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Twelve SmY homologs were identified [[Computational biology|computationally]] in ''[[Caenorhabditis elegans]]'', and ten in ''[[Caenorhabditis briggsae]]''.<ref name="MacMorris07" />
Twelve SmY homologs were identified [[Computational biology|computationally]] in ''[[Caenorhabditis elegans]]'', and ten in ''[[Caenorhabditis briggsae]]''.<ref name="MacMorris07" />
Several [[RNA|transcripts]] from these SmY [[gene]]s were [[Molecular cloning|cloned]] and [[Sequencing|sequenced]] in a systematic survey of small [[non-coding RNA]] transcripts in ''C. elegans''.<ref name="Deng06">{{cite journal
Several [[RNA|transcripts]] from these SmY [[gene]]s were [[Molecular cloning|cloned]] and [[Sequencing|sequenced]] in a systematic survey of small [[non-coding RNA]] transcripts in ''C. elegans''.<ref name="Deng06">{{cite journal
| author=Deng W, Zhu X, Skogerbø G, ''et al''
| author=Deng W, Zhu X, Skogerbø G, ''et al.''
| title=Organization of the Caenorhabditis elegans small non-coding transcriptome: genomic features, biogenesis, and expression
| title=Organization of the Caenorhabditis elegans small non-coding transcriptome: genomic features, biogenesis, and expression
| journal=Genome Research | volume=16 | issue=1 | pages=20–29 | year=2006 | month=January | pmid=16344563 | pmc=1356125
| journal=Genome Research | volume=16 | issue=1 | pages=20–29 | year=2006 | month=January | pmid=16344563 | pmc=1356125
Line 17: Line 17:


==Function==
==Function==
⚫
In ''[[C. elegans]]'', SmY RNAs [[copurification|copurify]] with [[spliceosome]] and with Sm, [[SL75p]], and [[SL26p]] proteins, while the better-characterized ''C. elegans'' [[SL1 RNA|SL1]] trans-splicing snRNA copurifies in a complex with Sm, SL75p, and SL21p (a [[Homology (biology)#Homology of sequences in genetics|paralog]] of SL26p).<ref name="Maroney96">{{cite journal

⚫
| author=Maroney PA, Yu YT, Jankowska M, Nilsen TW
⚫
In ''[[C. elegans]]'', SmY RNAs [[copurification|copurify]] with [[spliceosome]] and with Sm, [[SL75p]], and [[SL26p]] proteins, while the better-characterized ''C. elegans'' [[SL1 RNA|SL1]] trans-splicing snRNA copurifies in a complex with Sm, SL75p, and SL21p (a [[Homology (biology)#Homology of sequences in genetics|paralog]] of SL26p).<ref name="MacMorris07">{{cite journal
⚫
| title=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
⚫
| journal=RNA | volume=2 | issue=8 | pages=735–745 | year=1996 | month=August | pmid=8752084 | pmc=1369411 | doi=
⚫
| url=http://www.rnajournal.org/cgi/pmidlookup?view=long&pmid=8752084}}</ref><ref name="MacMorris07">{{cite journal
| author=MacMorris M, Kumar M, Lasda E, Larsen A, Kraemer B, Blumenthal T
| author=MacMorris M, Kumar M, Lasda E, Larsen A, Kraemer B, Blumenthal T
| title=A novel family of C. elegans snRNPs contains proteins associated with trans-splicing
| title=A novel family of C. elegans snRNPs contains proteins associated with trans-splicing
| journal=RNA | volume=13 | issue=4 | pages=511–520 | year=2007 | month=April | pmid=17283210 | pmc=1831854
| journal=RNA | volume=13 | issue=4 | pages=511–520 | year=2007 | month=April | pmid=17283210 | pmc=1831854
| doi=10.1261/rna.426707 | url=}}</ref><ref name="Maroney96">{{cite journal
| doi=10.1261/rna.426707 | url=}}</ref>
⚫
| author=Maroney PA, Yu YT, Jankowska M, Nilsen TW
⚫
| title=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
⚫
| journal=RNA | volume=2 | issue=8 | pages=735–745 | year=1996 | month=August | pmid=8752084 | pmc=1369411 | doi=
⚫
| url=http://www.rnajournal.org/cgi/pmidlookup?view=long&pmid=8752084}}</ref>
Loss of function of either SL21p or SL26p individually causes only a weak cold-sensitive [[phenotype]], whereas
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.
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.

Revision as of 12:53, 14 May 2009

Consensus secondary structure of SmY RNAs, deduced by manual comparative analysis.[clarification needed] 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.[1]

SmY ribonucleic acids (SmY RNAs) are a family of small nuclear RNAs found in some species of nematode worms. They are thought to be involved in mRNA trans-splicing.

SmY RNAs are about 70-90 nucleotides long and share a common secondary structure, with two stem-loops flanking a consensus binding site for Sm protein.[2][3] Sm protein is a shared component of spliceosomal snRNPs.

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.[1]

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 Caenorhabditis and Pristionchus species having 10-26 related paralogous copies, while other nematodes have 1-5.[1]

Discovery

The first SmY RNA was discovered in 1996 in purified Ascaris lumbricoides spliceosome preparations, as was another called SmX RNA that is not detectably homologous to SmY.[2] Twelve SmY homologs were identified computationally in Caenorhabditis elegans, and ten in Caenorhabditis briggsae.[3] Several transcripts from these SmY genes were cloned and sequenced in a systematic survey of small non-coding RNA transcripts in C. elegans.[4]

Function

In C. elegans, SmY RNAs copurify with spliceosome and 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][3] 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.

References

  1. ^ a b c Jones TA, Otto W, Marz M, Eddy SR, Stadler PF (2009). "A survey of nematode SmY RNAs". RNA Biol. 6 (1): 5–8. PMID 19106623.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  2. ^ 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)
  3. ^ a b c 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)
  4. ^ 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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