Biology subjects

Barbour, A. G.

Publications and source records attributed to Barbour, A. G..

6 recordsLinked to original sources

bioRxiv2026

Xist expression in male Peromyscus leucopus is associated with restricted chromatin repression and incomplete X-to-autosome dosage compensation

X-chromosome inactivation (XCI) equalizes X-linked gene dosage between XX females and XY males in eutherian mammals and is canonically initiated by the long noncoding RNA Xist, which coats one X chromosome and recruits Polycomb-mediated chromatin silencing. Xist expression has therefore been considered female-specific and central to balancing gene dosage between two X chromosomes in females and a single X chromosome in males. However, emerging evidence suggests that Xist can also be expressed in male cells in both healthy and pathogenic contexts, raising fundamental questions about the scope and constraints of Xist function. Here, we identify robust Xist expression in somatic cells of male white-footed deermice (Peromyscus leucopus), a placental mammal with a conventional XY karyotype. Unlike the chromosome-wide Xist RNA coating observed in females, male Xist RNA localizes as discrete nuclear puncta and is detected across multiple tissues by RNA-seq, RT-qPCR, and RNA fluorescence in situ hybridization. Integrative transcriptomic and chromatin profiling using CUT&Tag and single-nucleus Paired-Tag reveals that male Xist expression is not merely incidental but has measurable regulatory consequences. In females, Xist expression is associated with chromosome-wide enrichment of the repressive histone mark H3K27me3 and transcriptional silencing of X-linked genes. In males, although Xist transcription is also associated with H3K27me3, this interaction does not induce global X-chromosome inactivation. Instead, Xist selectively represses a subset of dosage-sensitive neural and mitochondrial X-linked genes, while the majority of X-linked genes remain largely active. Notably, with persistent Xist activity, neither males nor females achieve complete X-to-autosome dosage compensation in P. leucopus. These findings establish P. leucopus as a mammalian system in which male Xist operates outside the canonical female-specific XCI pathway, revealing a gene-selective model of X-chromosome regulation. Our results challenge the universality of prevailing XCI models and suggest that partial, context-dependent Xist activity represents a viable and evolutionarily stable dosage compensation strategy in mammals. Author SummaryIn mammals, females and males differ in their sex chromosome: females have two X chromosomes, while males have one. This difference creates a potential imbalance in gene dosage, which can disrupt development if not properly controlled. Typically, females compensate by turning off one chromosome through a process called X-chromosome inactivation (XCI), which is triggered by the long noncoding RNA Xist. In parallel, a process known as X-to-autosome dosage compensation balances X-linked gene expression relative to the rest of the genome. Because XCI occurs in females, Xist has long been considered to function only in female cells and be inactive in males. Here, we show that Xist is persistently expressed in male white-footed deermice (Peromyscus leucopus), a cricetid rodent with a conventional XY sex chromosome system. Unlike the large Xist RNA "cloud" that covers the inactive X chromosome in females, Xist RNA in males appears as small, discrete spots in the nucleus. By combining gene expression and chromatin profiling, we find that male Xist associates with the repressive histone mark H3K27me3 but does not switch off the entire X chromosome. Instead, Xist in males selectively reduces the activity of a limited set of X-linked genes, while most X-linked genes remain active. Surprisingly, we also find that neither male nor female P. leucopus achieves complete balance between X-linked and autosomal gene expression, despite the long-held view that such balance is essential for mammalian viability. By uncovering functional Xist activity in males of a non-model species and demonstrating incomplete dosage compensation in both sexes, this work challenges the traditional view of XCI as a strictly female-specific strategy and reveals an unexpected flexibility in how mammals regulate the X chromosome.

genetics↗

bioRxiv2026

SARS-CoV-2 virus infection of Peromyscus leucopus demonstrates that infection tolerance is not limited to agents for which deermice are reservoirs

