Characterization of three different clusters of 18S–26S ribosomal DNA genes in the sea urchin P. lividus: Genetic and epigenetic regulation synchronous to 5S rDNA

•Molecular characterization of 18S–26S rDNA clusters in common sea urchin•Regulation of rRNA synthesis by DNA methylation during sea urchin development•Silencing of biggest cluster in sea urchin adult tissue•Synchronous synthesis of 5S and 18S–26S rRNA in common sea urchin

We previously reported the characterization 5S ribosomal DNA (rDNA) clusters in the common sea urchin Paracentrotus lividus and demonstrated the presence of DNA methylation-dependent silencing of embryo specific 5S rDNA cluster in adult tissue. In this work, we show genetic and epigenetic characterization of 18S–26S rDNA clusters in this specie. The results indicate the presence of three different 18S–26S rDNA clusters with different Non-Transcribed Spacer (NTS) regions that have different chromosomal localizations. Moreover, we show that the two largest clusters are hyper-methylated in the promoter-containing NTS regions in adult tissues, as in the 5S rDNA. These findings demonstrate an analogous epigenetic regulation in small and large rDNA clusters and support the logical synchronism in building ribosomes. In fact, all the ribosomal RNA genes must be synchronously and equally transcribed to perform their unique final product.