Fig. 3: Unreprogrammed H3K9me3 directly blocks minor ZGA and delays LTR activation. | Nature Communications

Fig. 3: Unreprogrammed H3K9me3 directly blocks minor ZGA and delays LTR activation.

From: Unreprogrammed H3K9me3 prevents minor zygotic genome activation and lineage commitment in SCNT embryos

Fig. 3

a P-values (−log10 transformed) of representative gene motifs in rpgH3K9me3 (reprogrammed) and unrpgH3K9me3 (unreprogrammed) regions. b H3K9me3 signals on ZGA and MGA genes in late 1-cell and late 2-cell fertilized, SCNT and SCNT+Kdm4b embryos. c H3K9me3 signal on restrictedly activated minor ZGA genes in fertilized, SCNT and SCNT+Kdm4b embryos. d H3K9me3 signal around the Usp17lb, Usp17la and Gm16513 loci in CC, SCNT, SCNT+Kdm4b and fertilized embryos at the late 1-cell stage. e Expression level of Usp17l family genes in fertilized and SCNT embryos. n = 6 (SCNT) and n = 2 (Fertilized, from published data82 [GSE71434]) biologically independent samples. f The blastocyst rate of SCNT embryos after overexpression of Usp17l family genes. N indicates the total number of embryos. R indicates the number of replicates. g The mean expression level of MERVL-int and MT2_Mm in SCNT and fertilized embryos. n = 2 (Fertilized, from published data82 [GSE71434]) and n = 6 (SCNT) biologically independent samples. h The dynamics of the mean H3K9me3 signal of MERVL-int and MT2_Mm in SCNT and fertilized embryos. The number of biologically independent samples: n = 2 for SCNT-ICM and the fertilized group from a previous publication26 (GSE97778); n = 4 for CC and SCNT-6 hpa; n = 3 for SCNT-14 hpa, L2C, 4C, and 8C. i The mean H3K9me3 signals of MERVL-int and MT2_Mm loci in fertilized, SCNT and SCNT+Kdm4b embryos at the late 1-cell and late 2-cell stages. The number of biologically independent samples: n = 2 for SCNT+Kdm4b-L1C and the fertilized group from a previous publication26 (GSE97778); n = 3 for SCNT group and SCNT+Kdm4b-L2C. j The correlation of expression and H3K9me3 signal of LTRs in SCNT embryos compared with fertilized embryos. The Pearson correlation coefficient is shown. The red points indicate LTRs with significant changes in both H3K9me3 and expression levels. The gray points indicate other LTRs (e–i). Data are presented as mean values ± SEM (b). Statistical significance was calculated with a one-tailed Wilcoxon rank-sum test (f–h). Statistical significance was calculated with a two-tailed Student’s t test. ns, no significance. Source data are provided as a Source Data file.

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