Fig. 3: Housekeeping gene reactivation revealed by single-cell transcriptome.

a UMAP plot of the 64-cell stage samples from forward cross embryos. In total, 844 cells were divided into 9 clusters and annotated as 8 cell types. The animal (up) and vegetal (down) blastomeres of a Ciona embryo at the 64-cell stage are shown. Font color corresponds to cell types. b Expression ratio of paternal housekeeping genes to all genes in each cell at the 64-cell stage from forward cross embryos. Colors represent the level of the expression ratio. c Boxplot of the expression ratio of paternal housekeeping genes in each cell type at the 64-cell stage from forward cross embryos. n = 40, 43, 32, 187, 259, 150, 70, 20, 43 cells for each cell type from endoderm to epidermis (b). d UMAP plot of the 112-cell-stage samples from forward cross embryos. In total, 1002 cells were divided into 12 clusters and annotated as 9 cell types. Animal (up) and vegetal (down) blastomeres of a Ciona embryo at the 112-cell stage are shown. Font color corresponds to cell type. e Expression ratio of paternal housekeeping genes to all genes in each cell at the 112-cell stage from forward cross embryos. Colors represent the expression ratio. f Boxplot of the expression ratio of paternal housekeeping genes in each cell type at the 112-cell stage from forward cross embryos. n = 98, 60, 107, 138, 33, 29, 95, 181, 27, 48, 43, 143 cells for each cell type from endoderm to epidermis (b). g Whole-mount in situ hybridization of 60SL11, RPL13, SEC, KRR and HNRN in self-cross C. savignyi embryos and forward cross embryos at 32-, 64- and 112-cell stages. Scale bar: 50 μm. In each box plot, the horizontal black lines represent median values; boxes extend from 25th to 75th percentile of each group’s distribution of values; the vertical extending lines indicate adjacent values, and dots mark observations outside the range of adjacent values. The experiment was independently performed at least three times. Source data are provided as a Source Data file.