Initiation of zygotic transcription in mammals is poorly understood. In mice, zygotic transcription is first detected shortly after pronucleus formation in 1-cell embryos, but the identity of the transcribed loci and mechanisms regulating their expression are not known. Using total RNA-Seq, we have found that transcription in 1-cell embryos is highly promiscuous, such that intergenic regions are extensively expressed and thousands of genes are transcribed at comparably low levels. Striking is that transcription can occur in the absence of defined core-promoter elements. Furthermore, accumulation of translatable zygotic mRNAs is minimal in 1-cell embryos because of inefficient splicing and 3' processing of nascent transcripts. These findings provide novel insights into regulation of gene expression in 1-cell mouse embryos that may confer a protective mechanism against precocious gene expression that is the product of a relaxed chromatin structure present in 1-cell embryos. The results also suggest that the first zygotic transcription itself is an active component of chromatin remodeling in 1-cell embryos.

Bioinformatics Group Division of Biology Faculty of Science Zagreb University Zagreb Croatia

Bioinformatics Group Division of Biology Faculty of Science Zagreb University Zagreb Croatia Department of Informatics University of Oslo Oslo Norway

Department of Biology University of Pennsylvania Philadelphia PA USA

Department of Integrated Biosciences Graduate School of Frontier Sciences The University of Tokyo Kashiwa Japan

Department of Medical Genome Science Graduate School of Frontier Sciences The University of Tokyo Kashiwa Japan The University of Tokyo Tokyo Japan

Institute of Molecular Genetics Academy of Sciences of the Czech Republic Prague Czech Republic

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