Mapping parental DMRs predictive of local and distal methylome remodeling in epigenetic F1 hybrids.

F1 hybrids derived from a cross between two inbred parental lines often display widespread changes in DNA methylation and gene expression patterns relative to their parents. An emerging challenge is to understand how parental epigenomic differences contribute to these events. Here, we generated a large mapping panel of F1 epigenetic hybrids, whose parents are isogenic but variable in their DNA methylation patterns.

Predicting 3D chromatin interactions from DNA sequence using Deep Learning.

Gene regulation in eukaryotes is profoundly shaped by the 3D organization of chromatin within the cell nucleus. Distal regulatory interactions between enhancers and their target genes are widespread and many causal loci underlying heritable agricultural or clinical traits have been mapped to distal cis-regulatory elements. Dissecting the sequence features that mediate such distal interactions is key to understanding their underlying biology.

Heterochromatin is a quantitative trait associated with spontaneous epiallele formation.

Epialleles are meiotically heritable variations in expression states that are independent from changes in DNA sequence. Although they are common in plant genomes, their molecular origins are unknown. Here we show, using mutant and experimental populations, that epialleles in Arabidopsis thaliana that result from ectopic hypermethylation are due to feedback regulation of pathways that primarily function to maintain DNA methylation at heterochromatin.