Epigenetics and DNA Methylation

The paper introduces sciMETv3, a high-throughput single-cell DNA methylation profiling method, achieving 100-fold higher cell throughput and compatibility with multimodal assays.

BSReadSim generates realistic bisulfite sequencing reads by integrating genetic variants and methylation profiles across multiple sequencing technologies.

The paper evaluates low-pass nanopore sequencing for global methylation measurement in plants, finding that higher coverage is needed for accuracy compared to vertebrates and demonstrating consistent results across sample conditions.

This study benchmarks 15 DNA methylation age prediction methods across 142 datasets, finding that model performance depends on training data characteristics and providing a resource for future research.

This paper develops an epigenetic clock for Xenopus tropicalis using DNA methylation data, finding age-associated CpG sites enriched in heterochromatin marks similar to mammals.

This study reports Cryo-EM structures of DNMT3A2/3B3 bound to di-nucleosomes, revealing how linker length and H3K36 methylation influence DNA methylation.

The paper shows that DNA methylation ageing is reflected in correlations between genomic loci, with a preference for 500 bp apart sites, and links this to PRC2-dependent H3K27me3 dilution.

The paper shows that DNA methylation is reset in iPSCs compared to donor PBMCs, with unique methylation sites influenced by genetics in each cell type.

This study models age-linked rDNA hypermethylation in human cells using dCas9-directed DNA methylation and finds no detectable effect on rRNA transcription or cellular growth.

This study shows that disrupting BAP1, an epigenetic regulator, causes chromatin remodeling and leads to breast cancer stem cell-like properties and altered glycosylation.

This study shows that interchromosomal contacts between regulatory regions can establish stable transgenerational epigenetic inheritance in Drosophila through chromatin interactions mediated by GAGA-factor and Pleiohomeotic.

This study examines the impact of negative life events on epigenetic aging in twins, finding associations between life stressors and accelerated aging markers, which are reduced in monozygotic twins.

This study identifies SET-21 as a novel H3K23 histone methyltransferase that synergizes with SET-32 to promote transgenerational epigenetic inheritance via nuclear RNAi in C. elegans.

The paper identifies age-associated CpGs and non-linear methylation trajectories across 4,641 samples, highlighting complexities in epigenetic aging that current clocks may miss.

This paper develops a multiplex methylation-specific qPCR assay for cancer biomarker detection, achieving higher detection rates than singleplex methods.

This study shows maternal obesity causes oocyte genome hyper-methylation via increased DNMTs, which can be partially transmitted to F2 offspring, and melatonin reduces this hyper-methylation through the cAMP/PKA/CREB pathway.

The paper identifies and characterizes DNA methylation reader proteins in Arabidopsis thaliana, revealing context-specific binding preferences and functional roles.

The paper identifies a rice-specific mechanism for female-preferential RNA-directed DNA methylation mediated by OsCLSY3 recognizing a GC-rich DNA motif.

The paper shows that temperature perception in C. elegans can drive transgenerational epigenetic inheritance through RNAi factors and small RNAs.

The paper introduces epiCHAOS, a metric to quantify cell-to-cell epigenomic heterogeneity in single-cell data and shows its utility in assessing stemness and plasticity.

The paper shows that m4C DNA methylation regulates hemJ expression in Synechocystis, affecting tetrapyrrole biosynthesis and pigmentation.

The paper introduces SAM-DNMT3A, a CRISPR-based method to induce global DNA methylation, and shows it exploits a vulnerability in ER-positive breast cancers.

The paper identifies DNA methylation and gene expression changes in human blood after a meal, linking them to cardiometabolic health and obesity-related genes.

The paper presents whole-genome DNA methylomes of tree shrew brains, revealing conserved and divergent DNA methylation patterns on sex chromosomes compared to other mammals.

This study shows that changes in transposable element methylation during aging predict age and that demethylation of young L1s is linked to cancer.

The paper uses a genomic DNA methylation reporter system to track dynamic DNA methylation changes in cell cycle genes during iPSC cardiac differentiation, showing hypermethylation correlates with gene expression reduction.

This study examines how paternal environments and genetic backgrounds affect early embryonic development and identifies molecular responses to paternal conditions.

The paper shows that in mouse male germ cells, promoter chromatin states are shaped by H3K4me3 density and H3K27me3 dynamics, influencing gene expression during development.

This study shows FAK inhibition reduces DNA methylation and reactivates the tumor suppressor DAB2 in breast cancer cells, leading to decreased proliferation.