Af-CUT&Tag: a sensitive and antibody-free chromatin profiling method using genetically encoded tags and high-affinity binders fused to Tn5.
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| Autores principales: | , , , , , , , , , , , , , , |
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| Formato: | Artículo científico |
| Lenguaje: | en |
| Publicado: |
Nature communications
2026
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| _version_ | 1868266097715707904 |
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| author | Wang, Xindong Deng, Xusheng Qiu, Lu Liu, Junjia Shen, Hengxiang Du, Haoran Li, Weijie Song, Linxuan Deng, Wenhui Dong, Xiaoning Han, Yi Liu, Benchao Huang, Jialiang Li, Zengpeng Zhang, Yongyou |
| author_facet | Wang, Xindong Deng, Xusheng Qiu, Lu Liu, Junjia Shen, Hengxiang Du, Haoran Li, Weijie Song, Linxuan Deng, Wenhui Dong, Xiaoning Han, Yi Liu, Benchao Huang, Jialiang Li, Zengpeng Zhang, Yongyou Wang, Xindong Deng, Xusheng Qiu, Lu Liu, Junjia Shen, Hengxiang Du, Haoran Li, Weijie Song, Linxuan Deng, Wenhui Dong, Xiaoning Han, Yi Liu, Benchao Huang, Jialiang Li, Zengpeng Zhang, Yongyou |
| collection | PubMed - marine biology |
| contents | Af-CUT&Tag: a sensitive and antibody-free chromatin profiling method using genetically encoded tags and high-affinity binders fused to Tn5. Wang, Xindong Deng, Xusheng Qiu, Lu Liu, Junjia Shen, Hengxiang Du, Haoran Li, Weijie Song, Linxuan Deng, Wenhui Dong, Xiaoning Han, Yi Liu, Benchao Huang, Jialiang Li, Zengpeng Zhang, Yongyou Animals Chromatin Humans Transposases MicroRNAs Liver Regeneration Chromatin Assembly and Disassembly CRISPR-Cas Systems Transcription Factors Mice Conventional chromatin profiling techniques are often limited by antibody availability and performance. Here, we introduce Af-CUT&Tag, a target antibody-free method that overcomes these limitations by using CRISPR-integrated peptide tags (HiBiT/ALFA-tag) recognized by engineered binders (LgBiT/NbALFA) fused to a Tn5 transposase. Af-CUT&Tag eliminates dependence on traditional target antibodies, achieving robust specificity and sensitivity with as few as 500 cells. It provides high-quality chromatin profiles, with improved signal-to-noise ratios and library quality compared with conventional antibody-based counterparts, while also enabling single-cell resolution (scAf-CUT&Tag). Applying Af-CUT&Tag to Hippo effectors (YAP1/TAZ) during liver regeneration reveals dynamic chromatin remodeling, including YAP1/TAZ-mediated control of lipid metabolism (e.g., Lpin1, Fasn) and heme clearance (Hpx, Trf). We further identify miR-122 as a critical regulator of these processes, impacting liver regeneration. The versatility of Af-CUT&Tag in cell lines, bulk tissues, and single nuclei establishes it as a powerful tool for studying gene regulation in development, disease, and regeneration. |
| format | Artículo científico |
| id | pubmed_41547832 |
| institution | PubMed |
| language | en |
| publishDate | 2026 |
| publisher | Nature communications |
| record_format | pubmed |
| spellingShingle | Af-CUT&Tag: a sensitive and antibody-free chromatin profiling method using genetically encoded tags and high-affinity binders fused to Tn5. Wang, Xindong Deng, Xusheng Qiu, Lu Liu, Junjia Shen, Hengxiang Du, Haoran Li, Weijie Song, Linxuan Deng, Wenhui Dong, Xiaoning Han, Yi Liu, Benchao Huang, Jialiang Li, Zengpeng Zhang, Yongyou Animals Chromatin Humans Transposases MicroRNAs Liver Regeneration Chromatin Assembly and Disassembly CRISPR-Cas Systems Transcription Factors Mice Af-CUT&Tag: a sensitive and antibody-free chromatin profiling method using genetically encoded tags and high-affinity binders fused to Tn5. Wang, Xindong Deng, Xusheng Qiu, Lu Liu, Junjia Shen, Hengxiang Du, Haoran Li, Weijie Song, Linxuan Deng, Wenhui Dong, Xiaoning Han, Yi Liu, Benchao Huang, Jialiang Li, Zengpeng Zhang, Yongyou Animals Chromatin Humans Transposases MicroRNAs Liver Regeneration Chromatin Assembly and Disassembly CRISPR-Cas Systems Transcription Factors Mice Conventional chromatin profiling techniques are often limited by antibody availability and performance. Here, we introduce Af-CUT&Tag, a target antibody-free method that overcomes these limitations by using CRISPR-integrated peptide tags (HiBiT/ALFA-tag) recognized by engineered binders (LgBiT/NbALFA) fused to a Tn5 transposase. Af-CUT&Tag eliminates dependence on traditional target antibodies, achieving robust specificity and sensitivity with as few as 500 cells. It provides high-quality chromatin profiles, with improved signal-to-noise ratios and library quality compared with conventional antibody-based counterparts, while also enabling single-cell resolution (scAf-CUT&Tag). Applying Af-CUT&Tag to Hippo effectors (YAP1/TAZ) during liver regeneration reveals dynamic chromatin remodeling, including YAP1/TAZ-mediated control of lipid metabolism (e.g., Lpin1, Fasn) and heme clearance (Hpx, Trf). We further identify miR-122 as a critical regulator of these processes, impacting liver regeneration. The versatility of Af-CUT&Tag in cell lines, bulk tissues, and single nuclei establishes it as a powerful tool for studying gene regulation in development, disease, and regeneration. |
| title | Af-CUT&Tag: a sensitive and antibody-free chromatin profiling method using genetically encoded tags and high-affinity binders fused to Tn5. |
| topic | Animals Chromatin Humans Transposases MicroRNAs Liver Regeneration Chromatin Assembly and Disassembly CRISPR-Cas Systems Transcription Factors Mice |
| url | https://pubmed.ncbi.nlm.nih.gov/41547832/ |