A VIM2/4 deletion, and premature truncations of CMT2 and FBX5, drive DNA methylation changes after colonization of a novel habitat

Epigenetic Regulation of Divergent Co-Expression Between Whole-Genome Duplication and Transposed Duplication Genes and Its Impact on Catechin Accumulation in Camellia sinensis

Background/Objectives: Whole-genome duplication (WGD) and transposed duplication (TRD) are two principal evolutionary drivers of plant genome expansion, yet the molecular mechanisms underlying their divergent co-expression patterns remain poorly characterized. Methods: In this study, based on the reference genome of tea plant (Camellia sinensis ‘Yunkang 10’, YK10), we integrated publicly available transcriptomic, ATAC-seq, H3K27ac ChIP-seq, whole-genome bisulfite sequencing (WGBS), and SNP data from eight tissues and performed a multi-layered analysis of co-expression divergence across 4071 WGD and 10,174 TRD gene pairs. Results: WGD gene pairs exhibited significantly higher co-expression rates (44.3%) than TRD pairs (33.0%), with gene length and sequence similarity jointly promoting co-expression. Chromatin accessibility and H3K27ac modification were each positively correlated with expression and co-expression; however, under equivalent chromatin accessibility conditions, TRD gene expression remained systematically attenuated, and this reduced expression state was significantly associated with elevated levels of CG, CHG, and CHH methylation, suggesting that these epigenetic marks may collectively participate in the transcriptional repression of TRD genes. Promoter-proximal SNPs exerted disproportionately deleterious effects on TRD co-expression, demonstrating that the combined effects of genetic variation and epigenetic modifications are associated with enhanced transcriptional divergence. Weighted gene co-expression network analysis (WGCNA) revealed that WGD modules showed significant associations with EC, GC, and EGC accumulation, whereas WRKY and bHLH transcription factors in the TRD MEblue module exhibited strong associations with EGCG and ECG. Conclusions: This study systematically characterizes multi-omics association patterns related to duplicate gene co-expression divergence, providing insights into potential hierarchical regulation. It offers mechanistic clues for catechin metabolic regulation and provides candidate targets for metabolite-directed breeding.

Chromatin-Assisted Targeting Enables Precise DNA Methylation Editing in Plants

SunTag-NOVA robustly installed DNA methylation and repressed transcription at the endogenous FWA, FT and TMM genes with minimal genome-wide off-target consequences, and establishes SunTag-NOVA as a specific epigenome-editing platform for plants.

MOP1 affects DNA methylation, nucleosome occupancy, histone modifications and chromatin conformation at the b1 allele involved in paramutation

A new set of DNA methylation variants in the human genome show predominant tissue-specificity and sensitivity to reprogramming with a potential for disease susceptibility

DNA methylation is associated with genomic architecture, genetic variation and dispersal-related traits in an expanding invasion.

The importance of epigenetics in invasion biology is debated. In particular, the role of epigenetic mechanisms, such as DNA methylation, as potential drivers of rapid adaptation compensating for reduced genetic diversity remains an open question. Introduced to Australia 90 years ago, cane toads (Rhinella marina) are spreading at an ever-increasing rate. Across the invasion range, toads display overall low genetic diversity, yet paradoxically show high phenotypic variation in dispersal-related traits. Here, we use a common-garden experiment to investigate the role of DNA methylation in fostering rapid evolution in this system. We show that toads from newly established populations show distinct DNA methylation profiles to toads from long-colonized areas, particularly in genes putatively involved in dispersal. Epigenetic changes were strongly associated with genetic variation and often overlapped with transposable elements. Our results indicate that epigenetic changes following environmental perturbations have the potential to generate phenotypic variation at ecologically relevant traits in genetically depauperate invasive populations, their molecular interplay with gene activity being complex and probably context-dependent. This article is part of the theme issue 'Ecological epigenetics at the intersection of behaviour and life history variation in non-model animals'.

CTCF delimits a DNA methylation transition at the intergenic region between the embryonic and adult α-globin genes

ABSTRACT Transcriptional activation of cell-type-specific genes is achieved by multiple mechanisms that guarantee chromatin accessibility at cis-regulatory elements and the long-range interactions between them. Generally, DNA methylation counteracts these processes and promotes gene silencing in vertebrates. CTCF is a conserved and essential multifunctional transcription factor relevant for establishing and maintaining chromatin architecture and accessibility, while its precise role in regulating DNA methylation remains to be determined. We focused on the highly abundant and previously studied erythroid-specific αD gene (HBAD) to systematically investigate the role of CTCF binding on DNA methylation, chromatin accessibility, and gene expression using a chicken erythroid cell differentiation system. The perturbation of CTCF binding at the intergenic region between the embryonic π and the adult αD gene resulted in DNA methylation propagation towards the αD gene, which was accompanied by decreased chromatin accessibility, GATA-1 binding, and gene expression. Notably, chromatin conformation analyses revealed that CTCF binding enables αD transcriptional activation independently of its architectural function. We observed a similar role of CTCF on DNA methylation and gene expression in the human orthologous gene HBA2. Our findings support a conserved role of CTCF in preventing DNA methylation spreading and gene silencing of cell-type-specific genes along differentiation.