Epigenomics articles from across Nature Portfolio

DNA methylation is an age biomarker, but nonlinear aspects of its age-related dynamics are not well characterized. Here, the authors identify loci that undergo sudden methylation changes at specific life stages in the aging colon of male mice.

scGHOST offers a computational tool to annotate single-cell subcompartments from scHi-C or imaging data through graph representation learning with constrained random walk sampling.

Here the authors uncover p53’s role as the master regulator of spatio-temporal genome organization. p53 controls the expression of 340 distal genes through newly formed and pre-existing loops between p53-bound enhancers and promoters.

DNA methylation from cell-free DNA (cfDNA) can be profiled using whole genome bisulfite sequencing (WGBS). Here, the authors develop a computational method, FinaleMe, that predicts DNA methylation and tissues of-origin in cfDNA and validate its performance using paired deep and shallow-coverage whole-genome sequencing (WGS) and WGBS data.

An epigenetic study on free-ranging spotted hyenas (Crocuta crocuta) suggests that genes are differentially methylated between high-ranking and low-ranking females (cubs and adults) which may reflect rank-specific differences in access to resources.

Beaksedges harbour multiple centromeres in each chromosome, yet crossover distribution is distally biased, like in monocentric species, but with no correlation with (epi)genomic features. This study suggests that synapsis dynamics starting from chromosomal ends is key to the recombination pattern.

The effect of DNA methylation on gene expression has been known for decades. However, the mechanism by which DNA methylation functions to repress transcription has remained a major question in the field. Wang et al. now narrow this gap through their examination of the methylation binding protein MBD2 and expose how DNA methylation is read upstream of transcriptional repression.