Epigenetics analysis articles from across Nature Portfolio

FFPE tissues are widely used to preserve clinical specimens, but formalin-induced crosslinking limits their use in epigenomic profiling. Here, the authors present spatial FFPE-ATACseq, enabling in situ chromatin accessibility mapping while preserving tissue architecture in archived samples.

The discovery that DNA methylation of different CpG sites can serve as digital barcodes of clonal identity led to the development of EPI-Clone, an algorithm that enables single-cell lineage tracing through cellular differentiation at scale.

The role of germline variation in cancer remains underexplored. Here, the authors investigate the landscape of germline structural variants on tumour DNA methylation across pediatric brain and central nervous system tumour patients and suggest disease implications.

Germ layer specification during zygotic genome activation is regulated by chromatin state. Here, the authors use single-cell multiome profiling in Drosophila to show that H3K27me3 and H3K27ac at cis-regulatory elements control cell type-specific gene expression and developmental progression.

In this Protocol Extension, the authors describe procedures for spatial barcoding in tissue sections using a microfluidic chip followed by sequencing-based joint genome-wide profiling of transcriptome and open chromatin or histone modifications.

In this Tools of the Trade article, Min Liu and Aibin He describe TACIT, a single-cell method that maps histone modifications at near genome-wide coverage, and its extension CoTACIT, which simultaneously maps up to six histone modifications in the same cell.

We developed a method that improves the detection of haplotype-assigned chromatin interactions in humans by over tenfold, using far less data than traditional methods. This advance enabled an almost complete diploid 3D genome map, making high-order phased chromatin interaction studies more accessible to researchers.

In this Tools of the Trade article, Bercin Cenik describes the development and use of TurboCas, an enzyme that pairs catalytically dead Cas9 with the proximity-labelling enzyme miniTurbo to map the regulatory proteins that shape transcription.

Now a protocol enables simultaneous measurement of gene expression and chromatin state in intact tissues, unlocking the relationship between tissue architecture and gene regulation.

The structure of chromatin bound by Polycomb repressive complex 1 (PRC1) and how it contributes to transcription repression are unknown. Here, cryo-electron tomography (cryo-ET) of PRC1–chromatin condensates reveal randomly oriented neighboring nucleosomes in a stable, open chromatin mesh that might exclude large protein complexes to repress transcription.