The human RNA-DNA interactome is cell type-specific and dynamic

Integrated single-cell profiling of RNA and DNA interactomes reveals targetable chromatin architectures in cancer

Mapping genome-wide RNA-RNA and RNA-DNA interactions in nuclear hubs of male and female Drosophila cells

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

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

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-residue resolution, how nucleosome-core variation reshapes cellular function. Genome-scale interaction mapping identified hundreds of regulatory connections spanning chromatin, as well as actin organization, endocytosis, and membrane trafficking. Interactions were residue-specific and differed between H2A and H2A.Z, revealing a regulatory landscape encoded by single residues. Transcriptome profiling showed limited expression changes and little overlap between differentially expressed genes and regulatory partners, indicating that non-chromatin connections are not readily explained by altered transcription. L2 substitutions also preferentially conferred benefits under cell wall and membrane stress. Thus, the nucleosome is linked to cellular-periphery functions beyond classical chromatin regulation, identifying histone variation as a source of phenotypic innovation.

Chromatin is dispensable for bacterial life

Inside cells, DNA is intimately associated with proteins, forming chromatin. The protein constituents of chromatin vary across the tree of life: histones are the principal building blocks of chromatin in eukaryotes and many archaea, whereas bacteria typically encode a collection of nucleoid-associated proteins (NAPs) that wrap, bend, bridge or coat the DNA. Although chromatin proteins appear to be a universal feature of cellular life, DNA-templated processes such as transcription, replication, and DNA repair can take place in vitro in the absence of chromatin, raising the possibility that cellular systems might exist – or could be built – that lack chromatin proteins. To explore this possibility, the molecular consequences and potential systemic adjustments required for life without chromatin, we serially deleted the nine most abundant NAPs from E. coli (hupA, hupB, ihfA, ihfB, hns, stpA, fis, dps, lrp), resulting in a strain (ΔNAP9) that lacks its native chromatin. Using an array of different techniques, we document change – and sometimes surprising lack thereof – in compaction, composition and 3D architecture of the nucleoid, supercoiling, prophage activity, growth, viability, and genetic make-up of ΔNAP9. Most notably, we find that ΔNAP9 exhibits global dysregulation of gene expression, marked by a striking homogenization of transcriptional output across the genome that is reminiscent of the effects of histone depletion in eukaryotic cells. Our results reinforce the notion that chromatin plays a key role in compartmentalizing the use of genomic information, enabling both the localized suppression of selfish elements and dynamic reprogramming of genome activity in response to environmental change. At the same time, the successful construction of ΔNAP9 demonstrates that bacterial cells can carry out basic cellular functions in the absence of co-evolved chromatin proteins, highlighting the potential for radical (re-)engineering of prokaryotic chromatin and systems of gene expression.