligned with tissue anatomy while revealing complementary chromatin- and RNA-defined spatial patterns. Multiscale features, including A/B compartments, topologically associating domains, and chromatin loops, were associated with region- and cell-type-specific transcriptional programs. In mouse embryos, Spatial Hi-C-RNA resolved coordinated chromatin and transcriptional remodeling during neuronal maturation across developmental stages. In human melanoma, chromatin architecture delineated intratumoral subregions not detected by RNA alone and linked tumor-state transitions to changes in compartments, domain boundaries, and regulatory programs. Spatial Hi-C-RNA thus provides a broadly applicable framework for investigating genome structure–function relationships in development and disease within native tissue environments.

Reading the maps: Organization and function of chromatin types in Drosophila

Decoding the regulatory genome: single-cell four-omics integration

In a recent study published in Nature, Chen et al. introduced CHARM (single-cell assay for Chromatin conformation, Histone modi fi cation, chromatin Accessibility, and RNA expression Multi-omics pro fi ling), a platform that simultaneously captures four regulatory modalities within the same nucleus. 1 This integrated strategy provides a comprehensive framework for dissecting how multiple layers of epigenetic regulation converge to control gene expression at single-cell resolution. Gene regulation in eukaryotic cells is governed by a complex interplay of molecular and spatial mechanisms. Chromatin accessibility determines whether regulatory elements such as promoters and enhancers are available for transcription factor binding. Histone modi fi cations de fi ne chromatin states that either promote or repress transcription. In parallel, the three-dimensional organization of the genome establishes spatial proximity between distal regulatory elements and their target genes. Although each of these regulatory layers has been extensively studied, understanding how they operate together within the same cell has remained a major challenge. 2 Previous technologies have provided valuable insights into individual modalities. ATAC-seq pro fi les chromatin accessibility, CUT&Tag captures histone modi fi cations, and Hi-C reveals three-dimensional genome architecture. Recent single-cell platforms such as ChAIR and scHiCAR jointly pro fi le chromatin accessibility, RNA, and 3D contacts, but their 3D contact capture is anchored at accessible chromatin or candidate cis-regulatory elements, introducing structural bias into chromatin architecture reconstruction. 3,4 Moreover, regulatory modalities not captured by these platforms, such as histone modi fi cations, require separate pro fi ling and computational integration for broader cross-modality analysis. CHARM is distinguished from previous platforms by adding histone modi fi cation as a fourth same-cell modality and by using restriction-enzyme-based Hi-C

Mapping protein-DNA interactions across biological scales: principles, scalability and applications.

A comparative overview of major PDI technologies organized according to the biological scale at which they operate is provided, including sequence- and chromatin-based binding prediction, multi-omics integration, and regulatory network inference.

Reversing aging-like 3D genome disorganization in a Drosophila interphase model

Recent experimental evidence suggests that aging may arise from the progressive deterioration of the epigenetic landscape, while reversing the trend can result in cell and tissue rejuvenation. A mechanistic understanding of how restoration of a key component of this landscape – the 3D structure of the genome – can be accomplished is lacking. Here we investigate lamina-dependent disruption and recovery of the 3D architecture of the Drosophila melanogaster genome at TAD resolution (∼ 100 kb), using a model of the entire nucleus; weakening of chromatin–lamina interactions mimics an aging-associated loss of chromatin organization. We characterize this loss using the Shannon entropy of appropriately normalized Hi-C contact matrices. Our main finding is that lamina-depletion-induced increases in Hi-C map disorder, deterioration of chromosome territories, and cell-to-cell conformational heterogeneity are largely reversible when WT-like LAD–nuclear-envelope interactions are restored. The original and recovered conformational states of chromatin are nearly indistinguishable by bulk Hi-C contact matrix; the corresponding Pearson correlation coefficient is 0.999902. The direct experimentally testable prediction is that restoration of functional LAD–lamina interactions will promote recovery of young/WT-like 3D chromatin architecture after lamina-dependent architectural disruption.

Reading the maps: Organization and function of chromatin types in Drosophila