A Comprehensive DNA Methylome BodyMap across 12 Organs/Tissues from Spaceflight Mice

Methylome-transcriptome integration reveals molecular signatures of intrinsic aerobic capacity in aged skeletal muscle.

BACKGROUND Intrinsic aerobic capacity is a critical determinant of metabolic health and healthy aging, yet its epigenomic and transcriptomic features in aged skeletal muscle, and whether these intrinsic differences are accompanied by distinct exercise-related molecular responses, remain unclear. METHODS Soleus muscle from aged selectively bred high- and low-running capacity rats (HCR and LCR; 23-24 months) was profiled by reduced representation bisulfite sequencing (RRBS) and RNA sequencing (RNA-seq). Differentially methylated regions (DMRs) were annotated, functionally enriched, integrated with differentially expressed genes (DEGs), and correlated with maximal oxygen uptake (VO₂max). An age-comparable voluntary-running cohort was further analyzed by RNA-seq and selected protein profiling to assess exercise adaptation. RESULTS RRBS identified broad baseline methylome remodeling, including 7196 significant DMRs, with a higher proportion of hypermethylated regions in HCR muscle. These DMRs were mainly localized to open-sea CpGs, while gene-associated DMRs were predominantly intronic and exonic, and showed context-dependent functional enrichment. Baseline RNA-seq identified 322 DEGs between HCR and LCR muscle. Methylome-transcriptome integration revealed 72 DMR-DEG pairs representing 53 unique genes, mostly located in open-sea, intronic, and exonic regions. Exploratory VO2max analysis identified 63 DMRs associated with aerobic capacity. Chronic voluntary running induced more DEGs in HCR than in LCR muscle, while pathway-level responses in both lines converged on mitochondrial and oxidative metabolism. Selected protein profiling further revealed mainly baseline LCR-HCR differences, with limited additional exercise-associated changes. CONCLUSION Intrinsic high aerobic capacity in aged skeletal muscle is associated with hypermethylation-enriched methylome remodeling, feature-dependent functional enrichment, distinct transcriptional signatures, and oxidative-metabolic protein differences. These findings provide a multi-layer molecular framework for understanding intrinsic aerobic-capacity divergence in aged skeletal muscle and highlight candidate regulatory regions for future functional validation.

Intermittent fasting rewires tissue-specific gene–transposable element regulatory networks

Abstract Intermittent fasting (IF) is a dietary intervention known to promote systemic health benefits, yet its impact on genome-wide transcriptional regulatory networks, particularly those involving transposable elements (TEs), remains poorly understood. This study investigates the multitissue transcriptomic response to chronic IF in mice, focusing on TE regulation and its integration with host gene networks. We subjected C57BL/6 mice to 16 h of daily fasting for 4 months and performed RNA-seq on liver, skeletal muscle, and cortex tissues. Using locus-specific TE quantification, we found that IF induces profound, tissue-specific changes in TE expression, with the liver showing the strongest response (5,359 differentially expressed TEs), followed by skeletal muscle (620), while minimal changes were observed in the cortex. Integrated co-expression network analysis (WGCNA) in the liver and muscle revealed IF-responsive TEs that co-vary with nearby genes, forming distinct co-expression modules. Functional enrichment of genes proximal to co-expressed TEs within these modules highlighted clear tissue-specific regulatory programs. In the liver, the enriched terms were predominantly associated with translation and metabolism, whereas in skeletal muscle, the enriched pathways were involved in muscle contraction, mitochondrial organization, and chromatin modification. Furthermore, correlation analysis revealed strong, significant co-expression between TEs and their proximal genes within these modules, suggesting that TEs may exert potential cis-regulatory effects on adjacent genes. Taken together, our results provide a high-resolution atlas of TE regulation under IF and demonstrate that TEs are integral components of tissue-specific transcriptional networks reshaped by fasting. These findings offer new insights into how dietary interventions influence gene regulatory systems.

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

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.

Integration of methylome and transcriptome reveals age-associated signatures of stage-specific dynamics and regulatory remodeling in dogs.

Dynamic Atlas and Functional Regulatory Network of the Whole-Brain Proteome Across 24-Hour Temporal States in Vespertilio sinensis

As the only mammals capable of powered flight, bats exhibit extreme metabolic fluctuations adapted to flight and a nocturnal lifestyle, making them unique models for studying diurnal rhythms and energy homeostasis. We performed directDIA-based quantitative proteomics on whole-brain tissues of Vespertilio sinensis across four distinct 24-hour physiological states: Rest, Sleep, Wake, and Activity. Among the 7652 identified proteins, a total of 643 differentially expressed proteins (DEPs) were screened via pairwise comparisons across timepoints. Time-series clustering further resolved two statistically significant temporal expression modules (Module 3 and Module 9). Combined with functional enrichment of DEPs and phase set enrichment analysis (PSEA) of 574 rhythmic proteins, our multi-layered omics results collectively uncovered stage-specific molecular adaptive patterns. The Active state upregulated oxidative phosphorylation and thermogenesis for high energy demands, the Rest state activated immune clearance and autophagy to eliminate flight-induced metabolic damage, the Sleep state suppressed global transcription, calcium signaling and DNA repair to reduce neural energy consumption, and the Wake state (pre-dusk) pre-activated sulfur biosynthesis, antioxidant defense, and energy metabolic pathways to prepare for upcoming nocturnal activity. Parallel transcriptomic and proteomic rhythmic analysis further identified 19 conserved oscillatory molecules at both molecular layers, revealing partial transcript-protein rhythmic decoupling in the bat brain and refining the diurnal regulatory landscape. As the first systematic atlas of the bat whole-brain proteome across a 24-hour cycle, this study uncovers molecular strategies maintaining brain homeostasis, providing a foundation for understanding diurnal physiological adaptation, flight energy regulation, and circadian output pathways.

Exploratory longitudinal analysis of a PIN1-associated gene panel in PBMCs during orbital spaceflight

Spaceflight exposes astronauts to a combination of microgravity, radiation, circadian disruption, isolation, and operational stress that may influence immune and transcriptional regulation. In this exploratory study, we examined peripheral blood mononuclear cell RNA-sequencing data from three Axiom-3 astronauts sampled before launch (L−7) and on International Space Station Days 4, 7, and 10. A separate Galactic-07 participant sampled before launch and 3 h after suborbital flight was included for descriptive context only. The analysis focused on a preselected panel comprising PIN1 and ten biologically associated genes involved in cell-cycle regulation, stress responses, transcriptional control, innate immunity, and oxidative responses. Participant-adjusted longitudinal analysis identified significant overall time-associated variation in PIN1, TP53, PML, MYC, NCF1, NCF2, IRF3, POLR2A, and SFN after Benjamini–Hochberg correction. Several additional genes exhibited descriptive downward expression patterns without meeting the adjusted significance threshold. Because the cohort was small and the measurements were limited to bulk-PBMC mRNA abundance, the findings do not establish altered PIN1 protein activity, a mission-specific regulatory network, or biomarker performance. Instead, they provide hypothesis-generating evidence supporting further evaluation of PIN1-associated transcriptional responses in larger astronaut cohorts using protein-level, functional, and cell-type-resolved analyses.