Epigenetics and DNA Methylation

The paper characterizes the epigenomic and 3D genomic landscape of human subcutaneous adipose tissue at the cell-type level and links epigenomic variation to abdominal obesity risk.

This paper introduces two single-cell sequencing methods for detecting 5mC and 5hmC, showing increased 5hmC in aging mouse hippocampus.

This study reports the structure of the AMT complex bound to OCR protein, revealing its substrate binding mechanism and conformational changes during 6mA methylation.

This study identifies a specific epigenetic mechanism that silences PAX2 to initiate most endometrial cancers.

The paper identifies non-linear DNA methylation patterns with aging, showing peaks or troughs in middle age and linking them to disease onset.

This study identifies a novel mechanism where YEATS2 and GCDH regulate histone crotonylation, promoting EMT in head and neck cancer.

The paper shows how DNA methylation aging emerges from a hierarchy of molecular processes across different timescales.

This study shows TET1 acts as a tumor suppressor in lung adenocarcinoma by promoting antitumor immunity and inhibiting cell proliferation and migration.

The paper identifies a causal epigenetic link between TRIM61 methylation and age at menarche through genome-wide DNA methylation analysis and Mendelian randomisation.

The paper shows chronic heterochromatin loss in neurons leads to ERV de-repression, inflammation, and cognitive decline in mice.

The paper identifies reactive CpGs and RNA expression changes in early COVID-19 using eQTM analysis, showing reversible molecular shifts linked to disease severity and recovery.

ComputAgeBench benchmarks epigenetic aging clocks by comparing 13 models on 66 harmonized blood DNA methylation datasets to evaluate their ability to distinguish healthy individuals from those with aging-accelerating conditions.

Snappy identifies DNA methylation sites in bacteria using Oxford Nanopore reads without requiring control samples or motif enrichment heuristics.

The paper identifies methylation-dependent genetic effects on regulatory elements in diverse human genomes using a multiplexed mSTARR-seq assay, revealing 8,020 sites with genetic effects, 42.3% of which vary with methylation state.

This study shows that formaldehyde exposure alters histone methylation and acetylation in human cells, with changes resembling those in cancer and Alzheimer's disease.

This paper shows that CGGBP1 from higher amniotes restricts cytosine methylation and maintains GC-rich transcription factor binding sites in repressed promoters, influencing TFBS evolution.

This study examines DNA methylation changes in crucian carp brains during anoxia and reoxygenation, identifying differentially methylated regions and their association with gene expression.

This study identifies DNA hypomethylation, not DNA damage, as the primary mechanism of azacytidine and decitabine anti-cancer activity, linking it to chromatin regulators like USP48.

The paper shows that non-methylation factors cause age-predictive pseudomethylation signals in methylation arrays, affecting epigenetic clocks.

The paper identifies USP48 as a regulator of chromatin stability and DNA damage response to hypomethylating agents, showing its loss increases susceptibility to these drugs in AML.

The paper introduces a data repository containing epigenomic data from mice exposed to various environmental toxicants, enabling research on disease susceptibility.

The paper characterizes persistent epigenomic and transcriptomic changes in mice exposed to environmental toxicants across life stages, revealing widespread gene expression and chromatin alterations.

This study examines how early-life exposure to environmental toxicants alters TE chromatin accessibility and expression in mouse liver, revealing exposure-specific and sex-dependent effects.

The paper develops a mathematical model to investigate how allostery and nucleation contribute to H3K27 methylation dynamics in early Drosophila embryogenesis.

The paper investigates the evolutionary origins of DNA methylation, finding it was likely acquired from bacterial donors to silence transposable and viral elements across eukaryotes.

The paper identifies heterogeneous DNA methylation loss and LINE-1 activation in multiple myeloma, linking them to KZFP expression reduction and disease progression.

The paper creates a DNA methylation aging atlas across 17 human tissues, identifying conserved and tissue-specific aging signatures and potential therapeutic targets.