Yusuke Hokii et al. (2006) East Asia C. elegans Meeting "Spatio temporal distribution patterns of C.elegans small ncRNAs"

Yusuke Hokii, Yuko Endo, Yuko Mizuki, Chisato Ushida, Yuki Sugawara, Fumitoshi Harada, Hyouta Himeno, Takayuki Konno, Akira Muto

[East Asia C. elegans Meeting, 2006]

CeR 3, 4, 6, 7, 8, 9, 19 RNAs that were encoded in the regions corresponding to the introns of protein coding genes were isolated from Caenorhabditis elegans. These seven RNAs showed typical snoRNA secondary structures. CeR 19 RNA is included in C/D snoRNA and the other RNAs were classified in H/ACA snoRNAs. Four of the seven isolated snoRNAs (CeR 6, 7, 9, 19) could form base pairings with parts of rRNAs, suggesting that they have a potential to guide pseudouridylation and methylation of rRNAs. CeR 6 RNA may guide modification of U1254 of 18S rRNA. The predicted targets of CeR 7 RNAs are U778 and U827 of 18S rRNA, U866, U1058, U2400 and U2546 of 26S rRNA and U89 of 5.8S rRNA. CeR 9 RNA guides probably pseudouridylation of U513 of 18S rRNA. CeR 19 RNA has two base paring sites that ribose 2 O methylation of U308 of 26S rRNA and C642 of 18S rRNA. In the recent study of Schmitz et al. the targets of CeR 3, 4 and 8 RNA were predicted. These RNAs perhaps guide modification U3035 (CeR 3), U2558 (CeR 4), U2098 and U3035 (CeR 8) of rRNAs, respectively. Here we examined whole mount in situ hybridization to know the localization of these RNAs in cells and their spatiotemporal distribution patterns in worms. As expected, all these RNAs are localized in the nucleolus of most cells of the worm. Their expressions were observed from early embryonic stage to adult. Chemical modification experiments of rRNAs indicated that a predicted target of CeR 9 RNA, U513 of 18S rRNA, was pseudouridine. Further analysis will reveal the whole positions of C.elegans rRNA pseudouridine and demonstrate whether the potential target sites of CeR RNAs are indeed modified or not.

Yusuke Hokii et al. (2010) East Asia Worm Meeting "A small nucleolar RNA functions in rRNA processing in C. elegans."

Shigenori Oka, Kazumi Sakata, Toshinobu Fujiwara, Yumi Sasano, Akira Muto, Hyouta Himeno, Mayu Sato, Hiroshi Sakamoto, Akito Taneda, Ryuzo Shingai, Yusuke Hokii, Chisato Ushida

[East Asia Worm Meeting, 2010]

CeR-2 RNA, which is also known as CeN21 or Ce9 RNA, is one of the C. elegans non-protein-coding RNAs (ncRNAs) of unknown function. The characterization of this RNA by RNomic studies has failed to classify it into any known ncRNA family. Here, we examined the spatiotemporal expression patterns and found that this is expressed in most cells from the early embryo to adult stages. The subcellular localization is analogous to that of fibrillarin, a major nucleolar protein. Knockdown of nop56, a component of C/D small nucleolar ribonucleoproteins, but not of H/ACA snoRNP proteins, resulted in the aberrant nucleolar localization of CeR-2 RNA. A mutant worm with a reduced amount of cellular CeR-2 RNA showed changes in its pre-rRNA processing pattern compared with that of the wild-type strain N2. These results suggest that CeR-2 RNA is a C/D snoRNA involved in the processing of rRNAs.