{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,6,18]],"date-time":"2026-06-18T20:52:17Z","timestamp":1781815937242,"version":"3.54.5"},"posted":{"date-parts":[[2026,6,15]]},"group-title":"Genetics","reference-count":84,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,6,15]],"date-time":"2026-06-15T00:00:00Z","timestamp":1781481600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.biorxiv.org\/about\/FAQ#license"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["R01GM141424"],"award-info":[{"award-number":["R01GM141424"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["R01AI157513"],"award-info":[{"award-number":["R01AI157513"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,6,16]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  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\n                  <jats:italic>Xist<\/jats:italic>\n                  , which coats one X chromosome and recruits Polycomb-mediated chromatin silencing.\n                  <jats:italic>Xist<\/jats:italic>\n                  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\n                  <jats:italic>Xist<\/jats:italic>\n                  can also be expressed in male cells in both healthy and pathogenic contexts, raising fundamental questions about the scope and constraints of\n                  <jats:italic>Xist<\/jats:italic>\n                  function. Here, we identify robust\n                  <jats:italic>Xist<\/jats:italic>\n                  expression in somatic cells of male white-footed deermice (\n                  <jats:italic>Peromyscus leucopus<\/jats:italic>\n                  ), a placental mammal with a conventional XY karyotype. Unlike the chromosome-wide\n                  <jats:italic>Xist<\/jats:italic>\n                  RNA coating observed in females, male\n                  <jats:italic>Xist<\/jats:italic>\n                  RNA localizes as discrete nuclear puncta and is detected across multiple tissues by RNA-seq, RT-qPCR, and RNA fluorescence\n                  <jats:italic>in situ<\/jats:italic>\n                  hybridization. Integrative transcriptomic and chromatin profiling using CUT&amp;Tag and single-nucleus Paired-Tag reveals that male\n                  <jats:italic>Xist<\/jats:italic>\n                  expression is not merely incidental but has measurable regulatory consequences. In females,\n                  <jats:italic>Xist<\/jats:italic>\n                  expression is associated with chromosome-wide enrichment of the repressive histone mark H3K27me3 and transcriptional silencing of X-linked genes. In males, although\n                  <jats:italic>Xist<\/jats:italic>\n                  transcription is also associated with H3K27me3, this interaction does not induce global X-chromosome inactivation. Instead,\n                  <jats:italic>Xist<\/jats:italic>\n                  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\n                  <jats:italic>Xist<\/jats:italic>\n                  activity, neither males nor females achieve complete X-to-autosome dosage compensation in\n                  <jats:italic>P. leucopus<\/jats:italic>\n                  . These findings establish\n                  <jats:italic>P. leucopus<\/jats:italic>\n                  as a mammalian system in which male\n                  <jats:italic>Xist<\/jats:italic>\n                  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\n                  <jats:italic>Xist<\/jats:italic>\n                  activity represents a viable and evolutionarily stable dosage compensation strategy in mammals.\n                <\/jats:p>\n                <jats:sec>\n                  <jats:title>Author Summary<\/jats:title>\n                  <jats:p>\n                    In 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\n                    <jats:italic>Xist<\/jats:italic>\n                    . 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,\n                    <jats:italic>Xist<\/jats:italic>\n                    has long been considered to function only in female cells and be inactive in males. Here, we show that\n                    <jats:italic>Xist<\/jats:italic>\n                    is persistently expressed in male white-footed deermice (\n                    <jats:italic>Peromyscus leucopus<\/jats:italic>\n                    ), a cricetid rodent with a conventional XY sex chromosome system. Unlike the large\n                    <jats:italic>Xist<\/jats:italic>\n                    RNA \u201ccloud\u201d that covers the inactive X chromosome in females,\n                    <jats:italic>Xist<\/jats:italic>\n                    RNA in males appears as small, discrete spots in the nucleus. By combining gene expression and chromatin profiling, we find that male\n                    <jats:italic>Xist<\/jats:italic>\n                    associates with the repressive histone mark H3K27me3 but does not switch off the entire X chromosome. Instead,\n                    <jats:italic>Xist<\/jats:italic>\n                    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\n                    <jats:italic>P. leucopus<\/jats:italic>\n                    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\n                    <jats:italic>Xist<\/jats:italic>\n                    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.\n                  <\/jats:p>\n                <\/jats:sec>","DOI":"10.64898\/2026.06.11.731719","type":"posted-content","created":{"date-parts":[[2026,6,16]],"date-time":"2026-06-16T02:40:15Z","timestamp":1781577615000},"source":"Crossref","is-referenced-by-count":0,"title":["<i>Xist<\/i>\n                  expression in male\n                  <i>Peromyscus leucopus<\/i>\n                  is associated with restricted chromatin repression and incomplete X-to-autosome dosage compensation"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0009-0008-3076-7057","authenticated-orcid":false,"given":"Maria De Lourdes","family":"Andrade Ludena","sequence":"first","affiliation":[{"name":"Department of Developmental and Cell Biology, Charlie Dunlop School of Biological Sciences, University of California, Irvine, Irvine, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-1524-0265","authenticated-orcid":false,"given":"Jonathan V.","family":"Duong","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aqsa","family":"Motiwala","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher L","family":"Hartl","sequence":"additional","affiliation":[{"name":"Epigenome Technologies, San Diego, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anthony D.","family":"Long","sequence":"additional","affiliation":[{"name":"Department of Systems Biology, Charlie Dunlop School of Biological Sciences, University of California, Irvine, Irvine, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0719-5248","authenticated-orcid":false,"given":"Alan G.","family":"Barbour","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, CA, USA"},{"name":"Department of Medicine, School of Medicine, University of California, Irvine, Irvine, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0044-6403","authenticated-orcid":false,"given":"Sha","family":"Sun","sequence":"additional","affiliation":[{"name":"Department of Developmental and Cell Biology, Charlie Dunlop School of Biological Sciences, University of California, Irvine, Irvine, CA, USA"},{"name":"Department of Systems Biology, Charlie Dunlop School of Biological Sciences, University of California, Irvine, Irvine, CA, 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