GSE39849
Chromatin dynamics and genome-wide profiling of repetitive elements during early mammalian embryogenesis.
We have used repetitive elements, including retrotransposons, as model loci to address how and when  heterochromatin forms during development. High throughput RNA-sequencing using a  Nano-CAGE protocol throughout early embryogenesis revealed that the expression of  repetitive elements is abundant in embryonic cells, highly dynamic and stage-specific,  with most repetitive elements becoming repressed before implantation. Furthermore, we  show that Line L1 elements and IAP retrotransposons become reactivated from both  parental genomes in mouse embryos after fertilisation, indicating an open chromatin  configuration at the beginning of development. Our data show that the reprogramming process that follows  fertilisation is accompanied by a robust transcriptional activation of retrotransposons  and suggests that expression of repetitive elements is initially regulated through an  RNA-dependent mechanism in mammals. Overall design: Genome Wide profiling of CAGE transcripts using Nano-CAGE and RNAseq in oocytes and 3 different stages of mouse pre-implantation development