ArticleGenome research2016
Single-cell analyses of X Chromosome inactivation dynamics and pluripotency during differentiation.
Article in Genome research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
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Who cites it
63 citing papers in PubMed.
- A universal 6iL/E4 culture system for deriving and maintaining embryonic stem cells across mammalian species.Cell research · 2026Article
- Gata3 dosage governs primitive endoderm versus trophectoderm specification in embryonic stem cells.EMBO reports · 2026Article
- saseR: juggling offsets unlocks RNA-seq tools for fast and scalable differential usage, aberrant splicing and expression retrieval.Genome biology · 2026Article
- Single-cell omics uncover gene dynamics shaping embryonic and extra embryonic lineages in pig blastocysts.iScience · 2026Article
- Impact of sperm fractionation on chromosome positioning, chromatin integrity, DNA methylation, and hydroxymethylation level.Cellular & molecular biology letters · 2025Article
- Dynamic dosage changes in X-linked transposable elements during mammalian dosage compensation.Nature communications · 2025Article
- X-chromosome upregulation operates on a gene-by-gene basis at RNA and protein levels.Nature communications · 2025Article
- X-Linked Gene Dosage and SOX2 Act as Key Roadblocks for Human Germ Cell Specification in Klinefelter Syndrome.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Aging activates escape of the silent X chromosome in the female mouse hippocampus.Science advances · 2025Article
- Deep learning-based models for preimplantation mouse and human embryos based on single-cell RNA sequencing.Nature methods · 2025Article
- Unravelling lipid heterogeneity: Advances in single-cell lipidomics in cellular metabolism and disease.BBA advances · 2025Review
- Genetic gradual reduction of OGT activity unveils the essential role of O-GlcNAc in the mouse embryo.PLoS genetics · 2025Article
- Lineage-specific dynamics of loss of X upregulation during inactive-X reactivation.Stem cell reports · 2024Article
- Modeling X chromosome inactivation using t5iLA naive human pluripotent stem cells.BMC biology · 2024Article
- A system to analyze the initiation of random X-chromosome inactivation using time-lapse imaging of single cells.Scientific reports · 2024Article
- The effect of data transformation on low-dimensional integration of single-cell RNA-seq.BMC bioinformatics · 2024Article
- Single-Cell Transcriptome Sequence Profiling on the Morphogenesis of Secondary Hair Follicles in Ordos Fine-Wool Sheep.International journal of molecular sciences · 2024Article
- Single-cell analysis of human prepuce reveals dynamic changes in gene regulation and cellular communications.BMC genomics · 2023Article
- RBBP4 is an epigenetic barrier for the induced transition of pluripotent stem cells into totipotent 2C-like cells.Nucleic acids research · 2023Article
- Comparative developmental genomics of sex-biased gene expression in early embryogenesis across mammals.Biology of sex differences · 2023Article
3 more citing papers are in PubMed but not listed here.
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Pluripotency, differentiation, and X Chromosome inactivation (XCI) are key aspects of embryonic development. However, the underlying relationship and mechanisms among these processes remain unclear. Here, we systematically dissected these features along developmental progression using mouse embryonic stem cells (mESCs) and single-cell RNA sequencing with allelic resolution. We found that mESCs grown in a ground state 2i condition displayed transcriptomic profiles diffused from preimplantation mouse embryonic cells, whereas EpiStem cells closely resembled the post-implantation epiblast. Sex-related gene expression varied greatly across distinct developmental states. We also identified novel markers that were highly enriched in each developmental state. Moreover, we revealed that several novel pathways, including PluriNetWork and Focal Adhesion, were responsible for the delayed progression of female EpiStem cells. Importantly, we "digitalized" XCI progression using allelic expression of active and inactive X Chromosomes and surprisingly found that XCI states exhibited profound variability in each developmental state, including the 2i condition. XCI progression was not tightly synchronized with loss of pluripotency and increase of differentiation at the single-cell level, although these processes were globally correlated. In addition, highly expressed genes, including core pluripotency factors, were in general biallelically expressed. Taken together, our study sheds light on the dynamics of XCI progression and the asynchronicity between pluripotency, differentiation, and XCI.
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