SmY RNA: Difference between revisions
Content deleted Content added
Mindmatrix (talk | contribs) link Non-coding RNA, Consensus sequence, Sequencing and protein |
Citation bot (talk | contribs) Add: doi-access. | Use this bot. Report bugs. | Suggested by Abductive | Category:Small nuclear RNA | #UCB_Category 237/300 |
||
| (47 intermediate revisions by 32 users not shown) | |||
| Line 1: | Line 1: | ||
{{Infobox rfam |
|||
{{Cleanup-jargon|date=December 2008}} |
|||
| Name = SmY spliceosomal RNA |
|||
'''SmY ribonucleic acids''' ('''SmY RNAs''') are a family 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 |
|||
| image =SmY-structure.png |
|||
| author=Maroney PA, Yu YT, Jankowska M, Nilsen TW |
|||
| width = 290 |
|||
| 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 |
|||
| caption = Consensus [[secondary structure]] of SmY RNAs. 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="Jones09" /> |
|||
| journal=RNA | volume=2 | issue=8 | pages=735–745 | year=1996 | month=August | pmid=8752084 | pmc=1369411 | doi= |
|||
| Symbol = SmY |
|||
| url=http://www.rnajournal.org/cgi/pmidlookup?view=long&pmid=8752084}}</ref><ref name="MacMorris07">{{cite journal |
|||
| AltSymbols = |
|||
| author=MacMorris M, Kumar M, Lasda E, Larsen A, Kraemer B, Blumenthal T |
|||
| Rfam = RF01844 |
|||
| title=A novel family of C. elegans snRNPs contains proteins associated with trans-splicing |
|||
| miRBase = |
|||
| journal=RNA | volume=13 | issue=4 | pages=511–520 | year=2007 | month=April | pmid=17283210 | pmc=1831854 |
|||
| miRBase_family = |
|||
| doi=10.1261/rna.426707 | url=}}</ref> |
|||
| RNA_type = snRNA, splicing |
|||
| Tax_domain =[[Chromadorea]] |
|||
| GO = |
|||
| SO = |
|||
| CAS_number = |
|||
| EntrezGene = |
|||
| HGNCid = |
|||
| OMIM = |
|||
| PDB = |
|||
| RefSeq = |
|||
| Chromosome = |
|||
| Arm = |
|||
| Band = |
|||
| LocusSupplementaryData = |
|||
}} |
|||
'''SmY ribonucleic acids''' ('''SmY RNAs''') are a family of [[small nuclear RNA]]s found in some species of [[nematode]] worms. They are thought to be involved in [[mRNA]] [[trans-splicing]]. |
|||
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. |
|||
[[File:SmY-phylogeny.png|thumb|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="Jones09" />]] |
|||
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 [[homology (biology)#Paralogy|paralogous]] copies, while other nematodes have 1–5.<ref name="Jones09" /> |
|||
==Discovery== |
|||
The first SmY RNA was discovered in 1996 in purified ''[[Ascaris|Ascaris lumbricoides]]'' [[spliceosome]] preparations, as was another called [[SmX RNA]]<!--same as from [[SMX]]/[[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" /> 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" /> |
|||
A systematic survey of [[2,2,7-trimethylguanosine (TMG)]] [[5′ cap]]ped transcripts in ''C.elegans'' using anti TMG [[antibodies]] identified two TMG capped SmY transcripts.<ref name="Jia07" /> Sequence analysis of the potential Sm binding sites in these transcripts indicated the SmY, [[U5 spliceosomal RNA|U5 snRNA]], [[Small nucleolar RNA U3|U3 snoRNA]] and the [[Trans-splicing|spliced leader]] RNAs transcripts ([[SL1 RNA|SL1]] and [[SL2 RNA|SL2]]) all contain a very similar consensus SM binding sequence (AAU<sub>4</sub>–<sub>5</sub>GGA). The predicted SM binding sites identified in the [[U1 spliceosomal RNA|U1]], [[U2 spliceosomal RNA|U2]] and [[U4 spliceosomal RNA|U4]] snRNA transcripts varied from this consensus.<ref name="Jia07" /> |
|||
==Function== |
==Function== |
||
In ''[[Caenorhabditis elegans|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" /><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 to have a function in trans-splicing. |
|||
==References== |
|||
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" /> |
|||
{{reflist|refs= |
|||
Twelve SmY homologs were identified 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 |
|||
| author=Deng W, Zhu X, Skogerbø G, ''et al'' |
|||
| 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 |
|||
| doi=10.1101/gr.4139206 | url=}}</ref> |
|||
SmY RNAs are about 70-90 nucleotides 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 to have a function in trans-splicing. |
|||
<ref name="Deng06">{{cite journal |
