Epigenetics and DNA Methylation

This study performs a meta-analysis of epigenetic age acceleration across 93 datasets and 23K samples, highlighting geographic, ethnic, and gender differences in aging rates.

The paper uses WGBS to analyze DNA methylation changes during adipocyte differentiation and identifies context-dependent gene expression related to DMRs.

The paper characterizes the developmental trajectories of adult epigenetic clock sites using longitudinal cohort data, finding divergent patterns, early individual variation, and enrichment for genetic and prenatal environmental factors.

The paper develops improved models for detecting 6mA using Nanopore sequencing, achieving higher accuracy than existing methods.

The paper quantifies higher order interactions in DNA methylation data from Kabuki syndrome patients and controls, revealing reduced epigenome complexity and novel biological relationships.

This study identifies DNA methylation signatures in wild baboons linked to early life adversity, showing exposure-dependent effects and functional relevance of methylation changes.

This study develops a targeted long-read bisulfite sequencing method to analyze promoter methylation in severe preterm birth, finding significant hypomethylation of the MIR155HG gene promoter.

This study investigates DNA methylation dynamics during lamprey embryogenesis, revealing extensive maternal-to-paternal epigenome remodeling and its link to programmed genome rearrangement.

This study shows that targeting EZH2 and HDACs together induces ferroptosis in hematological malignancies by upregulating cholesterol biosynthesis and causing metabolic stress.

The paper identifies an alternative splicing event in SUZ12 that generates two PRC2 subtypes, SUZ12-S and SUZ12-L, with distinct roles in PRC2 function and H3K27 methylation.

This study uses longitudinal meta-regression to examine how DNA methylation effects on child health outcomes vary by timing, finding larger effects in childhood but noisier associations and time-specific signals.

This study compares 5mC detection accuracy between Nanopore R9 and R10 chemistries using human datasets, finding high concordance and strong correlation with Illumina bisulfite methods.

The paper shows that a mutation in Khdc3 in ancestral mice leads to transgenerational metabolic defects in offspring through epigenetic changes in gametes.

The paper shows that RNase A treatment during ChIP-seq falsely reduces PRC2 chromatin occupancy signals, revealing limitations in using this method to study RNA-dependent chromatin regulation.

This paper develops an epigenetic score to objectively measure alcohol consumption using blood-based DNA methylation and validates it across multiple cohorts, finding associations with brain health metrics.

The paper discovers novel DNA cytosine deaminases and develops a nondestructive single-enzyme methylation sequencing method for high-coverage methylome mapping of low-input DNA.

This paper introduces Active-Seq, a method to profile hypomethylated regions by enriching non-modified CpG sites, showing its effectiveness in various DNA sources.

This paper introduces RTFS, a method for pre-selecting CpGs for disease prediction models, and shows it performs well for predicting type 2 diabetes onset risk.

This study develops a single-nucleus CUT&RUN assay to analyze histone modifications in HNSCC cell lines, revealing how epigenetic changes contribute to cancer progression and heterogeneity.

Torch-eCpG is a GPU-accelerated tool for eQTM mapping that is faster and scales with increasing methylation loci.

This study identifies DNA methylation changes during bumblebee development, suggesting sex-specific erasure in ovaries and enrichment in sperm, marking the first such finding in insects.

The paper identifies kidney-specific methylation patterns that correlate with kidney function and show changes during disease progression.

The paper shows how Cdx2 binds different DNA motifs in developing and adult cells, leading to distinct gene activation patterns through methylation-dependent and -independent mechanisms.

The paper develops low-input and single-cell methods for Infinium DNA methylation BeadChips, improving detection rates and data quality for small sample sizes.

This study investigates the role of Dnmt1 in oocyte production in Bemisia tabaci by knocking it down and analyzing gene expression and methylation patterns, finding specific effects on the Wnt pathway.

The paper shows DNA hypomethylation in zebrafish leads to Cdk4/6 activation, ATR-mediated replication stress, and cell cycle arrest, which restricts liver growth.

This study identifies a self-regulatory mechanism of the 6mA methyltransferase AMT1 in Tetrahymena thermophila, showing that AMT1 modulates its own transcription through 6mA methylation and affects cell fitness.

The paper shows sparse CBX2 nucleates Polycomb proteins to form condensates that regulate facultative heterochromatin and cellular differentiation in mESCs.

The paper investigates methylome stability and parental effects in Lombardy poplar, finding stable CG methylation patterns and weak parental carry-over effects on phenotypic traits.

The paper defines and maps CpG islands and their methylation status in the T2T-YAO genome, comparing it to T2T-CHM13 and finding differences in CpG density and methylation patterns.