The North American deermouse Peromyscus leucopus is reservoir for several zoonotic agents, including bacterial, protozoan, and viral. It is remarkable for indiscernible or limited fitness consequences of these infections, a trait known as infection tolerance. But experimental infections have largely been of pathogens that P. leucopus naturally harbors. We asked whether infection tolerance extended to an agent, like SARS-CoV-2 virus, it had presumably not encountered before. Following protocols for experiments with mice and hamsters, we infected 8 female and 8 male P. leucopus of heterogeneous stock and compared responses of these animals on days 3 or 6 to those of 14 controls inoculated with virus-free medium. Serologic and virologic confirmation of infection was obtained for all exposed deermice. Moderate inflammation in lungs was histologically evident in infected animals, but no histological changes were noted in brains, even when viral RNA was present. Fourteen (88%) animals displayed no or only mild sickness; two had more severe illness. Genome-wide RNA-seq revealed an interferon-stimulated response on day 3 superceded mainly by a cell-mediated response by day 6. In brains transcription of the interferon-stimulated genes Isg15 and Mx2 positively correlated with viral RNA levels. The findings confirmed susceptibility of this species of Peromyscus to SARS-CoV-2 virus. For most infected outbred animals the immune response was swift and effective in controlling the pathogen and without evidence of excessive inflammation. Whatever is the basis for P. leucopus trait of infection tolerance, it extended to at least one pathogen that for it would be novel. ImportancePeromyscus leucopus is North American rodent that is reservoir for several agents of human disease, while exhibiting minimal illness, a phenotype termed infection tolerance. Whether this trait is pathogen-specific or represents a broader strategy has remained uncertain. By experimentally infecting P. leucopus with SARS-CoV-2 virus, which it is unlikely to have encountered, we investigated whether infection tolerance extends to a novel virus. Despite disseminated infection and lung pathology, most animals showed only mild or no disease. Expression analyses revealed early interferon-stimulated responses followed by cell-mediated responses with only limited production of inflammatory mediators interferon-gamma and nitric oxide synthase 2. Compared with results with a mouse model of infection, deermice displayed higher baseline expression of antiviral genes and quicker resolution of interferon responses. These findings suggest that infection tolerance is a strategy that limits immunopathology generally while resisting microbes, which has implications for understanding reservoir competence and host resilience.

microbiology↗

bioRxiv2025

Dermal fibroblast cultures recapitulate differences between deermice and mice in responses to a Toll-like receptor agonist

The white-footed deermouse Peromyscus leucopus is a primary reservoir for the agents of Lyme disease and other zoonoses in North America and manifests infection tolerance for the bacteria, protozoa, and viruses it hosts. In previous in vivo studies P. leucopus and M. musculus differed in the degree of sickness and profiles of biomarkers after exposure to bacterial lipopolysaccharide, a TLR4 agonist. As an approach for assessing immunity of mammals in nature and for longitudinal studies of colony animals in the laboratory, we evaluated using bulk and single cell RNA-seq primary dermal fibroblast cultures of P. leucopus and M. musculus in their short-term responses to a TLR2 agonist lipopeptide. By single cell RNA-seq cultures of both species comprised at least two types of fibroblasts, which were further differentiated in their responses to TLR agonists. With continued passage the mouse cell population lost viability, while the deermouse cell population spontaneously transformed into a cell line stably maintained under standard conditions. Bulk RNA-seq revealed distinctive profiles for deermouse and mouse cells in arginine metabolism gene expression, high baseline transcription of the antioxidant transcription factor Nfe2l2 (Nrf2) in deermouse fibroblasts, and the transcription of the aging-associated cytokine interleukin-11 in agonist-treated mouse fibroblasts but not deermouse fibroblasts. In both species cultures there was increased transcription of several types of endogenous retrovirus (ERV) and transposable elements (TE) after exposure to the agonist. The transcribed ERV/TE sequences in M. musculus cells were generally longer in length and with greater potential for translation than sequences in treated P. leucopus cells. The results indicate feasibility of this in vitro model for both laboratory- and field-based studies and that inherent differences between deermice and mice in cell-autonomous innate immune responses and ERV/TE activation can be demonstrated in dermal fibroblasts as well as the animals themselves.

immunology↗

bioRxiv2023

The white-footed deermouse, an infection tolerant reservoir for several zoonotic agents, tempers interferon responses to endotoxin in comparison to the mouse and rat

