Eight novel small RNAs, designated CeR-3, CeR-4, CeR-5, CeR-6, CeR-7, CeR-8, CeR-9 and CeR-19 RNA, were isolated from C. elegans . They are encoded in the regions corresponding to the introns of protein-coding genes. These RNA genes also exist in the C. briggsae genome. The position of each RNA gene in C. briggsae genome is nearly identical to that of C. elegans except for the case of CeR-5 RNA gene. The corresponding sequence of CeR-5, located in the fourth intron of the Y38F2AR.12 gene, was found in the anti-sense strand of the fifth intron of the homologous protein gene of C. briggsae . CeR-3, 4, 6, 7, 8 and 9 showed typical H/ACA snoRNA secondary structures and CeR-19 showed a C/D snoRNA structure. CeR-3, 4, 6 and 8 RNAs, are encoded in the regions corresponding to the introns of the ribosomal protein genes. The CeR-4 RNA sequence is also found in the second intron of the ribosomal protein S23 gene. A sequence identical to that of CeR-6 RNA locates in the first intron of
rps-29 ; the second intron of
rps-29 also has sequence homologous to CeR-6 RNA. The CeR-7 sequence is present in the gene encoding Nop56p, a protein component of box C/D snoRNP. CeR-9 and CeR-19 RNA genes are located in the introns of the W08G11.3 and D1054.3 genes, which are similar to the genes encoding S. cerevisiae Mlp2p and O. sativa SGT1, respectively. At present, the products of these two genes are not known to be related to the RNA-mediated phenomena, in contrast to the products of the host genes of the CeR-3, 4, 6, 7 and 8 RNA genes, which are known to function in the translation- or translation-related machineries. Since many snoRNAs in other organisms function in the modification of rRNAs and U snRNAs by forming base pairs with the target sites, we searched for the sequences of C. elegans rRNAs and U snRNAs which make base pairs with CeR-3, 4, 6, 7, 8, 9 and 19 RNAs, respectively. Twelve potential base pairing interactions were found, predicting ten probable pseudouridylation sites and two methylation sites in C. elegans rRNAs. Target sequences of CeR-3, 4 and 8 RNAs could not be found. These novel C. elegans snoRNAs may have functions other than modification of rRNAs and U snRNAs.