A cost-effective tsCUT&Tag method for profiling transcription factor binding landscape

Transcription factor binding landscape (TFBL) is necessary to dissect gene regulatory network for important agronomic traits. However, a low-cost and high-throughput chromatin profiling method in vivo is still lacked in plants. Here, we developed a transient and simplified CUT&Tag method (tsCUT&Tag) that combines transient expression of transcription factor proteins in protoplasts with a simplified CUT&Tag without nucleus extraction. tsCUT&Tag exhibited better data quality and higher signal resolution with lower sequencing depth compared to traditional ChIP-seq. Furthermore, we proved a strategy combining tsCUT&Tag with deep learning which has great potentials for profiling TFBL across the whole life cycle of plants.