Epigenetics and DNA Methylation

The paper investigates whether epigenetic mosaicism in somatic tissues of Pistacia terebinthus trees persists in reproductive cells, finding that intraplant methylation variation is retained in pollen.

mIDEA predicts and interprets protein-methylated-DNA interactions using a structure-aware energy matrix, improving binding-site prediction with methylation data.

The paper shows that PRC1 and PRC2 are independently recruited to hypomethylated pericentromeric heterochromatin in mESCs without requiring specific mediators.

This paper introduces SACOMA, a spatially-aware unsupervised method to identify co-methylated regions in DNA methylation data, improving sensitivity and false-positive control.

UMBS-seq improves 5-methylcytosine detection in low-input DNA by reducing degradation and noise, outperforming existing methods in yield and efficiency.

The paper identifies an isoform-specific regulatory mechanism of AEBP2 on PRC2 activity, showing the long isoform inhibits PRC2 while the short isoform enhances it.

The paper introduces dimelo-toolkit, a Python package for analyzing multimodal long-read epigenetic data, demonstrating its use with a novel DiMeLo-seq protocol to study chromatin state in GM12878 cells.

This paper introduces DMCTHM, a method using TMCMC and HMMs to identify DMCs in cancer epigenetics, outperforming existing methods and uncovering new DMCs in colorectal cancer.

This study identifies 49 CpG sites associated with generalized anxiety disorder across three ancestries but finds limited replication in an independent cohort.

This study shows that drug-treated colorectal cancer cells switch from EZH2-mediated repression to KDM6A-mediated activation, enabling reinitiation of proliferation and tumor relapse.

OpTiles dynamically defines tiling windows for methylation data based on CpG distribution and variability, improving reliability and annotation of targeted methylation datasets.

DMRU is a generative deep-learning model that identifies condition-specific DNA methylation in plants with high accuracy across species and conditions.

This study reveals the molecular mechanism of DNMT3A-3L-mediated de novo DNA methylation through structural analysis of its chromatin interactions and regulatory dynamics.

The paper deconvolves cancer methylation patterns to show that most methylation changes in B-cell cancers are proliferation-driven, not disease-specific, and identifies SLC22A15 as a novel tumour suppressor.

This study shows that elevated methionine increases DNA methylation of transposable elements in Arabidopsis, leading to their silencing without changing methyltransferase expression.

The paper examines DNA methylation's role in gene expression and chromatin structure in stick insects, finding it correlates with chromatin compartments and may inhibit gene expression near TSS.

The paper uses CROP-seq to identify histone modifying enzymes regulating inflammatory macrophage activation, finding Kdm5c modulates inflammatory responses by balancing baseline and inducible activation.

The paper identifies long Polycomb loops as a biomarker for sensitivity to Polycomb inhibition in certain cancers, particularly in AMLs with specific mutations.

This study shows TET1's non-catalytic activity helps maintain chromatin structure to prevent abnormal methylation in male germ cells.

This study investigates how DNA methylation and H3K9me3 maintain transgene silencing and shows that targeted DNA demethylation can reverse it in mammalian cells.

This study identifies sex-specific epigenetic changes in the nucleus accumbens of male and female mice exposed to chronic morphine, revealing shared biological dysregulation and potential therapeutic targets.

This study identifies altered DNA methylation patterns in the upper respiratory airway of COVID-19 patients, highlighting changes in immune-related genes and potential implications for airway health.

This study evaluates the robustness of epigenetic clocks to common SNPs across diverse ancestries and finds they remain stable despite cSNP-CpG overlaps.

This study examines epigenetic, microbiome, and immune differences in early-onset colorectal cancer (EOCRC) compared to average-onset CRC, finding accelerated epigenetic aging and stronger immune-microbe correlations in EOCRC.

This study shows that SETDB1 automethylation on H3K9-like motifs is essential for its function in ESCs, affecting chromodomain interactions and H3K9me3 establishment.

This study shows that dietary serine restriction alters H3K27me3 and H3K4me3 histone modifications, reducing tumor growth and plasticity in head and neck cancer.

This study compares CDO1 promoter methylation levels in gastric cancer and chronic gastritis patients with and without H. pylori infection, finding higher methylation in cancer and H. pylori-positive gastritis.

The paper investigates the roles of TRIM28, DNA methylation, and p53 in regulating gene and transposon expression in human embryonic and trophoblast stem cells, revealing divergent responses to genomic instability.

This paper uses nanopore long-read sequencing to characterize native CpG methylation and identify allele-specific methylation regions in the prostate genome.

This study develops an epigenetic clock using DNA methylation patterns to accurately predict the age of haddock, achieving 93% accuracy with 111 CpG loci.