Epigenetics and DNA Methylation

This study evaluates the responsiveness of DNA methylation aging biomarkers across 51 longevity interventions, identifying factors influencing their response and highlighting the utility of explainable clocks.

This study identifies quinoline-based compounds that inhibit DNA methyltransferases and other DNA-targeting enzymes, with compound 11 inducing DNA damage response in cancer cells.

This paper develops a vector system to manipulate histone H3 methylation in neurons, enabling the study of its role in cell differentiation and identity.

The paper evaluates methylation clocks in genetically diverse populations and finds they are less accurate in admixed cohorts and fail to consistently predict age acceleration in Alzheimer's disease cases.

The paper presents a method to directly measure methylation in ancient DNA, showing it is cost-effective and applicable to a wide range of samples.

The paper introduces MethylSeqLogo, a method that integrates DNA methylation data into sequence logos to better represent transcription factor binding specificity.

This paper develops two epigenetic clocks for rhesus macaques and finds that early life adversity, specifically infant maltreatment, is associated with epigenetic age acceleration.

The paper analyzes DNA methylation in dogs to identify age-related patterns, finding that LINE1 transposons show hypomethylation with age, varying by breed size and sex.

The paper evaluates how new DNA methylation arrays affect existing epigenetic age models and develops a cross-compatible model for 450k, EPICv1, and EPICv2 arrays.

This study shows that using updated reference genomes like T2T-CHM13 and pangenomes increases CpG detection in DNA methylation analysis and improves probe specificity in arrays, leading to more accurate findings in cancer studies.

The paper uses single-cell multi-omics to study EEC differentiation in mucinous colorectal cancer, identifies STAT3 as a regulator, and discovers a rare cancer cell type with neuron-like features.

PoreMeth2 identifies differentially methylated regions using Nanopore sequencing, revealing epigenomic changes in cancer and glial cells.

The paper develops an epigenetic clock for dogs using DNA methylation data to show that larger breeds age faster and have higher mortality risk.

The paper identifies methylation markers associated with age and BRD susceptibility in dairy cattle using RRBS, finding age-related and disease-specific differentially methylated genes.

The paper examines if prenatal exposure to genocide or trauma affects epigenetic aging in second-generation clocks among Rwandan adults, finding significant age acceleration linked to prenatal stress.

This study shows that H3.3K36M mutation reduces epigenetic memory and promoter methylation by disrupting the conversion of H3K9me3 domains into DNA methylation.

PCBS is an R package that provides fast and accurate analysis of whole-genome bisulfite sequencing data, offering improved accuracy and flexibility over existing tools.

MethyLasso identifies DNA methylation patterns and differentially methylated regions by segmenting whole-genome data, outperforming existing methods in benchmarking.

The paper identifies TBKBP1 as a key gene whose demethylation enhances cytotoxic activity in CMV-specific CD8+ T cells, suggesting it as a therapeutic target.

This study investigates DNA methylation changes in sepsis, finding that transcription factor promoters are demethylated, potentially driving cytokine expression during inflammation.

This study compares epigenetic aging rates between lab-reared and rewilded mice, finding faster aging in rewilded mice with implications for environmental influences on aging.

This study shows KDM5A and KDM5B regulate ERV expression and immune response by modulating KRAB-ZNF genes, with degradation of KDM5A causing rapid ERV activation.

This study measures MBD1 binding kinetics to methylated DNA with varying patterns and structural motifs, revealing that tandem CpG sites and DNA forks enhance binding, leading to a mechanistic model of epigenetic boundary maintenance.

The paper shows that transposable elements can transmit epigenetic changes across generations in Arabidopsis thaliana, often near stress-responsive genes, and these changes can affect gene expression and be subject to selection.

The paper reveals a mechanism by which automethylated PRC2 dimerizes on chromatin to allosterically activate another PRC2 protomer for H3K27me3 methylation.

This study shows TET2 and TET3 regulate Drosha and microRNAs in iNKT cells, linking DNA demethylation to gene expression and lineage specification.

The paper shows that multi-generational exposure to biotic stress increases epimutation rates in Arabidopsis, mediated by ROS1, affecting low-methylation genes.

The paper assesses the reliability of Infinium probes on Illumina Methylation arrays, identifies unreliable probes, and provides a method to exclude them using dynamic thresholds.

This study identifies epigenetic changes in HCC that affect cis-regulatory elements and retrotransposons, linking them to gene dysregulation and poor prognosis.

The paper benchmarks sample pooling for DNA methylation analysis in natural populations, finding that pooling captures similar global signals but detects more differentially methylated regions than individual libraries.