GSE162903
Base-editor-mediated multiplexed inactivation of DNA methyltransferases reveals essential roles of miRNAs in mouse gastrulation
Here, we first establish an easy Multi-Stop system to simultaneously inactivate genes involved in DNA methylation and demethylation in zygotes through introduction of the stop codon by hA3A-eBE-Y130F-mediated base editor (BE). While Multi-Stop-derived Dnmt-null embryos display embryonic lethal due to gastrulation failure. Moreover, mutation combinations between Tet and Dnmt families show severe embryonic lethal and Dnmt1 or Dnmt3a/3b is indispensable for mouse gastrulation. Then WGBS and RNA-seq analysis of different mutant embryos reveals genes jointly maintained by Dnmt1 and Dnmt3a/3b that are critical for gastrulation. Overall design: We used WGBS (Whole Genome Bisulfite Sequencing) and RNA-seq to analyze the change of DNA methylation and transcription in DNMT and TET mutant embryos. WGBS data of E7.5 whole embryos from eight groups of 32 samples, including E7.5-control, E7.5-Dnmt1-KO, E7.5-Dnmt3a/3b-DKO, E7.5-Dnmt1/3a/3b-TKO, E7.5-Tet1/2/3;Dnmt1/3a/3b-6KO, E7.5-Tet1/2/3; Dnmt3a/3b-5KO, E7.5-Tet1/2/3; Dnmt1-4KO, E7.5-Tet1/2; Dnmt3a/3b-4KO. WGBS data of E6.5 and E7.5 embryo from 16 groups of 48 samples, including Ex-E6.5-control, Ex-E6.5-Dnmt1-KO, Ex-E6.5-Dnmt3a/3b-DKO, Ex-E6.5-Dnmt1/3a/3b-TKO, Em-E6.5-control, Em-E6.5-Dnmt1-KO, Em-E6.5-Dnmt3a/3b-DKO, Em-E6.5-Dnmt1/3a/3b-TKO, Ex-E7.5-control, Ex-E7.5-Dnmt1-KO, Ex-E7.5-Dnmt3a/3b-DKO, Ex-E7.5-Dnmt1/3a/3b-TKO, Em-E7.5-control, Em-E7.5-Dnmt1-KO, Em-E7.5-Dnmt3a/3b-DKO, Em-E7.5-Dnmt1/3a/3b-TKO. RNA-seq data of E6.5 and E7.5 embryo from 16 groups of 48 samples, including Ex-E6.5-control, Ex-E6.5-Dnmt1-KO, Ex-E6.5-Dnmt3a/3b-DKO, Ex-E6.5-Dnmt1/3a/3b-TKO, Em-E6.5-control, Em-E6.5-Dnmt1-KO, Em-E6.5-Dnmt3a/3b-DKO, Em-E6.5-Dnmt1/3a/3b-TKO, Ex-E7.5-control, Ex-E7.5-Dnmt1-KO, Ex-E7.5-Dnmt3a/3b-DKO, Ex-E7.5-Dnmt1/3a/3b-TKO, Em-E7.5-control, Em-E7.5-Dnmt1-KO, Em-E7.5-Dnmt3a/3b-DKO, Em-E7.5-Dnmt1/3a/3b-TKO.