ArticleCell genomics2024
Quantification of escape from X chromosome inactivation with single-cell omics data reveals heterogeneity across cell types and tissues.
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Article in Cell genomics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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22citing papers in PubMed
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Who cites it
22 citing papers in PubMed.
- Modulating the degree of X-inactivation escape to establish causal links to sex-biased disease.Nature reviews. Molecular cell biology · 2026Article
- Escape from X-chromosome inactivation: from gene discovery to regulatory mechanisms.Biochemical Society transactions · 2026Review
- Human GPR174 deficiency drives polyclonal lymphoproliferative disease via defects in T cell function.medRxiv : the preprint server for health sciences · 2026Article
- Peripheral and Central miRNA Signatures in Alzheimer's Disease: Tissue-Specific Variability, Sex-Associated Differences, and Implications for Blood-Based Biomarkers.International journal of molecular sciences · 2026Review
- Review
- Age-related erosion of X chromosome inactivation in human tissues.bioRxiv : the preprint server for biology · 2026Article
- Machine learning reveals X chromosome transcriptional signatures that classify systemic lupus erythematosus in females.BMC rheumatology · 2026Article
- Article
- The impact of sex on the immune system explored at the single-cell level.American journal of human genetics · 2026Article
- Cell-type specific allelic dampening of sex-linked genes in sex chromosome aneuploidy.bioRxiv : the preprint server for biology · 2026Article
- Escape from X inactivation drives sex differences in gene expression.Molecular biology and evolution · 2026Article
- Escape from X inactivation varies across genes and tissues and shapes sex-biased sex chromosome gene expression.BMC genomics · 2026Article
- Opportunities for RNA sequencing in physiology: from big data to understanding homeostasis and heterogeneity.Function (Oxford, England) · 2026Review
- Single nuclei and spatial profiling of sacrococcygeal teratomas reveals cellular composition and X inactivation heterogeneity.NPJ precision oncology · 2026Article
- Cell-specific epigenome-wide DNA methylation in peripheral CD4(+) lymphocytes from patients with primary biliary cholangitis.Journal of translational autoimmunity · 2025Article
- X chromosome inactivation across primary human tissues is mostly complete, with significant implications for genetic and clinical studies.BMC genomics · 2025Article
- FemXpress: Systematic Analysis of X Chromosome Inactivation Heterogeneity in Female Single-Cell RNA-Seq Samples.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- X-linked competition - implications for human development and disease.Nature reviews. Genetics · 2025Review
- Role of X chromosome and dosage-compensation mechanisms in complex trait genetics.American journal of human genetics · 2025Article
- Escape from X-chromosome inactivation at KDM5C is driven by promoter-proximal DNA elements and enhanced by domain context.Human molecular genetics · 2025Article
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Authors and funding
36 authors.
Yoshihiko TomofujiDepartment of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan; Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan; Department of Genome Informatics, Graduate School of Medicine, the University of Tokyo, Tokyo 113-8654, Japan. Electronic address: ytomofuji@sg.med.osaka-u.ac.jp.
Ryuya EdahiroDepartment of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan; Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan.
Kyuto SoneharaDepartment of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan; Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan; Department of Genome Informatics, Graduate School of Medicine, the University of Tokyo, Tokyo 113-8654, Japan.
Yuya ShiraiDepartment of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan.
Kian Hong KockGenome Institute of Singapore (GIS), Agency for Science, Technology and Research (A∗STAR), Singapore 138672, Republic of Singapore.
Qingbo S WangDepartment of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan; Department of Genome Informatics, Graduate School of Medicine, the University of Tokyo, Tokyo 113-8654, Japan.
Shinichi NambaDepartment of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Department of Genome Informatics, Graduate School of Medicine, the University of Tokyo, Tokyo 113-8654, Japan.
Jonathan MoodyLaboratory for Genome Information Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.
Yoshinari AndoRIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.
Akari SuzukiLaboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.
Tomohiro YataDepartment of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Department of Neurology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan.
Kotaro OgawaDepartment of Neurology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan.