|||
==Structure== |
|||
| vauthors=Deng W, Zhu X, Skogerbø G, etal |
|||
| 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 |date=January 2006 |
|||
| pmid=16344563 | pmc=1356125 | doi=10.1101/gr.4139206 |
|||
}}</ref> |
|||
<ref name="Jia07">{{Cite journal |
|||
SmY RNAs conserve a consensus secondary structure with two stem-loops, flanking a consensus Sm protein binding site. |
|||
| vauthors = Jia D, Cai L, He H, Skogerbø G, Li T, Aftab N, Chen R |
|||
| title = Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap structures in ''Caenorhabditis elegans'' |
|||
| url= | journal = BMC Molecular Biology | volume = 8 | pages = 86 | date = September 2007 |
|||
| pmid = 17903271 | pmc = 2200864 | doi = 10.1186/1471-2199-8-86 |
|||
| doi-access = free |
|||
}}</ref> |
|||
<ref name="Jones09">{{cite journal |
|||
[[Image:SmY-structure.png|thumb|center|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.]] |
|||
| vauthors=Jones TA, Otto W, Marz M, Eddy SR, Stadler PF |
|||
| title=A survey of nematode SmY RNAs |
|||
| journal=RNA Biol |volume=6 |issue=1 |pages=5–8 |year=2009 |
|||
| pmid=19106623 |doi= 10.4161/rna.6.1.7634 |doi-access=free |
|||
| url=http://www.landesbioscience.com/journals/rna/abstract.php?id=7634 |
|||
}}</ref> |
|||
<ref name="MacMorris07">{{cite journal |
|||
==Phylogenetic range== |
|||
| vauthors=MacMorris M, Kumar M, Lasda E, Larsen A, Kraemer B, Blumenthal T |
|||
{{Refimprovesect|date=December 2008}} |
|||
| title=A novel family of ''C. elegans'' snRNPs contains proteins associated with trans-splicing |
|||
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. |
|||
| journal=RNA | volume=13 | issue=4 | pages=511–520 |date=April 2007 |
|||
| pmid=17283210 | pmc=1831854 | doi=10.1261/rna.426707 |
|||
}}</ref> |
|||
<ref name="Maroney96">{{cite journal |
|||
[[Image:SmY-phylogeny.png|thumb|center|400px|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.]] |
|||
| vauthors=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 |date=August 1996 |
|||
| pmid=8752084 | pmc=1369411 | doi= |
|||
| url=http://www.rnajournal.org/cgi/pmidlookup?view=long&pmid=8752084 |
|||
}}</ref> |
|||
}} |
|||
==References== |
|||
{{reflist|1}} |
|||
==External links== |
|||
* {{Rfam|id=RF01844|name=SmY spliceosomal RNA}} |
|||
[[Category:Non-coding RNA]] |
[[Category:Non-coding RNA]] |
||
[[Category:Small nuclear RNA]] |
|||
[[Category:RNA splicing]] |
|||
[[Category:Nematode nucleic acids]] |
|||
Latest revision as of 03:37, 25 November 2023
| SmY spliceosomal RNA | |
|---|---|
 Consensus secondary structure of SmY RNAs. 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] | |
| Identifiers | |
| Symbol | SmY |
| Rfam | RF01844 |
| Other data | |
| RNA type | snRNA, splicing |
| Domain(s) | Chromadorea |
| PDB structures | PDBe |
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.
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
[edit]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]
A systematic survey of 2,2,7-trimethylguanosine (TMG) 5′ capped transcripts in C.elegans using anti TMG antibodies identified two TMG capped SmY transcripts.[5] Sequence analysis of the potential Sm binding sites in these transcripts indicated the SmY, U5 snRNA, U3 snoRNA and the spliced leader RNAs transcripts (SL1 and SL2) all contain a very similar consensus SM binding sequence (AAU4–5GGA). The predicted SM binding sites identified in the U1, U2 and U4 snRNA transcripts varied from this consensus.[5]
Function
[edit]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
[edit]- ^ 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. doi:10.4161/rna.6.1.7634. PMID 19106623.
- ^ a b c Maroney PA, Yu YT, Jankowska M, Nilsen TW (August 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.
- ^ a b c MacMorris M, Kumar M, Lasda E, Larsen A, Kraemer B, Blumenthal T (April 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.
- ^ Deng W, Zhu X, Skogerbø G, et al. (January 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.
- ^ a b Jia D, Cai L, He H, Skogerbø G, Li T, Aftab N, Chen R (September 2007). "Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap structures in Caenorhabditis elegans". BMC Molecular Biology. 8: 86. doi:10.1186/1471-2199-8-86. PMC 2200864. PMID 17903271.