Germline genomic and methylomic dynamics following three generations of early-life metabolic challenges

de Anca Prado, V.; Pertille, F.; Andersson, D.; Mourin-Fernandez, M.; Godia, M.; Jimenez-Chillaron, J. C.; Ruegg, J.; Guerrero-Bosagna, C.

doi:10.64898/2026.07.21.739755

bioRxiv · 10.64898/2026.07.21.739755

Germline genomic and methylomic dynamics following three generations of early-life metabolic challenges

de Anca Prado, V.·Pertille, F.·Andersson, D.·Mourin-Fernandez, M.·Godia, M.·Jimenez-Chillaron, J. C.·Ruegg, J.·Guerrero-Bosagna, C.

View original source ↗Export metadata ↓

Abstract

Environmental and dietary factors can exert multigenerational effects on health and development. In this study, we investigated whether early-life metabolic challenge affects the germline genome and epigenome across three generations. Using a murine model of early life obesity via litter size reduction (overnutrition group, ON) and a control group (CT), we followed the paternal lineage focusing on germline genomic and methylation changes employing Genotyping-by-Sequencing (GBS) coupled with methyl-immunoprecipitation (GBS-MeDIP). We found that unrelated ON families clustered together based on identified Single-Nucleotide Polymorphism (SNP), suggesting that the treatment may have genomic impact. Copy number variations (CNVs) events were identified in ON individuals, being enriched in Long Interspersed Nuclear Elements (LINEs) and Long Terminal Repeats (LTRs). While Principal Component Analysis (PCA) of the methylome showed no clear treatment effect, pathway enrichment and regional analyses revealed methylation changes associated with transposable elements and developmental genes. Notably, the ON group exhibited a disruption in the methylation of Repetitive Elements (RE), which was significant in the same type of RE that were also enriched in the observed CNVs. The ON also showed reduced emergence of novel SNPs in offspring compared to the CT group. These findings suggest that multigenerational metabolic challenge can constrain genetic variability and induce genome instability, potentially mediated by transposable element activity rather than widespread changes in DNA methylation. This work highlights the importance of studying both genome and epigenome dynamics under realistic, multigenerational exposure scenarios and suggests that early metabolic challenges can have long-lasting impacts on genomic architecture and evolutionary potential.

Explore related subjects

genomics Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

de Anca Prado, V., Pertille, F., Andersson, D., Mourin-Fernandez, M., Godia, M., Jimenez-Chillaron, J. C., Ruegg, J., Guerrero-Bosagna, C.. 2026-07-24. Germline genomic and methylomic dynamics following three generations of early-life metabolic challenges. https://doi.org/10.64898/2026.07.21.739755

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

RNA isoform-resolved multiplexed sequencing with bioorthogonal barcoding

RNA isoform dysregulation drives disease pathogenesis and is the target of FDA-approved splice-switching therapeutics. However, multiplexed sequencing methods discard splice junction information because only 3' termini are barcoded and counted. Here, we repurpose acylation and click chemistries to conjugate bioorthogonal barcodes (bobcodes) directly onto multiple internal positions along cellular RNAs. Bobcoded RNAs from multiple samples are pooled for multiplexed cDNA synthesis, during which reverse transcriptase switches from each RNA template onto its tethered bobcode with greater than 99% accuracy in species mixing experiments. Bobcode attachment intervals set cDNA insert sizes without a library fragmentation step, and priming with poly(dT) or random hexamers selects between 3'-end counting and full-length isoform capture. A bioorthogonal barcode-sequencing (BOB-seq v0.1) drug screen identifies transcriptome-wide on- and off-target RNA splicing effects and outperforms existing multiplexing RNA sequencing methods in workflow simplicity, sample-to-sample variability, and barcoding accuracy. Bobcodes add isoform resolution to scalable multiplexed RNA sequencing.

genomics↗

bioRxiv2026

Integrative Nanopore and Illumina sequencing reveals age-associated tRNA modification and CCA-tail dynamics in yeast

Aging is characterized by a progressive loss of proteostasis. Transfer RNAs (tRNAs) are essential regulators of translation, yet their dynamics during aging remain poorly understood due to challenges in sequencing highly modified RNAs. Here we present a benchmarked Nanopore direct RNA sequencing (RNA004 chemistry) resource that profiles the Saccharomyces cerevisiae tRNAome during replicative aging at single-molecule resolution. Using in vitro transcribed tRNA controls, we establish modification detection thresholds and validate key findings with orthogonal Illumina sequencing. While overall tRNA abundance remains largely stable, our resource reveals age-associated terminal A cleavage at the 3' CCA tail of mature tRNAs, targeted T-loop and anticodon modification changes, and single-molecule evidence of modification co-occurrence. This dataset provides a resource for exploring tRNA regulation, translation fidelity, and longevity.

genomics↗

bioRxiv2026

A hydrogen-producing mitochondrion in an anaerobic eukaryotrophic rhizarian

Diverse eukaryotes thrive under low oxygen conditions, in part through highly modified mitochondrion-related organelles (MROs) that use alternate metabolic pathways to support ATP production and cofactor recycling. Anaerobic lifestyles have evolved repeatedly across the eukaryotic tree of life, each providing an independent opportunity to understand how eukaryotes adapt to life in low oxygen conditions. Here, we use single-cell transcriptomics to reconstruct the MRO metabolism of PCE SSF, a benthic eukaryotrophic flagellate and the first cultivated representative of Novel Clade 12 (NC12; Rhizaria), an independently anaerobic rhizarian lineage. PCE SSF possesses an anaerobic hydrogen-producing mitochondrion capable of hydrogenosome-type substrate-level phosphorylation. It also retains a nearly complete but likely branched tricarboxylic acid pathway that lacks citrate synthase and malate dehydrogenase. The function of citrate synthase may instead be fulfilled by the typically cytosolic ATP citrate lyase, previously reported in this context only in the anaerobic cercozoan, Brevimastigomonas motovehiculus. Unlike B. motovehiculus, however, PCE SSF retains only Complex II and the NuoE/NuoF subunits of the electron transport chain and lacks a mitochondrial genome. Together, these features indicate an atypical and reduced mitochondrial metabolism, highlighting the diversity of evolutionary solutions to anaerobic energy metabolism in eukaryotes.

genomics↗