The white-footed deermouse Peromyscus leucopus, a long-lived rodent, is a key reservoir for agents of several zoonoses, including Lyme disease. While persistently infected, this deermouse is without apparent disability or diminished fitness. For a model for inflammation elicited by various pathogens, the endotoxin lipopolysaccharide (LPS) was used to compare genome-wide transcription in blood by P. leucopus, Mus musculus and Rattus norvegicus and adjusted for white cell concentrations. Deermice were distinguished from the mice and rats by LPS response profiles consistent with non-classical monocytes and alternatively-activated macrophages. LPS-treated P. leucopus, in contrast to mice and rats, also displayed little transcription of interferon-gamma and lower magnitude fold-changes in type 1 interferon-stimulated genes. This was associated with comparatively reduced transcription of endogenous retrovirus sequences and cytoplasmic pattern recognition receptors in the deermice. The results reveal a mechanism for infection tolerance in this species and perhaps other animal reservoirs for agents of human disease.

microbiology↗

bioRxiv2020

The infection-tolerant mammalian reservoir of Lyme disease and other zoonoses broadly counters the inflammatory effects of endotoxin

Animals that are competent natural reservoirs of zoonotic diseases commonly suffer little morbidity from the pathogens they persistently harbor. The mechanisms of this infection tolerance and the trade-off costs are poorly understood. We used exposure to a single dose of lipopolysaccharide (LPS) endotoxin as an experimental model of inflammation to compare the responses of the cricentine rodent Peromyscus leucopus, the white-footed deermouse, to that of Mus musculus, the standard laboratory model for pathogenesis studies. Four hours after injection with either LPS or saline, blood and spleen and liver tissues were collected postmortem and subjected to RNA-seq, untargeted metabolomics, and specific RT-qPCR. This was followed by analysis of differential expression at the gene, pathway, and empirical network levels. The deermice showed the same signs of sickness as the mice with LPS exposure, and in addition demonstrated comparable increases in levels of corticosterone and expression of interleukin (IL)-6, tumor necrosis factor, IL-1{beta}, and acute phase reactants, including C-reactive protein. But whereas the M. musculus response to LPS was best-characterized by network analysis as cytokine-associated, the P. leucopus response was dominated by pathway terms associated with neutrophil activity. Dichotomies between the species in expression profiles of arginase 1 and nitric oxide synthase 2, as well as the ratios of IL-10 to IL-12, were consistent with a type M1 polarized macrophage response in the mice and a type M2 or alternatively-activated response in the deermice. Analysis of metabolites in the plasma and RNA in the tissues revealed differences between the two species in tryptophan metabolism during response to LPS. Two up-regulated genes in particular signified the difference between the species: Slpi (secretory leukocyte proteinase inhibitor) and Ibsp (integrin-binding protein sialoprotein). The latter was previously unrecognized in the context of inflammation or infection. Key RNA-seq findings in P. leucopus were replicated in a second LPS experiment with older animals, in a systemic bacterial infection model, and with cultivated fibroblasts. Taken together, the results indicate that the deermouse possesses several adaptive traits to moderate effects of inflammation and oxidative stress ensuing from infection. This seems to be at the cost of infection persistence and that is to the benefit of the pathogen.

systems biology↗

bioRxiv2020

Lactobacilli and other gastrointestinal microbiota of Peromyscus leucopus, reservoir host for agents of Lyme disease and other zoonoses in North America

The cricetine rodent Peromyscus leucopus is an important reservoir for several human zoonoses, including Lyme disease, in North America. Akin to hamsters, the white-footed deermouse has been unevenly characterized in comparison to the murid Mus musculus. To further understanding of P. leucopus total genomic content, we investigated gut microbiomes of an outbred colony of P. leucopus, inbred M. musculus, and a natural population of P. leucopus. Metagenome and whole genome sequencing were combined with microbiology and microscopy approaches. A focus was the genus Lactobacillus, four diverse species of which were isolated from forestomach and feces of colony P. leucopus. Three of the species--L. animalis, L. reuteri, and provisionally-named species "L. peromysci"--were identified in fecal metagenomes of wild P. leucopus but not discernibly in samples from M. musculus. L. johnsonii, the fourth species, was common in M. musculus but absent or sparse in wild P. leucopus. Also identified in both colony and natural populations were a Helicobacter sp. in feces but not stomach, and a Tritrichomonas sp. protozoan in cecum or feces. The gut metagenomes of colony P. leucopus were similar to those of colony M. musculus at the family or higher level and for major subsystems. But there were multiple differences between species and sexes within each species in their gut metagenomes at orthologous gene level. These findings provide a foundation for hypothesis-testing of functions of individual microbial species and for interventions, such as bait vaccines based on an autochthonous bacterium and targeting P. leucopus for transmission-blocking.

microbiology↗