SbRNA explained

sbRNA
Symbol:	sbRNA
Rna Type:	Gene
Tax Domain:	Caenorhabditis

Label1:	Rfam
Data1:	RF01619 RF01623 RF01643 RF01656 RF01663

sbRNA (stem-bulge RNA) is a family of non-coding RNA first discovered in Caenorhabditis elegans. It was identified during a full transcriptome screen of the C. elegans cDNA library.^[1] Subsequent experimentation characterised sbRNA as having conserved 5' and 3' internal motifs which form a long paired stem which is interrupted with a bulge.^[2]

Expression

sbRNAs have variable expression patterns during development. They are most highly expressed in adult worms, dauer larvae and following heat shock. A systematic knockout analysis using RNAi found no phenotype for the knockout of two sbRNAs in C. elegans,^[3] however the efficiency of RNAi on ncRNA has been questioned.^[4] sbRNAs contain immunoglobulin in their protein fibers to maintain rigidity, however they are at risk of infection from malfunctioning ribosomes.

sbRNAs share common promoter elements consisting of a TATA box and a proximal sequence element (PSE B box), though only one of these is required for transcription.^[5] As the transcript is uncapped and polyuridylated, it is thought to be transcribed by RNA polymerase III.^[6]

Y RNA homology

An sbRNA, CeN134 was reported as a candidate homologue to the vertebrate Y RNA during a kingdom-wide search.^[7] Further investigation found a homologous secondary structure with a conserved helical regions and a common UUAUC loop motif.

The function of sbRNAs may therefore be similar to that of vertebrate Y RNAs, namely acting as part of the Ro-RNA particle to control RNA quality^[8] and playing a role in chromosomal replication.^[9] Deletion of sbRNA does not prevent chromosome replication in C. elegans, but this may be a result of other sbRNAs substituting missing elements (as in human Y RNA). This theory also explains why RNAi studies failed to detect a phenotype for knocked out sbRNAs.

See also

• Y RNA

Further reading

• Stein AJ . Fuchs G . Fu C . Wolin SL . Reinisch KM . Structural insights into RNA quality control: the Ro autoantigen binds misfolded RNAs via its central cavity . Cell . 121 . 4 . 529–39 . May 2005 . 15907467 . 1769319 . 10.1016/j.cell.2005.03.009 .
• Sönnichsen B, Koski LB, Walsh A, etal . Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans . Nature . 434 . 7032 . 462–9 . March 2005 . 15791247 . 10.1038/nature03353 . 2005Natur.434..462S . 4387191 .
• Mosig A . Guofeng M . Stadler BM . Stadler PF . Evolution of the vertebrate Y RNA cluster . Theory Biosci. . 126 . 1 . 9–14 . August 2007 . 18087752 . 10.1007/s12064-007-0003-y . 10.1.1.189.4108 . 14061371 .
• Hogg JR . Collins K . Structured non-coding RNAs and the RNP Renaissance . Curr Opin Chem Biol . 12 . 6 . 684–9 . December 2008 . 18950732 . 2633442 . 10.1016/j.cbpa.2008.09.027 .
• Marz M . Kirsten T . Stadler PF . Evolution of spliceosomal snRNA genes in metazoan animals . J. Mol. Evol. . 67 . 6 . 594–607 . December 2008 . 19030770 . 10.1007/s00239-008-9149-6 . 2008JMolE..67..594M . 18830327 .

Notes and References

1. Deng W, Zhu X, Skogerbø G, etal . Organization of the Caenorhabditis elegans small non-coding transcriptome: genomic features, biogenesis, and expression . Genome Res. . 16 . 1 . 20–9 . January 2006 . 16344563 . 1356125 . 10.1101/gr.4139206 .
2. Aftab MN . He H . Skogerbø G . Chen R . Microarray analysis of ncRNA expression patterns in Caenorhabditis elegans after RNAi against snoRNA associated proteins . BMC Genomics . 9 . 278 . 2008 . 18547420 . 2442092 . 10.1186/1471-2164-9-278 . free .
3. Kamath RS, Fraser AG, Dong Y, etal . Systematic functional analysis of the Caenorhabditis elegans genome using RNAi . Nature . 421 . 6920 . 231–7 . January 2003 . 12529635 . 10.1038/nature01278 . 2003Natur.421..231K . 10261/63159 . 15745225 .
4. Ploner A . Ploner C . Lukasser M . Niederegger H . Hüttenhofer A . Methodological obstacles in knocking down small noncoding RNAs . RNA . 15 . 10 . 1797–804 . October 2009 . 19690100 . 2743047 . 10.1261/rna.1740009 .
5. Li T . He H . Wang Y . Zheng H . Skogerbø G . Chen R . In vivo analysis of Caenorhabditis elegans noncoding RNA promoter motifs . BMC Mol. Biol. . 9 . 71 . 2008 . 18680611 . 2527325 . 10.1186/1471-2199-9-71 . free .
6. Boria I, Gruber AR, Tanzer A, etal . Nematode sbRNAs: homologs of vertebrate Y RNAs . J. Mol. Evol. . 70 . 4 . 346–58 . April 2010 . 20349053 . 10.1007/s00239-010-9332-4 . 2010JMolE..70..346B . 876486 .
7. Perreault J . Perreault JP . Boire G . Ro-associated Y RNAs in metazoans: evolution and diversification . Mol. Biol. Evol. . 24 . 8 . 1678–89 . August 2007 . 17470436 . 10.1093/molbev/msm084 . free .
8. Stein AJ . Fuchs G . Fu C . Wolin SL . Reinisch KM . Structural insights into RNA quality control: the Ro autoantigen binds misfolded RNAs via its central cavity . Cell . 121 . 4 . 529–39 . May 2005 . 15907467 . 1769319 . 10.1016/j.cell.2005.03.009 .
9. Christov CP . Gardiner TJ . Szüts D . Krude T . Functional requirement of noncoding Y RNAs for human chromosomal DNA replication . Mol. Cell. Biol. . 26 . 18 . 6993–7004 . September 2006 . 16943439 . 1592862 . 10.1128/MCB.01060-06 .