ArticleNature communications2021
Cellular macromolecules-tethered DNA walking indexing to explore nanoenvironments of chromatin modifications.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Proximity-activated DNA scanning encoded sequencing for massive access to membrane proteins nanoscale organization.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Visualizing epigenetic modifications and their spatial proximities in single cells using three DNA-encoded amplifying FISH imaging strategies: BEA-FISH, PPDA-FISH and Cell-TALKING.Nature protocols · 2025Article
- Bidirectional linkage of DNA barcodes for the multiplexed mapping of higher-order protein interactions in cells.Nature biomedical engineering · 2024Article
- Molecular robotic agents that survey molecular landscapes for information retrieval.Nature communications · 2024Article
- Development of a DNAzyme Walker for the Detection of APE1 in Living Cancer Cells.Analytical chemistry · 2023Article
- Hierarchical DNA branch assembly-encoded fluorescent nanoladders for single-cell transcripts imaging.Nucleic acids research · 2023Article
- Role of main RNA modifications in cancer: NSignal transduction and targeted therapy · 2022Review
- Applications of DNA-Functionalized Proteins.International journal of molecular sciences · 2021Review
- Walking through chromatin modifications.Nature methods · 2021Article
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Abstract
Exploring spatial organization and relationship of diverse biomolecules within cellular nanoenvironments is important to elucidate the fundamental processes of life. However, it remains methodologically challenging. Herein, we report a molecular recognition mechanism cellular macromolecules-tethered DNA walking indexing (Cell-TALKING) to probe the nanoenvironments containing diverse chromatin modifications. As an example, we characterize the nanoenvironments of three DNA modifications around one histone posttranslational modification (PTM). These DNA modifications in fixed cells are labeled with respective DNA barcoding probes, and then the PTM site is tethered with a DNA walking probe. Cell-TALKING can continuously produce cleavage records of any barcoding probes nearby the walking probe. New 3'-OH ends are generated on the cleaved barcoding probes to induce DNA amplification for downstream detections. Combining fluorescence imaging, we identify various combinatorial chromatin modifications and investigate their dynamic changes during cell cycles. We also explore the nanoenvironments in different cancer cell lines and clinical specimens. In principle, using high-throughput sequencing instead of fluorescence imaging may allow the detection of complex cellular nanoenvironments containing tens of biomolecules such as transcription factors.
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