Epigenetics and DNA Methylation

The paper profiles L1 DNA methylation at single-locus resolution across normal and cancer cells, revealing how methylation and transcription interact with L1 integration sites.

The paper improves transcription factor binding prediction by integrating CpG methylation data with PWM-based scores, showing better performance than standard PWM scores for most TFs.

This study shows that early life adversity causes sex-specific changes in DNA methylation of parvalbumin cells in the prefrontal cortex of rats, affecting cell counts and stress hormone responses.

This study shows that DNMT3B PWWP mutations cause hypermethylation of heterochromatin marked by H3K9me3, disrupting DNA methylation homeostasis and contributing to ICF syndrome, cancer, and aging.

The paper shows that non-CG DNA methylation and MeCP2 regulate long genes to maintain neuron type-specific gene programs at high resolution.

This study shows that reducing mitochondrial DNA copy number in human cells changes nuclear DNA methylation and gene expression, revealing pathways linked to disease.

The paper develops and validates deconvolution models using DNA methylation data to estimate cell-type proportions in the human cortex, finding glial cells are twice as abundant as neurons and linking cell-type proportions to Alzheimer's disease neuropathology.

The paper identifies maternal histone methyltransferases that antagonistically regulate monoallelic expression in C. elegans intestinal progenitor cells.

This study identifies UBP5 as an interactor of PRC2 in Arabidopsis, showing it regulates development and stress responses by counteracting PRC2-mediated repression through H2Aub erasure.

The paper introduces causality-enriched epigenetic clocks, DamAge and AdaptAge, to track detrimental and adaptive methylation changes linked to aging, showing their association with adverse outcomes and beneficial adaptations.

This paper introduces a transformer-based model to predict cell type-specific DNA methylation regulatory variants and improves fine mapping for brain disorders.

This study identifies MBD2 as a methyl reader that silences transposable elements during male gametogenesis by acting downstream of DNA methylation.

This study shows that Helicobacter pylori's methylome responds to acidity via the ArsRS two-component system and HsdM1, with differential methylation patterns affecting gene expression during acid stress.

This study identifies sex-based differences in DNA methylation and gene expression in late-gestation mouse placentas, revealing distinct patterns on the X chromosome and autosomes.

This study shows that Decitabine suppresses tumour growth in ER+ breast cancer by inducing DNA hypomethylation and altering 3D chromatin structure.

This paper develops a deep learning model that classifies 13 cancer types and non-cancer tissues using DNA methylation data with 98.2% accuracy, identifying methylation loci linked to cancer-related genes.

This study examines how DNA methylation and gene expression respond to elevated pCO2 in eastern oysters, finding sex-specific effects on transcriptional noise and gene regulation.

The paper investigates the conditional probability of symmetric DNA methylation in Arabidopsis plants using sequencing techniques and finds that CpG and CWG methylation sites influence each other over long distances.

The paper compares DNA methylation age in four premature aging mouse models, finding ERCC1 mice show the most significant increase in epigenetic age.

The paper maps DNA methylation quantitative trait loci (meQTL) in three tissues and uses Mendelian randomization to link DNAm to Alzheimer's and Parkinson's disease risk.

The paper develops a computational model to forecast H3K27 methylation dynamics in Drosophila with high temporal resolution and shows that PRC2 activity and replication frequency define methylated H3K27 pools.

This study identifies 48% differentially methylated positions and 37% variably methylated positions in blood methylomes across aging, revealing their roles in entropy and epigenetic clocks.

The paper predicts gene expression changes after HDACi treatment using machine learning with pre-treatment transcriptome and epigenomic data, achieving high accuracy in distinguishing up- and downregulated genes.

This study shows that TFAP2C deficiency in porcine embryos leads to developmental disorders by altering epigenetic modifications and gene expression.

The paper evaluates imputation methods and quality standards for predicting epigenetic age from single-cell DNA methylation data in humans.

The paper generates a single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain, identifying methylation patterns and regulatory networks across cell types and brain regions.

The paper introduces memo-eQTL, a method to identify DNA methylation-modulated eQTLs, and finds 1,731 novel memo-eQTLs in prostate samples that alter SNP-gene expression interactions through CTCF-based chromatin structure changes.

This study shows early moderate prenatal alcohol exposure affects DNA methylation in offspring, with some effects replicated in humans, and maternal diet can mitigate these effects.