Panzeri et al. use a Trim28^+/D9 mouse model with intrinsic developmental heterogeneity to show that ‘heavy’ and ‘light’ developmental morphs exhibit different timing, type and severity of cancer, linked to a relevant DNA hypomethylation signature.

CDX2 binds distinct targets in developing and adult intestinal epithelial cells based on the distribution of its motifs with and without CpG. Here, the authors show that loss of DNA methylation during development allows Cdx2 to activate target genes.

Mapping DNA methylomes in single cells is challenging, and thus studies using bulk samples remain common. Here, authors develop a transformer-based method for methylation pattern analysis to enhance bulk methylome deconvolution and cancer detection.

Koch and colleagues report that epigenetic clocks mirror age predictions based on the accumulation of somatic mutations and show that somatic mutations at CpG sites coincide with extensive remodeling of the surrounding methylome.

A rat study suggests that maternal stress induces epigenetic signatures in placenta and brain that persist across four generations of offspring, proposing that diseases may be inherited by experience-induced non-genetic mechanisms.

Despite theoretical expectations of balanced 1:1 sex ratios between females and males, many dioecious plant species exhibit sex ratio distortions. A recent study in persimmon shows how this can be caused by random inactivation of an X-chromosomal gene that is essential for seed development.

The insertion of the stress-responsive transposable element (TE) ONSEN into a critical flowering regulator gene confers an adaptive response to herbicide treatment in Arabidopsis thaliana natural accessions.

Aging-related DNA methylation changes are numerous. Their precise measurement has opened new avenues to explore aging-related disease pathology, including the construction of chronological and biological age predictors (termed DNA methylation ‘clocks’). Three studies investigate the substantial stochastic contribution to these epigenetic changes and further our understanding of aging biology, as well as of these predictors.

The replicational age of single cells provides a temporal reference for tracking cell fate transition trajectories. The computational framework EpiTrace measures cell age using single-cell ATAC-seq data, specifically by considering chromatin accessibility at clock-like genomic loci, enabling the reconstruction of the history of developmental and pathological processes.

The ATP-dependent chromatin remodeller DDM1 has a vital role in plant DNA methylation, influencing gene silencing and suppression of transposable elements. The structure of DDM1 in complex with nucleosome in different states of the ATP hydrolysis process reveals the molecular mechanism underlying chromatin remodelling by DDM1.