Super-CUT&Tag: A Sensitive, Spatially Resolved Approach for Epigenomic Profiling in Tissue Sections

Zhu, M.; Zha, Z.; Xuan, J.; Zhao, H.; Dai, J.; Liu, J.; Xia, Y.; Lin, H.; Yang, Y.; Chen, F.; Lin, S.; Liu, X.; Wu, L.; Zhu, Z.; Huang, J.; Zhang, H.; Yang, C.

doi:10.64898/2025.12.08.692886

bioRxiv · 10.64898/2025.12.08.692886

Super-CUT&Tag: A Sensitive, Spatially Resolved Approach for Epigenomic Profiling in Tissue Sections

Zhu, M.·Zha, Z.·Xuan, J.·Zhao, H.·Dai, J.·Liu, J.·Xia, Y.·Lin, H.·Yang, Y.·Chen, F.·Lin, S.·Liu, X.·Wu, L.·Zhu, Z.·Huang, J.·Zhang, H.·Yang, C.

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Abstract

Spatial profiling of protein-DNA interactions is essential for understanding gene regulatory processes, but current methods suffer from low sensitivity, limited resolution, and complex workflows. Here we introduce Super-CUT&Tag (Solid-phase interface embedded with an Ultra-dense DNA barcode array to Profile Epigenomic landscapes for spatially Resolved CUT&Tag), a robust spatial epigenomic method that directly transfers in situ protein-DNA interactions from tissue sections onto a pre-fabricated spatially barcoded array. Incorporating 3D polyamidoamine (PAMAM) dendrimers markedly improves chromatin capture efficiency, achieving several-fold higher sensitivity compared to current spatial CUT&Tag approaches. Using Super-CUT&Tag, we profile H3K27ac spatial landscape and uncover previously hidden active-chromatin heterogeneity across mouse embryonic tissues and stages. Integration with spatial transcriptomics further reveals spatiotemporal enhancer regulation dynamics of Neurod2 during corticogenesis. By overcoming key bottlenecks in sensitivity, resolution and usability, Super-CUT&Tag establishes a powerful platform for spatial epigenomic profiling in complex tissues.

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Zhu, M., Zha, Z., Xuan, J., Zhao, H., Dai, J., Liu, J., Xia, Y., Lin, H., Yang, Y., Chen, F., Lin, S., Liu, X., Wu, L., Zhu, Z., Huang, J., Zhang, H., Yang, C.. 2025-12-10. Super-CUT&Tag: A Sensitive, Spatially Resolved Approach for Epigenomic Profiling in Tissue Sections. https://doi.org/10.64898/2025.12.08.692886

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