Abstract
ABSTRACTStem bulge RNAs (sbRNAs) are a family of small non-coding stem-loop RNAs present in Caenorhabditis elegans and other nematodes, the function of which is unknown. Here, we report the first functional characterisation of nematode sbRNAs. We demonstrate that sbRNAs from a range of nematode species are able to reconstitute the initiation of chromosomal DNA replication in the presence of replication proteins in vitro, and that conserved nucleotide sequence motifs are essential for this function. By functionally inactivating sbRNAs with antisense morpholino oligonucleotides, we show that sbRNAs are required for S phase progression, early embryonic development and the viability of C. elegans in vivo. Thus, we demonstrate a new and essential role for sbRNAs during the early development of C. elegans. sbRNAs show limited nucleotide sequence similarity to vertebrate Y RNAs, which are also essential for the initiation of DNA replication. Our results therefore establish that the essential function of small non-coding stem-loop RNAs during DNA replication extends beyond vertebrates.
Highlights
Small non-coding RNAs, which are less than 200 nucleotides in length, are involved in a multitude of cellular processes
Conservation of nucleotide sequence and secondary structure predictions of C. elegans Stem-bulge RNAs (sbRNAs) To investigate the functionality of sbRNAs, we focused on the 19 family members in the model organism C. elegans, including the derived CeY RNA
DISCUSSION sbRNAs were recently identified as a family of small non-coding RNAs in nematodes (Aftab et al, 2008; Boria et al, 2010; Deng et al, 2006)
Summary
Small non-coding RNAs, which are less than 200 nucleotides in length, are involved in a multitude of cellular processes. These non-coding RNAs include small nucleolar (sno)RNAs that modify pre-rRNA, small nuclear (sn)RNAs that are involved in pre-mRNA splicing, micro (mi)RNAs that regulate mRNA translation and stability, and PIWIinteracting (pi)RNAs that mediate epigenetic and post-transcriptional gene silencing (reviewed by Morris and Mattick, 2014). Other non-coding RNAs have emerged, and these have important roles in genome stability. Stem-bulge RNAs (sbRNAs) are a recently identified family of non-coding RNAs found in nematode worms (Aftab et al, 2008; Boria et al, 2010; Deng et al, 2006). There have been expression level studies (Aftab et al, 2008; Boria et al, 2010; Deng et al, 2006), no function has been described for nematode sbRNAs to date
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