title: Long non-coding RNA exchange during the oocyte-to-embryo transition in mice.
abstract: The oocyte-to-embryo transition (OET) transforms a differentiated gamete into pluripotent blastomeres. The accompanying maternal-zygotic RNA exchange involves remodeling of the long non-coding RNA (lncRNA) pool. Here, we used next generation sequencing and de novo transcript assembly to define the core population of 1,600 lncRNAs expressed during the OET (lncRNAs). Relative to mRNAs, OET lncRNAs were less expressed and had shorter transcripts, mainly due to fewer exons and shorter 5' terminal exons. Approximately half of OET lncRNA promoters originated in retrotransposons suggesting their recent emergence. Except for a small group of ubiquitous lncRNAs, maternal and zygotic lncRNAs formed two distinct populations. The bulk of maternal lncRNAs was degraded before the zygotic genome activation. Interestingly, maternal lncRNAs seemed to undergo cytoplasmic polyadenylation observed for dormant mRNAs. We also identified lncRNAs giving rise to trans-acting short interfering RNAs, which represent a novel lncRNA category. Altogether, we defined the core OET lncRNA transcriptome and characterized its remodeling during early development. Our results are consistent with the notion that rapidly evolving lncRNAs constitute signatures of cells-of-origin while a minority plays an active role in control of gene expression across OET. Our data presented here provide an excellent source for further OET lncRNA studies.
authors.affiliation: Bioinformatics Group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia.
authors.forename: Rosa
authors.initials: R
authors.lastname: Karlic
authors.affiliation: Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic.
authors.forename: Sravya
authors.initials: S
authors.lastname: Ganesh
authors.affiliation: Bioinformatics Group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia.
authors.forename: Vedran
authors.initials: V
authors.lastname: Franke
authors.affiliation: Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic.
authors.forename: Eliska
authors.initials: E
authors.lastname: Svobodova
authors.affiliation: Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic.
authors.forename: Jana
authors.initials: J
authors.lastname: Urbanova
authors.affiliation: Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 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: Fugaku
authors.initials: F
authors.lastname: Aoki
authors.affiliation: Bioinformatics Group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia.
authors.forename: Kristian
authors.initials: K
authors.lastname: Vlahovicek
authors.affiliation: Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic.
authors.forename: Petr
authors.initials: P
authors.lastname: Svoboda
mesh_terms: D000818:Animals; D001757:Blastomeres / Q000378:metabolism; D004622:Embryo, Mammalian / Q000378:metabolism*; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D059014:High-Throughput Nucleotide Sequencing; D051379:Mice; D009865:Oocytes / Q000378:metabolism*; D062085:RNA, Long Noncoding / Q000235:genetics* / Q000378:metabolism; D017423:Sequence Analysis, RNA
chemical_list: D062085:RNA, Long Noncoding
keywords: endo-siRNA; lncRNA; oocyte; polyadenylation; zygote