title: Linking maternal and somatic 5S rRNA types with different sequence-specific non-LTR retrotransposons.
abstract: 5S rRNA is a ribosomal core component, transcribed from many gene copies organized in genomic repeats. Some eukaryotic species have two 5S rRNA types defined by their predominant expression in oogenesis or adult tissue. Our next-generation sequencing study on zebrafish egg, embryo, and adult tissue identified maternal-type 5S rRNA that is exclusively accumulated during oogenesis, replaced throughout the embryogenesis by a somatic-type, and thus virtually absent in adult somatic tissue. The maternal-type 5S rDNA contains several thousands of gene copies on chromosome 4 in tandem repeats with small intergenic regions, whereas the somatic-type is present in only 12 gene copies on chromosome 18 with large intergenic regions. The nine-nucleotide variation between the two 5S rRNA types likely affects TFIII binding and riboprotein L5 binding, probably leading to storage of maternal-type rRNA. Remarkably, these sequence differences are located exactly at the sequence-specific target site for genome integration by the 5S rRNA-specific Mutsu retrotransposon family. Thus, we could define maternal- and somatic-type MutsuDr subfamilies. Furthermore, we identified four additional maternal-type and two new somatic-type MutsuDr subfamilies, each with their own target sequence. This target-site specificity, frequently intact maternal-type retrotransposon elements, plus specific presence of Mutsu retrotransposon RNA and piRNA in egg and adult tissue, suggest an involvement of retrotransposons in achieving the differential copy number of the two types of 5S rDNA loci.
authors.affiliation: RNA Biology & Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, The Netherlands.
authors.forename: Mauro D
authors.identifier: 0000-0001-9832-6911
authors.initials: MD
authors.lastname: Locati
authors.affiliation: RNA Biology & Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, The Netherlands.
authors.forename: Johanna F B
authors.initials: JF
authors.lastname: Pagano
authors.affiliation: RNA Biology & Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, The Netherlands.
authors.forename: Wim A
authors.initials: WA
authors.lastname: Ensink
authors.affiliation: RNA Biology & Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, The Netherlands.
authors.forename: Marina
authors.initials: M
authors.lastname: van Olst
authors.affiliation: RNA Biology & Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, The Netherlands.
authors.forename: Selina
authors.initials: S
authors.lastname: van Leeuwen
authors.affiliation: Department of Molecular Cell Biology, Institute of Biology, Leiden University, Gorlaeus Laboratories - Cell Observatorium, Leiden 2333 CE, The Netherlands.
authors.forename: Ulrike
authors.initials: U
authors.lastname: Nehrdich
authors.affiliation: Department of Molecular Cell Biology, Institute of Biology, Leiden University, Gorlaeus Laboratories - Cell Observatorium, Leiden 2333 CE, The Netherlands.
authors.forename: Kongju
authors.initials: K
authors.lastname: Zhu
authors.affiliation: Department of Molecular Cell Biology, Institute of Biology, Leiden University, Gorlaeus Laboratories - Cell Observatorium, Leiden 2333 CE, The Netherlands.
authors.forename: Herman P
authors.initials: HP
authors.lastname: Spaink
authors.affiliation: RNA Biology & Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, The Netherlands.
authors.forename: Geneviève
authors.initials: G
authors.lastname: Girard
authors.affiliation: RNA Biology & Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, The Netherlands.
authors.forename: Han
authors.initials: H
authors.lastname: Rauwerda
authors.affiliation: RNA Biology & Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, The Netherlands.
authors.forename: Martijs J
authors.initials: MJ
authors.lastname: Jonker
authors.affiliation: RNA Biology & Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, The Netherlands.
authors.forename: Rob J
authors.initials: RJ
authors.lastname: Dekker
authors.affiliation: RNA Biology & Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, The Netherlands t.m.breit@uva.nl.
authors.forename: Timo M
authors.identifier: 0000-0002-6801-9969
authors.initials: TM
authors.lastname: Breit
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D002875:Chromosomes / Q000737:chemistry; D004625:Embryo, Nonmammalian; D047108:Embryonic Development / Q000235:genetics; D005260:Female; D059014:High-Throughput Nucleotide Sequencing; D008297:Male; D000072741:Maternal Inheritance; D009866:Oogenesis / Q000235:genetics; D012341:RNA, Ribosomal, 5S / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D018626:Retroelements; D020079:Terminal Repeat Sequences; D015027:Zebrafish / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D015053:Zygote / Q000254:growth & development / Q000378:metabolism
chemical_list: D012341:RNA, Ribosomal, 5S; D018626:Retroelements
keywords: 5S ribosomal RNA; embryogenesis; maternal rRNA; target-specific retrotransposon; zebrafish