ArticleNature methods2021
Single-cell joint detection of chromatin occupancy and transcriptome enables higher-dimensional epigenomic reconstructions.
Article in Nature methods, 2021. 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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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
63 citing papers in PubMed, 93 citations in OpenAlex.
- CTCF aligns single-cell TAD-like domain boundaries and stabilizes long-range active chromatin clusters.Science advances · 2026Article
- Genome-wide profiling of histone modifications and transcription factor binding at single-cell resolution by DeChIC-seq.Cell research · 2026Article
- Simultaneous single-cell profiling of chromatin, transcriptome and surface markers with OneCell CUT&Tag captures epigenomic reprogramming.Nature biotechnology · 2026Article
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- Histone Modifications in Cardiovascular Disease: Mechanisms and Therapeutic Opportunities.MedComm · 2026Review
- Enhancer Dynamics for Gene Regulation in the Cardiovascular System.Arteriosclerosis, thrombosis, and vascular biology · 2026Review
- A hitchhiker's guide to single-cell epigenomics: Methods and applications for cancer research.International journal of cancer · 2026Review
- The applications of single-cell multiomics in drug screening.Pharmaceutical science advances · 2025Review
- Review
- Regulation of Hepatic Stellate Cell Phenotypes in Metabolic Dysfunction-Associated Steatohepatitis.Gastroenterology · 2025Review
- Single-cell epigenomics and proteomics methods integrated in multiomics.Fundamental research · 2025Review
- Combinatorial profiling of multiple histone modifications and transcriptome in single cells using scMTR-seq.Science advances · 2025Article
- IT-scC&T-seq streamlines scalable, parallel profiling of protein-DNA interactions in single cells.Genome biology · 2025Article
- Single-cell multi-omics delineates the dynamics of distinct epigenetic codes coordinating mouse gastrulation.BMC genomics · 2025Article
- Advances and applications in single-cell and spatial genomics.Science China. Life sciences · 2025Review
- Single-cell parallel analysis of DNA damage and transcriptome reveals selective genome vulnerability.Nature methods · 2025Article
- Article
- Semi-automated IT-scATAC-seq profiles cell-specific chromatin accessibility in differentiation and peripheral blood populations.Nature communications · 2025Article
- Single-nucleus CUT&RUN elucidates the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression.Genome research · 2025Article
3 more citing papers are in PubMed but not listed here.
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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
Deciphering mechanisms in cell-fate decisions requires single-cell holistic reconstructions of multidimensional epigenomic states in transcriptional regulation. Here we develop CoTECH, a combinatorial barcoding method allowing high-throughput single-cell joint detection of chromatin occupancy and transcriptome. We used CoTECH to examine bivalent histone marks (H3K4me3 and H3K27me3) with transcription from naive to primed mouse embryonic stem cells. We also derived concurrent bivalent marks in pseudosingle cells using transcriptome as an anchor for resolving pseudotemporal bivalency trajectories and disentangling a context-specific interplay between H3K4me3/H3K27me3 and transcription level. Next, we revealed the regulatory basis of endothelial-to-hematopoietic transition in two waves of hematopoietic cells and distinctive enhancer-gene-linking schemes guiding hemogenic endothelial cell emergence, indicating a unique epigenetic control of transcriptional regulation for hematopoietic stem cell priming. CoTECH provides an efficient framework for single-cell coassay of chromatin occupancy and transcription, thus enabling higher-dimensional epigenomic reconstructions.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.