Locati Mauro D, Pagano Johanna F B, Ensink Wim A, van Olst Marina, van Leeuwen Selina, Nehrdich Ulrike, Zhu Kongju, Spaink Herman P, Girard Geneviève, Rauwerda Han, Jonker Martijs J, Dekker Rob J, Breit Timo M
RNA Biology & Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, The Netherlands.
Department of Molecular Cell Biology, Institute of Biology, Leiden University, Gorlaeus Laboratories - Cell Observatorium, Leiden 2333 CE, The Netherlands.
RNA. 2017 Apr;23(4):446-456. doi: 10.1261/rna.059642.116. Epub 2016 Dec 21.
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.
5S核糖体RNA是核糖体的核心组成部分，由基因组重复序列中组织的多个基因拷贝转录而来。一些真核生物物种有两种5S核糖体RNA类型，根据它们在卵子发生或成体组织中的主要表达来定义。我们对斑马鱼卵、胚胎和成体组织进行的新一代测序研究确定了母源型5S核糖体RNA，其仅在卵子发生过程中积累，在整个胚胎发育过程中被体细胞型所取代，因此在成体体细胞组织中几乎不存在。母源型5S核糖体DNA在4号染色体上包含数千个基因拷贝，呈串联重复，基因间区域较小，而体细胞型仅在18号染色体上有12个基因拷贝，基因间区域较大。两种5S核糖体RNA类型之间的九个核苷酸差异可能影响TFIII结合和核糖体蛋白L5结合，可能导致母源型核糖体RNA的储存。值得注意的是，这些序列差异恰好位于5S核糖体RNA特异性Mutsu逆转座子家族进行基因组整合的序列特异性靶位点处。因此，我们可以定义母源型和体细胞型MutsuDr亚家族。此外，我们还鉴定出另外四个母源型和两个新的体细胞型MutsuDr亚家族，每个亚家族都有自己的靶序列。这种靶位点特异性、经常完整的母源型逆转座子元件，加上卵子和成体组织中Mutsu逆转座子RNA和piRNA的特异性存在，表明逆转座子参与实现了两种类型5S核糖体DNA位点的不同拷贝数。
