Epigenetics and DNA Methylation

The paper analyzes how epistemic uncertainty affects the reliability of aging clocks in predicting rejuvenation effects during cellular reprogramming.

This study shows that DNA hydroxymethylation in gene bodies limits transcriptional changes with age in mouse and human tissues.

The paper compares biological age indicators across different blood cell types and finds cell type-specific associations with calendar age.

This study shows PRAME expression in melanoma is negatively regulated by TET2-mediated DNA hydroxymethylation, with reduced 5hmC levels correlating with PRAME upregulation.

The paper shows melanoma cells develop therapy resistance through AP-1-mediated cellular memories that encode transient gene expression and chromatin changes.

This study shows that loss of H3K9me3 in adult mice leads to premature aging, characterized by reduced lifespan, frailty, and accelerated epigenetic aging.

The paper develops a DNA methylation score to quantify the impact of maternal smoking on newborn health outcomes in European and South Asian populations, finding consistent associations with smaller birth size and lower birth weight.

The paper shows that DNA methylation in Amoebidium appalachense silences endogenized giant viruses, contributing 14% of its genes and revealing a dynamic process of viral integration and purging.

This study investigates the evolution of IBM1, an H3K9 demethylase, in flowering plants, showing its role in regulating gene body methylation and its dynamic evolution across species.

DMRIntTk integrates DMR sets from different methods using density peak clustering to enhance methylation difference proportions and comprehensiveness.

The paper shows that pre-implantation genome-wide methylation in European badgers is influenced by environmental factors and linked to early-life traits, suggesting an epigenetic mechanism for adaptive plasticity.

The paper maps 5mC and 5hmC modifications in mouse cortical cell types using Nanopore sequencing and RNA sequencing, revealing astrocytes as a major source of 5hmC and providing a resource for methylome analysis.

The paper introduces a directional functional class scoring method for Infinium DNA methylation data, showing improved performance in detecting pathway methylation differences in various biological contexts.

The paper resolves the paradox of global methylation perturbation having little effect on most genes by showing gene-specific protection through enhancer-silencer balance.

Rockfish improves 5-methylcytosine detection from Nanopore sequencing with higher accuracy and efficiency compared to existing methods.

This study identifies H3K27me1 as a chromatin scar that mediates lifelong stress susceptibility through its role in altering gene expression in the nucleus accumbens.

The paper investigates DNA methylation changes in ancient genomes to assess epigenetic impacts of the Neolithic transition but finds no systematic methylation differences related to diet or lifestyle.

mLiftOver converts DNA methylation data between Infinium platforms, enabling accurate integration and analysis across different array versions.

This study creates a DNA methylation database for gynecological cancers and develops qMSP assays for detection and classification.

The paper investigates the role of DNA methylation machinery in the reproduction and development of the pea aphid, showing its involvement in oocyte and embryo viability.

The paper shows that H3.2K4 antagonizes Polycomb group activity and promotes target gene expression in vivo.

The paper introduces BAllC, a binary format for single-cell DNA methylation data, and BAllCools, a toolkit to improve storage and operational efficiency.

This study compares the structural and functional differences between human and mouse DPPA3 in binding to UHRF1 PHD finger, showing weaker human DPPA3 binding and reduced inhibition of UHRF1 chromatin binding.

This paper introduces aging clock models that predict age-related diseases by analyzing DNA methylation in specific cellular pathways, showing strong predictive power for conditions like Alzheimer's and atherosclerosis.

The paper develops DNA methylation predictors for mammalian maximum lifespan, gestation time, and sexual maturity, showing species-level epigenetic signatures that differ from individual lifespan variation.

The paper uses de-novo somatic mutations to deconvolute 5mC methylation patterns in mixed tissues, showing improved accuracy in estimating methylation levels and detecting differentially-methylated sites.

This study analyzes the methylome of Populus nigra cv. 'Italica' under various environmental stresses and identifies stress-specific and generic methylation responses.

PT-seq is a high-sensitivity method for mapping phosphorothioate DNA modifications in complex microbial communities and metagenomic identification of PT-containing microbes.

The paper develops a computational framework to classify blood cell types from long-read sequencing data using DNA methylation patterns, showing accurate classification for some regions and cell types.

This study examines DNA methylation changes in mouse tissues due to lead and phthalate exposure, identifying tissue- and sex-specific DMRs and their association with genomic imprinting.