Extended Data Fig. 7: Knockout of upf3a, but not upf1 or upf3b, impairs GCR in capn3a^−/− and nid1a^−/− embryos.

a, Schematic diagram showing the genomic structure and a genetic mutation in zebrafish upf3a gene. ATG denotes the translation start codon; black lines denote introns; blue vertical bars denote exons. Red horizontal line through the letters denotes deletion of 17 bp in the upf3a gene. Numbers denote the amino acid positions of two domains in zebrafish Upf3a protein, and the length of the Upf3a^−/− mutant protein. b, Western blot analysis of Upf3a protein in wild-type and upf3a^−/− embryos at 12 hpf. Actb1 was used as the protein loading control. MZ, maternal–zygotic mutant embryos. c, Schematic diagram showing the genomic structure and a genetic mutation of zebrafish upf1 gene. Underlined residues denote the additional 4 bp in the upf1 gene. d, Schematic diagram showing the genomic structure and a genetic mutation of the zebrafish upf3b gene. Red horizontal line denotes deletion of 1 bp in the upf3b gene. e, Statistical analysis of the average liver sizes of three genotypes from the in-cross of upf3a^+/−;capn3a^−/− as indicated at 3.5 dpf. The number of embryos for each genotype is shown. upf3a none-MZ denotes upf3a none-maternal–zygotic mutant embryos. f, WISH of upf3a in the offspring from the in-cross of upf3a^+/− at the one-cell stage. g, Images of zebrafish larvae of different genotypes at 3, 4 and 5 dpf as shown. All larvae were from the in-cross of two homozygous parents (either single or double homozygous mutants). h, Statistical analysis of the average body lengths in the samples as shown in g. i, Statistical analysis of the average body lengths of three genotypes from the in-cross of upf3a^+/−;nid1a^−/− embryos at 4 dpf as indicated. j, Statistical analysis of the average body lengths in the 4-dpf larvae of four genotypes as indicated. The wild-type and upf1^−/− embryos were from the in-cross of upf1^+/−. The nid1a^−/− and upf1^−/−;nid1a^−/− embryos were from the incross of upf1^+/−;nid1a^−/−. k, Statistical analysis of the average body lengths in the 4-dpf larvae of the four genotypes as indicated. The wild-type and upf3b^−/− embryos were from the in-cross of upf3b^+/−. The nid1a^−/− and upf3b^−/−;nid1a^−/− embryos were from the in-cross of upf3b^+/−;nid1a^−/−. Each experiment was repeated three times with similar results, and a representative result is shown. n indicates the number of zebrafish embryos in each group. Data are mean ± s.d. from three biological replicates. *P < 0.05, **P < 0.01, ***P < 0.001, two-tailed t-test.