Dynamic landscapes and regulome of mRNA structure during zebrafish early embryogenesis

We resolved the RNA secondary structure during zebrafish early embryogenesis based on in vivo click selective 2'-hydroxyl acylation and profiling experiment (icSHAPE). We analyzed the RNA structure dynamics among different development stages. Also, we studied which factors regulate maternal gene decay by RNA structure switch. Overall design: icSHAPE of 12 samples from zebrafish embryos at six different early development stages and 4 samples from Elavl1a deficient zebrafish embryos at sphere and shield stages, including two treated with DMSO as control and two treated with NAIN3 for each stage or condition. RNA-seq of 6 samples from zebrafish embryos at 2, 4, 6 h.p.f. and 4 samples from Elavl1a deficient zebrafish embryos at 4 and 6 h.p.f. including two biological replicates. iCLIP-seq of 4 samples from flag-elavl1a mRNA injected zebrafish embryos at 4 and 6 h.p.f. including two biological replicates.