Drosophila melanogaster Raw sequence reads. Drosophila melanogaster

RNA exo- and endonucleases are essential for nuclear noncoding RNA (ncRNA) maturation. Substrate specificities of the Rex RNA nuclease family of Mg2+-dependent 3’-5’ single-stranded RNA DEDDh exonucleases, implicated in ncRNA maturation, is mostly unknown in higher eukaryotes. Here we studied the Drosophila melanogaster dNEF-sp 3’-5’ exonuclease (CG8368), a distant homolog of Saccharomyces cerevisiae Rex1p. Loss-of-function mutants of dNEF-sp accumulated 3’ extended, improperly trimmed snoRNAs and 5S rRNAs. Furthermore, while in higher eukaryotes an endonucleolytic cleavage, guided by snoRNA U8 and dependent on Ddx51 helicase, was proposed to generate the 3’ end of 28S rRNA, dNEF-sp mutants and knockdowns of the Ddx51 homolog Dbp73D additionally revealed accumulation of 3’ extended 28S rRNA precursors, demonstrating that 3’-exonucleolytic processing matured 3’ ends of 28S rRNA in D. melanogaster. dNEF-sp enzymatic activity was required for germline development and organismal survival, and loss-of-function of dNEF-sp lead to increased nucleolar size and defective ribosome export. Considering the conservation of this novel Rex exonuclease member in all higher eukaryotes, these finding may also be relevant in mammalian snoRNA maturation and ribosomal biogenesis.