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[[Image:SmY-structure.png|thumb|right|350px|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.<ref name="Jones" />]]
{{Technical (expert)}}
'''SmY ribonucleic acids''' ('''SmY RNAs''') are a type of [[small nuclear RNA]]s found in some [[nematode]] species. They are thought to be involved in mRNA [[trans-splicing]] because they [[copurification|copurify]] with [[spliceosome]]s and with some of the same [[protein]]s that associate with small [[ribonucleoprotein]] particles containing [[SL1 RNA|SL1]] and [[SL2 RNA|SL2]] trans-spliced leader RNAs.<ref name="Maroney96">{{cite journal
'''SmY ribonucleic acids''' ('''SmY RNAs''') are a type of [[small nuclear RNA]]s found in some worms. They are thought to be involved in [[mRNA]] [[trans-splicing]], though there is ongoing debate on this matter.
⚫
| 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><ref name="MacMorris07">{{cite journal
⚫
| 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
⚫
| journal=RNA | volume=13 | issue=4 | pages=511–520 | year=2007 | month=April | pmid=17283210 | pmc=1831854
⚫
| doi=10.1261/rna.426707 | url=}}</ref> However, it is important to note that there is some evidence that [[introns]] in specific sequence elements are not copurified by SmY, so there is ongoing debate about their role in protein association.


SmY RNAs are about 70-90 [[nucleotide]]s long and share a common [[secondary structure]], with two [[stem-loop]]s flanking a consensus [[binding site]] for [[LSm|Sm protein]].<ref name="Maroney96"/><ref name="MacMorris07"/> Sm protein is a shared component of [[spliceosome|spliceosomal]] [[snRNP]]s.
⚫
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 8-32 related [[homology_(biology)#Paralogy|paralogous]] copies, while other nematodes have 1-6.


[[Image:SmY-phylogeny.png|thumb|right|400px|Phylogenetic distribution of known and predicted SmY RNA genes, and the number of genes and [[pseudogene]]s found in each species. Gene numbers are based on computational analysis (using the program Infernal) of [[Genome project#Genome assembly|genome assemblies]]; in some cases these are draft genomes that may be incomplete.<ref name="Jones">{{cite web|url=ftp://selab.janelia.org/pub/publications/Jones09/Jones09-preprint.pdf|title=A Survey of Nematode SmY RNAs|last=Thomas A. Jones |coauthors=Wolfgang Otto; Manja Marz; Sean R. Eddy; Peter F. Stadler|date=2008-11-20|pages=pp. 13|accessdate=2008-12-20}}</ref>]]
[[Image:SmY-phylogeny.png|thumb|right|350px|Phylogenetic distribution of known and predicted SmY RNA genes, and the number of genes and [[pseudogene]]s found in each species. Gene numbers are based on computational analysis (using the program Infernal) of [[Genome project#Genome assembly|genome assemblies]]; in some cases these are draft genomes that may be incomplete.<ref name="Jones">{{cite web|url=ftp://selab.janelia.org/pub/publications/Jones09/Jones09-preprint.pdf|title=A Survey of Nematode SmY RNAs|last=Thomas A. Jones |coauthors=Wolfgang Otto; Manja Marz; Sean R. Eddy; Peter F. Stadler|date=2008-11-20|pages=pp. 13|accessdate=2008-12-20}}</ref>]]
⚫
SmY RNAs have been found in [[nematode]]s 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 8-32 related [[homology_(biology)#Paralogy|paralogous]] copies, while other nematodes have 1-6.


==Discovery==

⚫
The first SmY RNA was discovered in 1996 in purified ''[[Ascaris|Ascaris lumbricoides]]'' spliceosome preparations, as well as a second RNA called SmX that is not detectably [[Homology (biology)|homologous]] to SmY.<ref name="Maroney96" />
==Function==

⚫
The first SmY RNA was discovered in purified ''[[Ascaris|Ascaris lumbricoides]]'' spliceosome preparations, as well as a second RNA called SmX that is not detectably [[Homology (biology)|homologous]] to SmY.<ref name="Maroney96" />
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
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| 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
| doi=10.1101/gr.4139206 | url=}}</ref>
| doi=10.1101/gr.4139206 | url=}}</ref>
SmY RNAs are about 70-90 [[nucleotide]]s long, with a conserved [[Consensus sequence|consensus]] binding site for the [[LSm|Sm protein]], a shared component of spliceosomal [[snRNP]]s.<ref name="Maroney96"/><ref name="MacMorris07"/>
⚫
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 [[Homology (biology)#Homology of sequences in genetics|paralog]] of SL26p).<ref name="MacMorris07"/>
⚫
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 by some to have a function in trans-splicing.


==Structure==
==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="MacMorris07"/><ref name="Maroney96">{{cite journal
SmY RNAs conserve a consensus [[secondary structure]] with two [[stem-loop]]s, flanking a consensus Sm protein [[binding site]].
⚫
| 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><ref name="MacMorris07">{{cite journal
⚫
| 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
⚫
| journal=RNA | volume=13 | issue=4 | pages=511–520 | year=2007 | month=April | pmid=17283210 | pmc=1831854
| doi=10.1261/rna.426707 | url=}}</ref>
⚫
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.
⚫
[[Image:SmY-structure.png|thumb|right|400px|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.<ref name="Jones" />]]
⚫
However, there is some evidence that [[introns]] in specific sequence elements are not copurified by SmY, so there is ongoing debate about their role in protein association.


==References==
==References==
{{reflist|1}}
{{reflist|1}}

{{biology-stub}}


[[Category:Non-coding RNA]]
[[Category:Non-coding RNA]]

Revision as of 18:41, 20 December 2008

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.[1]

SmY ribonucleic acids (SmY RNAs) are a type of small nuclear RNAs found in some worms. They are thought to be involved in mRNA trans-splicing, though there is ongoing debate on this matter.

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 Rhabditid species having 8-32 related paralogous copies, while other nematodes have 1-6.

Discovery

The first SmY RNA was discovered in 1996 in purified Ascaris lumbricoides spliceosome preparations, as well as a second RNA called SmX 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).[3][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. However, there is some evidence that introns in specific sequence elements are not copurified by SmY, so there is ongoing debate about their role in protein association.

References

  1. ^ a b Thomas A. Jones (2008-11-20). "A Survey of Nematode SmY RNAs" (PDF). pp. pp. 13. Retrieved 2008-12-20. {{cite web}}: |pages= has extra text (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)
  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 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)
  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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