Tatsuhiko NaitoDepartment of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.
Ho NamkoongDepartment of Infectious Diseases, Keio University School of Medicine, Shinanomachi 160-8582, Japan.
Quy Xiao Xuan LinGenome Institute of Singapore (GIS), Agency for Science, Technology and Research (A∗STAR), Singapore 138672, Republic of Singapore.
Eliora Violain BuyaminGenome Institute of Singapore (GIS), Agency for Science, Technology and Research (A∗STAR), Singapore 138672, Republic of Singapore.
Le Min TanGenome Institute of Singapore (GIS), Agency for Science, Technology and Research (A∗STAR), Singapore 138672, Republic of Singapore.
Radhika SonthaliaGenome Institute of Singapore (GIS), Agency for Science, Technology and Research (A∗STAR), Singapore 138672, Republic of Singapore.
Kyung Yeon HanSamsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea.
Hiromu TanakaDivision of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Shinanomachi 160-8582, Japan.
Ho LeeDivision of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Shinanomachi 160-8582, Japan.
Asian Immune Diversity Atlas (AIDA) Network
Japan COVID-19 Task Force
Biobank Japan Project
Tatsusada OkunoDepartment of Neurology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan.
Boxiang LiuDepartment of Pharmacy, National University of Singapore, Singapore 117549, Republic of Singapore.
Koichi MatsudaDepartment of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Shirokanedai 108-8639, Japan.
Koichi FukunagaDivision of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Shinanomachi 160-8582, Japan.
Hideki MochizukiDepartment of Neurology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan.
Woong-Yang ParkSamsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea.
Kazuhiko YamamotoLaboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.
Chung-Chau HonLaboratory for Genome Information Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.
Jay W ShinGenome Institute of Singapore (GIS), Agency for Science, Technology and Research (A∗STAR), Singapore 138672, Republic of Singapore; Laboratory for Advanced Genomics Circuit, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.
Shyam PrabhakarGenome Institute of Singapore (GIS), Agency for Science, Technology and Research (A∗STAR), Singapore 138672, Republic of Singapore; Lee Kong Chian School of Medicine, Singapore 308232, Republic of Singapore; Cancer Science Institute of Singapore, Singapore 117599, Republic of Singapore.
Atsushi KumanogohIntegrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan; Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Department of Immunopathology, Immunology Frontier Research Center, Osaka University, Suita 565-0871, Japan.
Yukinori OkadaDepartment of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan; Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan; Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan; Department of Genome Informatics, Graduate School of Medicine, the University of Tokyo, Tokyo 113-8654, Japan; Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita 565-0871, Japan; Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe), Osaka University, Suita 565-0871, Japan. Electronic address: yuki-okada@m.u-tokyo.ac.jp.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Several X-linked genes escape from X chromosome inactivation (XCI), while differences in escape across cell types and tissues are still poorly characterized. Here, we developed scLinaX for directly quantifying relative gene expression from the inactivated X chromosome with droplet-based single-cell RNA sequencing (scRNA-seq) data. The scLinaX and differentially expressed gene analyses with large-scale blood scRNA-seq datasets consistently identified the stronger escape in lymphocytes than in myeloid cells. An extension of scLinaX to a 10x multiome dataset (scLinaX-multi) suggested a stronger escape in lymphocytes than in myeloid cells at the chromatin-accessibility level. The scLinaX analysis of human multiple-organ scRNA-seq datasets also identified the relatively strong degree of escape from XCI in lymphoid tissues and lymphocytes. Finally, effect size comparisons of genome-wide association studies between sexes suggested the underlying impact of escape on the genotype-phenotype association. Overall, scLinaX and the quantified escape catalog identified the heterogeneity of escape across cell types and tissues.
Indexed as
Single-Cell AnalysisX Chromosome InactivationAnimalsFemaleGenes, X-LinkedGenome-Wide Association StudyHumansLymphocytesMaleMiceMyeloid CellsOrgan SpecificitySequence Analysis, RNAsex differencessingle-cell omicsX chromosome
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