title: The first murine zygotic transcription is promiscuous and uncoupled from splicing and 3' processing.
abstract: 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.
authors.affiliation: Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.
authors.forename: Ken-Ichiro
authors.initials: K
authors.lastname: Abe
authors.affiliation: Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.
authors.forename: Ryoma
authors.initials: R
authors.lastname: Yamamoto
authors.affiliation: Bioinformatics Group, Division of Biology, Faculty of Science, Zagreb University, Zagreb, Croatia.
authors.forename: Vedran
authors.initials: V
authors.lastname: Franke
authors.affiliation: Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.
authors.forename: Minjun
authors.initials: M
authors.lastname: Cao
authors.affiliation: Department of Medical Genome Science, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan The University of Tokyo, Tokyo, Japan.
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Suzuki
authors.affiliation: Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.
authors.forename: Masataka G
authors.initials: MG
authors.lastname: Suzuki
authors.affiliation: Bioinformatics Group, Division of Biology, Faculty of Science, Zagreb University, Zagreb, Croatia Department of Informatics, University of Oslo, Oslo, Norway.
authors.forename: Kristian
authors.initials: K
authors.lastname: Vlahovicek
authors.affiliation: Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic svobodap@img.cas.cz rschultz@sas.upenn.edu aokif@k.u-tokyo.ac.jp.
authors.forename: Petr
authors.initials: P
authors.lastname: Svoboda
authors.affiliation: Department of Biology, University of Pennsylvania, Philadelphia, PA, USA svobodap@img.cas.cz rschultz@sas.upenn.edu aokif@k.u-tokyo.ac.jp.
authors.forename: Richard M
authors.initials: RM
authors.lastname: Schultz
authors.affiliation: Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan svobodap@img.cas.cz rschultz@sas.upenn.edu aokif@k.u-tokyo.ac.jp.
authors.forename: Fugaku
authors.initials: F
authors.lastname: Aoki
mesh_terms: D020413:3' Untranslated Regions / Q000502:physiology*; D000818:Animals; D002843:Chromatin / Q000378:metabolism; D042002:Chromatin Assembly and Disassembly / Q000502:physiology; D004622:Embryo, Mammalian / Q000166:cytology / Q000378:metabolism*; D018507:Gene Expression Regulation, Developmental / Q000502:physiology*; D051379:Mice; D012326:RNA Splicing / Q000502:physiology*; D014158:Transcription, Genetic / Q000502:physiology*; D015053:Zygote / Q000166:cytology / Q000378:metabolism*
chemical_list: D020413:3' Untranslated Regions; D002843:Chromatin
keywords: RNA‐Seq; gene expression; preimplantation mouse embryo; pre‐mRNA splicing; transcription