Global analysis of expression upon RNA Pol I inhibition (iPol I) in ESCs

Immediately following fertilisation, the genomes of mammalian embryos undergo extensive reprogramming to generate a totipotent zygote with the capacity to form the entire developing organism and associated extraembryonic tissues. The embryo must also switch from dependence on maternal transcripts to transcribing from its own genome, and is accompanied in mice by rapid and transient upregulation of MERVL transposons and MERVL-driven genes at the 2-cell stage. The mechanisms and requirement for MERVL and 2-cell (2C) gene upregulation are poorly understood. Moreover, this program must be rapidly shut off upon 2C exit and developmental progression. Here, we report that robust ribosomal RNA synthesis and nucleolar integrity are essential for exit from the 2C state. 2-cell embryos and 2C-like cells show immature nucleoli with altered structure and reduced function, and we reveal that nucleolar disruption induces conversion to the 2C-like state in ESCs. Mechanistically, the 2C/MERVL activator Dux is held in perinucleolar chromatin in ESCs and released into the nucleoplasm upon nucleolar disruption or direct inhibition of nucleolar phase separation, leading to its rapid upregulation. In embryos, nucleolar disruption prevents proper Dux silencing and leads to 2-4 cell arrest. Our findings reveal an intriguing link between rRNA synthesis, nucleolar maturation and gene repression during early development. Overall design: 3 replicates each of mouse ESCs at 0/2/4/8h after treatment with 1uM BMH-21 or CX-5461 used for RNA extraction and library generation (21 samples total)