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Peer-reviewedCC BY 4.0Nucleic Acids Research

Exploring DNA movement through the application of droplet-based high-efficiency chromatin conformation capture (DropHiChew) and loop velocity

  • Chen Zhang1,2
  • Yeming Xie3
  • Chen Tan3
  • Zhichao Chen3
  • Huimin Cao3
  • Mei Guo3
  • Luyang Zhao2
  • Zhe Weng4
  • Chong Tang5,3
5 affiliations
  1. 1Shenzhen Loop Area Institute , Shenzhen 518000,
  2. 2Shenzhen Salus BioMed Inc. Ltd. , Shenzhen 518000,
  3. 3BGI Genomics , Shenzhen 518083,
  4. 4NHC Key Laboratory of Male Reproduction and Genetics, Guangdong Provincial Reproductive Science Institute (Guangdong Provincial Fertility Hospital) , Guangzhou 510600,
  5. 5Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Longgang District , Shenzhen 518000,
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Abstract

This study presents a novel approach to understanding DNA movement dynamics. Chromatin conformation plays a crucial role in controlling gene expression and cellular processes, with abnormalities linked to diseases like cancer and genetic disorders. ​Current single-cell chromatin conformation methods face limitations in cost-effectiveness, accessibility, and capturing dynamic genome architecture.​​ Therefore, we develop ​DropHiChew, a droplet-based, highly efficient chromatin conformation capture method employing 10× Genomics single-cell systems for user-friendly, cost-effective implementation. Combined with our ​loop velocity algorithm—which estimates the speed and direction of cell development by quantifying chromatin movement—this approach accurately gauges the trajectory of DNA motion and cellular states even at shallow sequencing depth (50k contacts per cell). Validation demonstrates its applicability across biological systems, including HEK293T, spermiogenesis, and embryonic development. The integration of DropHiChew and loop velocity offers potential for diverse applications in chromatin capture studies. This paradigm provides a dynamic perspective on genome organization for disease modeling, cellular differentiation, and developmental biology.

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Cite

BibTeXRIS
BibTeX
@article{zhang2026exploring,
  title = {{Exploring DNA movement through the application of droplet-based high-efficiency chromatin conformation capture (DropHiChew) and loop velocity}},
  author = {Chen Zhang and Yeming Xie and Chen Tan and Zhichao Chen and Huimin Cao and Mei Guo and Luyang Zhao and Zhe Weng and Chong Tang},
  journal = {Nucleic Acids Research},
  year = {2026},
  month = oct,
  doi = {10.1093/nar/gkag995},
  url = {https://academic.oup.com/nar/article/doi/10.1093/nar/gkag995/9004255},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Exploring DNA movement through the application of droplet-based high-efficiency chromatin conformation capture (DropHiChew) and loop velocity
AU  - Chen Zhang
AU  - Yeming Xie
AU  - Chen Tan
AU  - Zhichao Chen
AU  - Huimin Cao
AU  - Mei Guo
AU  - Luyang Zhao
AU  - Zhe Weng
AU  - Chong Tang
PY  - 2026
DA  - 2026/10/01
JO  - Nucleic Acids Research
DO  - 10.1093/nar/gkag995
UR  - https://academic.oup.com/nar/article/doi/10.1093/nar/gkag995/9004255
AB  - This study presents a novel approach to understanding DNA movement dynamics. Chromatin conformation plays a crucial role in controlling gene expression and cellular processes, with abnormalities linked to diseases like cancer and genetic disorders. ​Current single-cell chromatin conformation methods face limitations in cost-effectiveness, accessibility, and capturing dynamic genome architecture.​​ Therefore, we develop ​DropHiChew, a droplet-based, highly efficient chromatin conformation capture method employing 10× Genomics single-cell systems for user-friendly, cost-effective implementation. Combined with our ​loop velocity algorithm—which estimates the speed and direction of cell development by quantifying chromatin movement—this approach accurately gauges the trajectory of DNA motion and cellular states even at shallow sequencing depth (50k contacts per cell). Validation demonstrates its applicability across biological systems, including HEK293T, spermiogenesis, and embryonic development. The integration of DropHiChew and loop velocity offers potential for diverse applications in chromatin capture studies. This paradigm provides a dynamic perspective on genome organization for disease modeling, cellular differentiation, and developmental biology.
SN  - 0305-1048
SN  - 1362-4962
ER  -