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SmY RNA

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Template:Technical (expert) SmY ribonucleic acids (SmY RNAs) are a family of small nuclear RNAs found in some nematode species. They are thought to be involved in mRNA trans-splicing because they copurify with spliceosomes and with some of the same proteins that associate with small ribonucleoprotein particles containing SL1 and SL2 trans-spliced leader RNAs.[1][2]

Function

The first SmY RNA was discovered in purified Ascaris lumbricoides spliceosome preparations, as well as a second RNA called SmX that is not detectably homologous to SmY.[1] Twelve SmY homologs were identified computationally in Caenorhabditis elegans, and ten in Caenorhabditis briggsae.[2] Several transcripts from these SmY genes were cloned and sequenced in a systematic survey of small non-coding RNA transcripts in C. elegans.[3] SmY RNAs are about 70-90 nucleotides long, with a conserved consensus binding site for the Sm protein, a shared component of spliceosomal snRNPs.[1][2] In C. elegans, SmY RNAs copurify in a complex with Sm, SL75p, and SL26p proteins, while the better-characterized C. elegans SL1 trans-splicing snRNA copurifies in a complex with Sm, SL75p and SL21p (a paralog of SL26p).[2] Loss of function of either SL21p or SL26p individually causes only a weak cold-sensitive phenotype, whereas knockdown of both is lethal, as is a SL75p knockdown. Based on these results, the SmY RNAs are believed to have a function in trans-splicing.

Structure

SmY RNAs conserve a consensus secondary structure with two stem-loops, flanking a consensus Sm protein binding site.

Consensus secondary structure of SmY RNAs, deduced by manual comparative analysis. A count of base pair substitutions observed in 68 structurally aligned sequences in the Rfam seed alignment is shown for each base pair, illustrating the extensive support for this predicted structure.

Phylogenetic range

SmY RNAs have been found in nematodes of class Chromadorea, which includes the most commonly studied nematodes (such as Caenorhabditis, Pristionchus, and Ascaris), but not in the more distantly related Trichinella spiralis in class Dorylaimia. The number of SmY genes in each species varies, with most Rhabditid species having 10-30 related paralogous copies, while other nematodes have 1-5.

Phylogenetic distribution of known and predicted SmY RNA genes, and the number of genes and pseudogenes found in each species. Gene numbers are based on computational analysis (using the program Infernal) of genome assemblies; in some cases these are draft genomes that may be incomplete.

References

  1. ^ a b c Maroney PA, Yu YT, Jankowska M, Nilsen TW (1996). "Direct analysis of nematode cis- and trans-spliceosomes: a functional role for U5 snRNA in spliced leader addition trans-splicing and the identification of novel Sm snRNPs". RNA. 2 (8): 735–745. PMC 1369411. PMID 8752084. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  2. ^ a b c d MacMorris M, Kumar M, Lasda E, Larsen A, Kraemer B, Blumenthal T (2007). "A novel family of C. elegans snRNPs contains proteins associated with trans-splicing". RNA. 13 (4): 511–520. doi:10.1261/rna.426707. PMC 1831854. PMID 17283210. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  3. ^ Deng W, Zhu X, Skogerbø G; et al. (2006). "Organization of the Caenorhabditis elegans small non-coding transcriptome: genomic features, biogenesis, and expression". Genome Research. 16 (1): 20–29. doi:10.1101/gr.4139206. PMC 1356125. PMID 16344563. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
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