ArticleNature biotechnology2023
scChIX-seq infers dynamic relationships between histone modifications in single cells.
Article in Nature biotechnology, 2023. 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.
- Article
- A hitchhiker's guide to single-cell epigenomics: Methods and applications for cancer research.International journal of cancer · 2026Review
- Single-cell sequencing technology in renal cancer: insights into tumor biology and clinical application.Biomarker research · 2025Review
- Retrospective and multifactorial single-cell profiling reveals sequential chromatin reorganization during X inactivation.Nature cell biology · 2025Article
- Ocelli: an open-source tool for the analysis and visualization of developmental multimodal single-cell data.NAR genomics and bioinformatics · 2025Article
- annATAC: automatic cell type annotation for scATAC-seq data based on language model.BMC biology · 2025Article
- Advances and applications in single-cell and spatial genomics.Science China. Life sciences · 2025Review
- Opportunities and challenges in the application of single-cell transcriptomics in plant tissue research.Physiology and molecular biology of plants : an international journal of functional plant biology · 2025Review
- scTrends: A living review of commercial single-cell and spatial 'omic technologies.Cell genomics · 2024Review
- Crossing epigenetic frontiers: the intersection of novel histone modifications and diseases.Signal transduction and targeted therapy · 2024Review
- Emerging toolkits for decoding the co-occurrence of modified histones and chromatin proteins.EMBO reports · 2024Review
- The chromatin accessibility dynamics during cell fate specifications in zebrafish early embryogenesis.Nucleic acids research · 2024Article
- Advances in single-cell omics and multiomics for high-resolution molecular profiling.Experimental & molecular medicine · 2024Review
- Nano-CUT&Tag for multimodal chromatin profiling at single-cell resolution.Nature protocols · 2024Review
- Single-cell Technologies Provide Novel Insights into Liver Physiology and Pathology.Journal of clinical and translational hepatology · 2024Review
- Single-cell joint profiling of multiple epigenetic proteins and gene transcription.Science advances · 2024Article
- Application and research progress of single cell sequencing technology in leukemia.Frontiers in oncology · 2024Review
- Combinatorial single-cell profiling of major chromatin types with MAbID.Nature methods · 2024Article
- Single-cell technologies for multimodal omics measurements.Frontiers in systems biology · 2023Review
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Authors and funding
6 authors.
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Abstract
Regulation of chromatin states involves the dynamic interplay between different histone modifications to control gene expression. Recent advances have enabled mapping of histone marks in single cells, but most methods are constrained to profile only one histone mark per cell. Here, we present an integrated experimental and computational framework, scChIX-seq (single-cell chromatin immunocleavage and unmixing sequencing), to map several histone marks in single cells. scChIX-seq multiplexes two histone marks together in single cells, then computationally deconvolves the signal using training data from respective histone mark profiles. This framework learns the cell-type-specific correlation structure between histone marks, and therefore does not require a priori assumptions of their genomic distributions. Using scChIX-seq, we demonstrate multimodal analysis of histone marks in single cells across a range of mark combinations. Modeling dynamics of in vitro macrophage differentiation enables integrated analysis of chromatin velocity. Overall, scChIX-seq unlocks systematic interrogation of the interplay between histone modifications in single cells.
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