Cellular macromolecules-tethered DNA walking indexing to explore nanoenvironments of chromatin modifications

Feng Chen, Min Bai, Xiaowen Cao, Jing Xue, Yue Zhao, Na Wu, Lei Wang, Dexin Zhang and Yongxi Zhao ()
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Feng Chen: Xi’an Jiaotong University
Min Bai: Xi’an Jiaotong University
Xiaowen Cao: Xi’an Jiaotong University
Jing Xue: Xi’an Jiaotong University
Yue Zhao: Xi’an Jiaotong University
Na Wu: Xi’an Jiaotong University
Lei Wang: Air Force Medical University
Dexin Zhang: Xi’an Jiaotong University
Yongxi Zhao: Xi’an Jiaotong University

Nature Communications, 2021, vol. 12, issue 1, 1-12

Abstract: 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.

Date: 2021
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DOI: 10.1038/s41467-021-22284-z

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