Abstract
Protein-mediated chromatin interactions can be revealed by coupling proximity-based ligation with chromatin immunoprecipitation. However, these techniques require complex experimental procedures and millions of cells per experiment, which limits their widespread application in life science research. Here, we develop a novel method, Hi-Tag, that identifies high-resolution, long-range chromatin interactions through transposase tagmentation and chromatin proximity ligation (with a phosphorothioate-modified linker). Hi-Tag can be implemented using as few as 100,000 cells, involving simple experimental procedures that can be completed within 1.5 days. Meanwhile, Hi-Tag is capable of using its own data to identify the binding sites of specific proteins, based on which, it can acquire accurate interaction information. Our results suggest that Hi-Tag has great potential for advancing chromatin interaction studies, particularly in the context of limited cell availability.
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Acknowledgement
This work was supported by the National Natural Science Foundation of China (32221005), the Earmarked Fund for CARS (CARS-35), the National Natural Science Foundation of China Outstanding Youth (32125035) and Major Project of Hubei Hongshan Laboratory (2021hszd003). We thank laboratory members for helpful discussions and critical reading of the paper. We thank the public technology service platform of Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Ministry of Education) and we would be grateful to Jing Xu and Shuang Xiao for their support of sample preparation, data acquisition and analysis. The computations in this paper were run on the bioinformatics computing platform of the National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University.
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Qi, X., Zhang, L., Zhao, Q. et al. Hi-Tag: a simple and efficient method for identifying protein-mediated long-range chromatin interactions with low cell numbers. Sci. China Life Sci. 67, 1027–1034 (2024). https://doi.org/10.1007/s11427-023-2441-0
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DOI: https://doi.org/10.1007/s11427-023-2441-0