Epigenetics and DNA Methylation

TranslAGE provides a standardized framework for benchmarking epigenetic aging biomarkers by harmonizing datasets and precomputing scores across multiple performance domains.

This paper estimates the age of breast cancers using an epigenetic clock based on methylation data, finding that younger tumors are more aggressive while older tumors show higher immune infiltration.

The paper develops CTexploreR to analyze cancer-germline genes, showing X-linked genes are DNA methylation dependent and exhibit maternal imprinting in early embryos.

The paper maps sex-associated DNA methylation in blood cell types using whole genome bisulfite sequencing data from the iMETHYL database, identifying cell-type specific differentially methylated sites and their functional implications.

This study identifies AEBP2 as a therapeutic target in EZH2-mutant lymphoma by showing its role in maintaining H3K27me2 levels through a PRC2.2 complex.

The paper examines age-related DNA methylation changes on sex chromosomes in two avian species, finding significant decreases on the female-specific W chromosome and species-specific patterns on the Z chromosome.

This study shows that KDM5 demethylases suppress R-loop formation in breast cancer cells, reducing DNA damage and enhancing immune-related gene expression without affecting normal cells.

The paper develops an explainable deep learning framework to predict health scores from blood DNA methylation, showing strong predictive accuracy and alignment with biological processes.

The paper investigates CLPB overexpression in breast cancer, finding hypomethylation of its promoter correlates with poor survival and suggests it as a potential therapeutic target.

The paper shows that maternal SETDB1 is essential for silencing 2-cell totipotency genes in mouse embryos, allowing development beyond the 8-cell stage.

The paper develops a machine learning model to predict methylation signatures distinguishing OSCC from normal tissue, achieving high accuracy on validation datasets.

The paper investigates DNA methylation differences in prostate cancer across African, European, and Asian ancestries, finding ancestry-driven methylation patterns linked to disease aggressiveness in African tumors.

The paper shows that PMD-C proteins in Arabidopsis counteract Polycomb silencing by targeting specific DNA motifs to maintain gene expression.

The paper identifies SENP7 and UTF1/VENTX as new loci influencing cPCDH methylation in blood and brain through a genome-wide association study.

The paper investigates how genetic background affects RNAi-induced changes in DNA methyltransferase expression in Daphnia pulex, finding significant genotypic differences and cross-reactivity in gene silencing.

The paper develops epigenetic clocks using long-read DNA methylation data from diverse ancestries, showing improved aging predictions and identifying ancestry-specific aging pathways.

This study identifies the mechanism by which AW1-51, a small activating RNA, promotes DNA demethylation and reactivation of the CEBPA gene in cancer.

This study identifies HDA-1 as essential for maintaining epigenome stability in Neurospora crassa by regulating H3K27me3 and heterochromatin integrity.

This study demonstrates that a small epigenome-wide association study (EWAS) with high methylmercury exposure variance can identify differentially methylated CpG sites and pathways related to MeHg toxicity.

This study investigates the barley methylome, identifies differentially methylated regions, and shows their association with gene expression and phenotypic traits, improving genomic prediction models.

The paper identifies TE-like methylated genes in maize endosperm that are demethylated and highly expressed, revealing a switch from heterochromatin to euchromatin that activates protein storage genes.

This study shows that Lantana camara leaf extract suppresses DNMT1, leading to tumor suppressor gene reactivation, G0/G1 arrest, apoptosis, and reduced migration in TNBC cells.

This study identifies cell-type-specific DNA methylation dynamics in the human cortex across development, highlighting prenatal periods as critical for epigenomic plasticity and linking changes to neurodevelopmental disorders.

This study profiles DNA methylation in COVID-19 patients and finds hypomethylation linked to neurological pathways in severe cases.

The paper shows HRDE-1 maintains transcriptional silencing in C. elegans without chromatin marks by promoting small RNA feedback loops.

This paper identifies GyrB3's role in transposon silencing through histone deacetylation, showing its interaction with HDA6 and its impact on DNA methylation and transposon activity.

This study identifies multiple epigenetic mechanisms that silence SSTR2 expression in PNETs, highlighting the role of DNMT3B, PRC complexes, histone demethylases, and chromatin remodelers, with potential therapeutic implications.

The paper identifies transcript-proximal methylation-associated regulatory sites (TMRs) by integrating RNA-seq and WGBS data, showing their enrichment in cancer and correlation with transcription.

The paper shows CDCA7A and CDCA7B maintain CG methylation in centromeric heterochromatin by remodeling H1-containing nucleosomes, with H1 having an inhibitory role.

This study shows Foxh1 recruits PRC2 to specific loci, silencing genes in ectoderm while activating them in endoderm during early embryogenesis.