Online now! Cell-free DNA #methylome and #fragmentome analysis for relapse monitoring of #EwingSarcoma

By S. Richardson, M. McCabe, @florentmouliere.bsky.social & colleagues @cancerresearchuk.org @manchester.ac.uk

➡️ doi.org/10.1038/s44321-026-00396-7

Photorespiration is linked to DNA methylation by formate as a one-carbon source - Nature Plants This study reveals that Arabidopsis reassimilates formate produced during photorespiration via the cytosolic folate cycle to fuel DNA methylation, forming a metabolic–epigenetic bridge that links elev...

#Photorespiration fuels C1 metabolism to support DNA methylation in Arabidopsis, linking photosynthetic C flux to #epigenome stability & showing how rising CO₂ can reshape the plant #methylome.

by #ValentinHankofer &
@martingroth.bsky.social

With contributions by
@andreaghirardo.bsky.social

A ternary-code DNA methylome atlas of mouse tissues - Genome Biology Background DNA cytosine modifications, including 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC), are key epigenetic regulators with distinct functions. Dissecting the ternary code (C, 5mC, 5hmC) across tissues and cell types remains a critical priority due to the limitations of traditional profiling methods based on bisulfite conversion. Results Here, we leverage the combined bisulfite and enzymatic (bACE) conversion with the Mouse Methylation BeadChip to generate 265 base-resolution ternary-code modification maps of 5mC and 5hmC across 29 mouse tissue types spanning 8–76 weeks of age and both sexes. Our atlas reveals a complex grammar of 5hmC distribution, jointly shaped by cell mitotic activity, chromatin states, and interplay with 5mC at the same and neighboring CpG sites. Of note, we demonstrate that 5hmC significantly complements 5mC-based biomarkers in delineating cell identity in both brain and non-brain tissues. Each modification state, including 5hmC alone, accurately discriminates tissue types, enabling high-precision machine learning classification of epigenetic identity. Furthermore, the ternary methylome variations extensively implicate gene transcriptional variation, with age-related changes correlated with gene expression in a tissue-dependent manner. Conclusions Our work reveals how tissue, sex, and age jointly govern the dynamics of the two cytosine modifications, augments the scope of DNA modification biomarker discovery, and provides a reference atlas to explore epigenetic dynamics in development and disease.

#Epigenetics profiling of C57BL/6 J mice across 29 tissues, both sexes, age range of 8–76 weeks for population-scale analysis doi.org/10.1186/s130... @SolmoeLee @KohliLab @zhouwanding.bsky.social #Methylome #Aging #TranslationalScience

#methylome #epigenetics #multiomics

New publication: High-resolution #methylome analysis uncovers stress-responsive genomic hotspots and drought-sensitive #transposableelement superfamilies in the clonal Lombardy #poplar, by @kjfverhoeven @wimvanderputten and others.
https://doi.org/10.1093/jxb/erae262

Somatic #Aneuploidy 🐭🧠

Single-cell DNA #Methylome

734 (100kbp-resolved) or 1433 (1Mbp-resolved) Aneuploid cells/415k total cells

#Pericyte -> highest aneuploidy rate

Strikingly enriched ploidy event
mChr16 trisomy-> hChr21 trisomy #DownSyndrome

bioRxiv 2023
www.biorxiv.org/content/10.1...

Interesting #Aorta Transcriptome+DNA #Methylome

Glucose-6-phosphate dehydrogenase/G6PD S188F CRISPR rat vs WT

1509 DEG->⏫DNMT1/2, TET2/3->
⏫5-hmC ie.⏬global DNA methylation

4222 differentially methylated regions
-> 29 hypomethylated + ⏫genes-> Lipid/ROS/Thermogenesis
www.mdpi.com/1422-0067/24...