ArticleNucleic acids research2013
Visualization of multivalent histone modification in a single cell reveals highly concerted epigenetic changes on differentiation of embryonic stem cells.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 37 citations in OpenAlex.
- Sequential-GAM constructs the single-cell geometric 3D genome structure.Nucleic acids research · 2026Article
- High-speed multiplexed DNA-PAINT imaging of nuclear organization using an expanded sequence repertoire.Nature communications · 2026Article
- Bivalent chromatin: a developmental balancing act tipped in cancer.Biochemical Society transactions · 2024Review
- Sequence divergence and retrotransposon insertion underlie interspecific epigenetic differences in primates.Molecular biology and evolution · 2022Article
- Tumor microenvironmental signals reshape chromatin landscapes to limit the functional potential of exhausted T cells.Science immunology · 2022Article
- Combination of a synthetic retinoid and a DNA demethylating agent induced differentiation of neuroblastoma through retinoic acid signal reprogramming.British journal of cancer · 2021Article
- Cellular macromolecules-tethered DNA walking indexing to explore nanoenvironments of chromatin modifications.Nature communications · 2021Article
- A Microfluidic Device for Modulation of Organellar Heterogeneity in Live Single Cells.Analytical sciences : the international journal of the Japan Society for Analytical Chemistry · 2021Article
- Super-enhancers in transcriptional regulation and genome organization.Nucleic acids research · 2019Article
- Design, Construction, and Validation of Histone-Binding Effectors in Vitro and in Cells.Biochemistry · 2018Article
- Emerin modulates spatial organization of chromosome territories in cells on softer matrices.Nucleic acids research · 2018Article
- Chd2 regulates chromatin for proper gene expression toward differentiation in mouse embryonic stem cells.Nucleic acids research · 2017Article
- Repo-Man/PP1 regulates heterochromatin formation in interphase.Nature communications · 2017Article
- Repression of somatic cell fate in the germline.Cellular and molecular life sciences : CMLS · 2015Review
- Single molecule and single cell epigenomics.Methods (San Diego, Calif.) · 2015Review
- Poised chromatin in the mammalian germ line.Development (Cambridge, England) · 2014Review
- Snf2h-mediated chromatin organization and histone H1 dynamics govern cerebellar morphogenesis and neural maturation.Nature communications · 2014Article
- Heterogeneity in immune responses: from populations to single cells.Trends in immunology · 2014Review
- Single Cell Analysis: From Technology to Biology and Medicine.Single cell biology · 2014Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Combinations of histone modifications have significant biological roles, such as maintenance of pluripotency and cancer development, but cannot be analyzed at the single cell level. Here, we visualized a combination of histone modifications by applying the in situ proximity ligation assay, which detects two proteins in close vicinity (∼30 nm). The specificity of the method [designated as imaging of a combination of histone modifications (iChmo)] was confirmed by positive signals from H3K4me3/acetylated H3K9, H3K4me3/RNA polymerase II and H3K9me3/H4K20me3, and negative signals from H3K4me3/H3K9me3. Bivalent modification was clearly visualized by iChmo in wild-type embryonic stem cells (ESCs) known to have it, whereas rarely in Suz12 knockout ESCs and mouse embryonic fibroblasts known to have little of it. iChmo was applied to analysis of epigenetic and phenotypic changes of heterogeneous cell population, namely, ESCs at an early stage of differentiation, and this revealed that the bivalent modification disappeared in a highly concerted manner, whereas phenotypic differentiation proceeded with large variations among cells. Also, using this method, we were able to visualize a combination of repressive histone marks in tissue samples. The application of iChmo to samples with heterogeneous cell population and tissue samples is expected to clarify unknown biological and pathological significance of various combinations of epigenetic modifications.
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