2025 Hyper Recent •CC0 1.0 Universal

This work is dedicated to the public domain. No rights reserved.

Access Preprint From Server
July 17th, 2025
Version: 1
California Institute of Technology
genomics
biorxiv

Transcriptomic responses to endurance exercise training in rats

Oakes, C. G.Open in Google Scholar•Pachter, L.Open in Google Scholar

The bio-molecular changes of exercise, and how to best optimize them for improved performance, are an important human health research question. A recent study by the Molecular Transducers of Physical Activity Consortium (MoTrPAC) used a cohort of Rattus norvegicus to produce a whole-organism molecular map of the temporal effects of endurance exercise training. This dataset, encompassing hundreds of assays across 19 different tissues, can be used to evaluate the predictive power of gene expression, understand isoform-level changes in response to exercise, and with modern tools can be examined for associations with viral infection. Our analysis of the RNA-seq data reveals that gene expression can accurately predict the amount of exercise a rat was trained in. Additionally, we find biologically relevant isoform-level differences in expression that are masked in gene-level analysis. Finally, we find a potential novel respiratory virus that may negatively impact physiological measurements. This more comprehensive analysis provides a blueprint for directing similar analyses with respect to physiological perturbations across organisms.

Similar Papers

biorxiv
Thu Jul 17 2025
Persistent cortical excitatory neuron dysregulation in adult Chd8 haploinsufficient mice.
CHD8 mutations cause autism spectrum disorder, cognitive deficits, and macrocephaly. Chd8+/- mouse models exhibit macrocephaly and transcriptional pathology, with inconsistent findings regarding neurogenesis, neuron function, and behavior. Via stereology and single nuclei transcriptomics (snRNA-seq), we found increased Chd8+/- cortical volume was not explained by increase in neuron number. Differe...
Canales, C. P.
•
Lozano, S. A.
•
Frost, N. A.
•
Cichewicz, K.
...•
Nord, A. S.
biorxiv
Thu Jul 17 2025
Mitochondrial clone tracing within spatially intact human tissues
Understanding tissue development and intra-tissue evolution requires the ability to trace clones in intact tissues coupled with high-plex molecular profiling preserving spatial context. However, current lineage tracing tools are incompatible with spatial omics. Here, we present SUMMIT (Spatially Unveiling Mitochondrial Mutations In Tissues), a spatially-resolved lineage tracing technology that int...
Bracht, S. A.
•
Rong, J.
•
Gier, R. A.
•
DeMarshall, M.
...•
Shaffer, S. M.
biorxiv
Thu Jul 17 2025
Conservation of chromatin states and their association with transcription factors in land plants
The complexity of varied modifications of chromatin composition is integrated in archetypal combinations called chromatin states that predict the local potential for transcription. The degree of conservation of chromatin states has not been established amongst plants, and how they interact with transcription factors is unknown. Here we identify and characterize chromatin states in the flowering pl...
Shukla, V.
•
Axelsson, E.
•
Hisanaga, T.
•
Haseloff, J.
...•
Berger, F.
biorxiv
Thu Jul 17 2025
Telomere replication stress-induced DNA damage response triggers inflammatory signaling via canonical and non-canonical STING pathways
Telomeres are protected by the shelterin complex, but they are also common fragile sites and are particularly susceptible to replicative stress. We found that depletion of telomeric repeat-binding factor 1 (TRF1), a key shelterin component essential for telomere replication, in mouse embryonic fibroblasts (MEFs) activated ATR- and subsequent ATM-dependent DNA damage responses. TRF1 loss increased ...
Zhu, W.
•
Gong, Y.
•
Wang, Y.
•
Gorospe, M.
•
Liu, Y.
biorxiv
Thu Jul 17 2025
A multi-omics analysis of human fibroblasts overexpressing an Alu transposon reveals widespread disruptions in aging-associated pathways
During aging and cellular senescence, repetitive elements are frequently transcriptionally derepressed across species and cell types. Among these, the most abundant repeats by copy number in the human genome are Alu retrotransposons. Though Alu elements are often studied for their mutagenic potential, there is increasing appreciation for their contributions to other biological functions, including...
Bravo, J. I.
•
Tewelde, E.
•
King, C. D.
•
Bons, J.
...•
Benayoun, B. A.
biorxiv
Thu Jul 17 2025
A Complete Telomere-to-Telomere Diploid Reference Genome for Indian Population
Human reference genomes have been instrumental in advancing genomic and biomedical research, but South and Southeast Asian populations are underrepresented, despite accounting for a large proportion of world population. As a part of effort on generating reference genomes for these populations, we present the first gapless, telomere-to-telomere (T2T) diploid genome assembly created by using a trio ...
Sarashetti, P.
•
Lipovac, J.
•
Jia, Q.
•
Wang, L.
...•
Liu, J.
biorxiv
Thu Jul 17 2025
Characterisation of β-tubulin isotypes in Uncinaria stenocephala and implications for benzimidazole resistance in hookworms
Uncinaria stenocephala is a widespread hookworm of dogs across Europe, Canada, southern Australia, and other temperate regions, where it often outnumbers infections caused by Ancylostoma caninum. Although a putative {beta}-tubulin isotype-1 mutation associated with resistance has been detected in U. stenocephala, clinical resistance to benzimidazoles has not yet been confirmed. Benzimidazole resis...
Stocker, T.
•
Slapeta, J.
biorxiv
Wed Jul 16 2025
UniversalEPI: robust prediction of cell type-specific and differential chromatin interactions from DNA sequence and chromatin accessibility
Enhancer-promoter interactions (EPIs) play a central role in gene regulation, but experimental techniques such as Hi-C for mapping these interactions remain costly and labor-intensive. Computational methods have been developed to predict EPIs in silico from DNA sequences and chromatin information; however, there are major challenges with the generalizability and accuracy of predictions by existing...
Grover, A.
•
Zhang, L.
•
Muser, T.
•
Häfliger, S.
...•
Boeva, V.
biorxiv
Wed Jul 16 2025
Distribution Patterns of rRNA Copy Number Repeats in Prokaryotic Genomes
Unlike tandem repeats in eukaryotes, ribosomal RNA (rRNA) operons across prokaryotic genomes are widely distributed. Here, I examined the distribution of 16S ribosomal RNA gene copies using all entries from the Ribosomal RNA Operon Copy Number Database with a copy number of 2 or greater, using a metric-normalized range-that allows for comparisons between copy number. Normalized range varied across...
Williamson, M. R.