Fig. 4: Application of Af-CUT&Tag in liver partial hepatectomy model.

a. Schematic diagram of Rosa26-CAG-LSL-Cas9-tdTomato mice injected with rAAV2/8-type virus carrying Yap1/Taz-HiBiT knock-in template for liver cell-specific gene knock-in. b. Western blot detected the expression levels of HiBiT and YAP1 in Yap1-HiBiT liver tissue protein (top), and detected the expression levels of HiBiT and TAZ in Taz1-HiBiT liver tissue protein (bottom). The blots shown are representative of results obtained from multiple independent experiments. c. Comparison of the Fraction of Reads in Peaks (FRiP) for Yap1/Taz signals in Af-CUT&Tag and Nano-CUT&Tag profiles in liver tissue cells. The bar plot represents the mean FRiP value for each condition, with pre- and post-hepatectomy (PHx-pre and PHx-post) samples indicated by distinct colored points. Statistical significance was assessed using a unpaired t-test to compare the mean values between the two groups. d. Peak in promoter, reads in promoter, PCR Bottlenecking Coefficient 1 (PBC1), Non-Redundant Fraction (NRF), and duplication ratio comparison of Yap1/Taz signal in Af-CUT&Tag and Nano-CUT&Tag in liver tissue cells. e. Comparison of unique reads per cell detected by the scAf-CUT&Tag method targeting Yap1 between PHx-pre and PHx-post samples without downsampling the data. The mean number of unique reads per cell is 1153 for PHx-pre and 5844 for PHx-post. Data are shown on a log10 scale. Violin plots illustrate the distribution of unique reads per cell, with the central line representing the median, the box edges corresponding to the 25th and 75th percentiles, and the upper and lower edges of the violin indicating the maximum and minimum values. f. Uniform manifold approximation and projection (UMAP) plots of Yap1 signals for PHx-pre (left) and PHx-post (right) (PHx-pre: n = 12,775; PHx-post: n = 12,812). g. Chromatin landscapes showing comparing bulk Af-CUT&Tag maps with scAf-CUT&Tag maps (PHx-pre Yap1 cluster3 and PHx-post Yap1 cluster 2), both in aggregate over all single cells and individual cells, at regions of enrichment of Yap1. Cells were ordered by read coverage within the regions depicted.