Metabolism of non-coding RNA (Homo sapiens)

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3, 6, 165, 171413, 171, 2, 4, 7, 9...11m3G capped Spliceosomal snRNA m7G capped Spliceosomal snRNA SMN complex snRNP Sm core complex SMNSM protein complex SMNSM protein complex SMN complex nucleoplasmcytosolSpliceosomal m3G capped snRNA loaded with the SM complex SMNSM protein complex m7G capped snRNACBCPHAX complex Nup62 Complex m7G capped Spliceosomal snRNA snRNP Sm core complex SMNSM protein complex SMN complex Nup107 Complex Spliceosomal m7G capped snRNAs with SMNSM protein complex bound snRNP Sm core complex Spliceosome snRNAs Cap Binding Complex m3G capped Spliceosomal snRNA SMN complex Spliceosome snRNAs m3G capped Spliceosomal snRNA Methylosome SMN complex Spliceosome snRNAs snRNP Sm core complex SMN complex Spliceosome snRNAs Spliceosomal m3G capped snRNASMNSMSnurportin complex snRNP Sm core complex Cap Binding Complex Spliceosome snRNAs Nuclear Pore Complex Spliceosomal m3G capped snRNAs with SMNSM protein complex bound SMN1 SMN1 SNRPE SNRPB2xMe-SNRPB SNRPGSMN complexCLNS1A TPR GEMIN6 NUP98-5 NUP62 SNRPF GEMIN7 SEH1L-2 GEMIN4 U2 snRNA 2xMe-SNRPD1 GEMIN7 U2 snRNA SNRPD2 U4 snRNA U5 snRNA U5 snRNA GEMIN4 SNRPD2 GEMIN2 SNUPN SNRPD2 U2 snRNA RANBP2 Nuclear Pore Complex SMN1 2xMe-SNRPB SMNSM protein complexRAE1 GEMIN6 U4 snRNA NUP85 NUP210 Spliceosomal m3G capped snRNASMNSMSnurportin complex3-methylguanosine cap GEMIN2 NUP155 GEMIN2 U4 snRNA 2xMe-SNRPD3 2xMe-SNRPD1 GEMIN4 3-methylguanosine cap SNRPG SNRPD2PRMT5GEMIN6 NUP107 SMN1 2xMe-SNRPD3 SNRPD1SMN1 m7G capped Spliceosomal snRNANUP37 NUP133 DDX20 U1 snRNA U6 snRNA SNRPF NUP35 2xMe-SNRPD3 NUP88 3-methylguanosine cap MethylosomeGEMIN4 DDX20 SNRPFU6 snRNA U1 snRNA 2xMe-SNRPB U5 snRNA 2xMe-SNRPB WDR77 U1 snRNA PHAXGEMIN4 SMN complex2xMe-SNRPD1 SNRPF GEMIN5 U4 snRNA SNRPG SNRPEm7G capped snRNACBCPHAX complexDDX20 GEMIN7 GEMIN7 NCBP2 GEMIN5 DDX20 NUPL2 NCBP1 SNRPF SMN1 PHAXU1 snRNA SNRPF NUP153 SNRPE GEMIN6 NUP93 SNUPN2xMe-SNRPD3 2xMe-SNRPD1 SNRPD2 2xMe-SNRPD1 SNRPD2 Spliceosomal m7G capped snRNAs with SMNSM protein complex boundGEMIN6 Nup45 AdoMetU2 snRNA GEMIN2 NUP188NUP43 SNRPE SNRPG U6 snRNA NCBP1 Spliceosomal m3G capped snRNAs with SMNSM protein complex boundNUPL1-2 U6 snRNA TGS17-methylguanosine cap Spliceosomal m3G capped snRNA loaded with the SM complexU5 snRNA 2xMe-SNRPD3NUP160 GEMIN2 7-methylguanosine cap GEMIN4 NUP54 U6 snRNA GEMIN6 U2 snRNA 7-methylguanosine cap 2xMe-SNRPD3 GEMIN5 SNRPG U5 snRNA NUP205GEMIN7 SNRPE GEMIN5 U1 snRNA POM121 SNRPG GEMIN5 U4 snRNA GEMIN7 NUP50 DDX20 DDX20 SNRPE 3-methylguanosine cap GEMIN5 NCBP2 2xMe-SNRPB Cap Binding Complex AAAS NUP214 GEMIN2 8, 10, 15


Description

The term non-coding is commonly employed for RNA that does not encode a protein, but this does not mean that such RNAs do not contain information nor have function. There is considerable evidence that the majority of mammalian and other complex organism's genomes is transcribed into non-coding RNAs, many of which are alternatively spliced and/or processed into smaller products. Around 98% of all transcriptional output in humans is non-coding RNA. RNA-mediated gene regulation is widespread in higher eukaryotes and complex genetic phenomena like RNA interference are mediated by such RNAs. These non-coding RNAs are a growing list and include rRNAs, tRNAs, snRNAs, snoRNAs siRNAs, 7SL RNA, 7SK RNA, the RNA component of RNase P RNA, the RNA component of RNase MRP, and the RNA component of telomerase. Original Pathway at Reactome: http://www.reactome.org/PathwayBrowser/#DB=gk_current&FOCUS_SPECIES_ID=48887&FOCUS_PATHWAY_ID=194441

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Ontology Terms

 

Bibliography

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  1. Plessel G, Fischer U, Lührmann R.; ''m3G cap hypermethylation of U1 small nuclear ribonucleoprotein (snRNP) in vitro: evidence that the U1 small nuclear RNA-(guanosine-N2)-methyltransferase is a non-snRNP cytoplasmic protein that requires a binding site on the Sm core domain.''; PubMed Europe PMC Scholia
  2. Fontoura BM, Blobel G, Matunis MJ.; ''A conserved biogenesis pathway for nucleoporins: proteolytic processing of a 186-kilodalton precursor generates Nup98 and the novel nucleoporin, Nup96.''; PubMed Europe PMC Scholia
  3. Charroux B, Pellizzoni L, Perkinson RA, Shevchenko A, Mann M, Dreyfuss G.; ''Gemin3: A novel DEAD box protein that interacts with SMN, the spinal muscular atrophy gene product, and is a component of gems.''; PubMed Europe PMC Scholia
  4. Charroux B, Pellizzoni L, Perkinson RA, Yong J, Shevchenko A, Mann M, Dreyfuss G.; ''Gemin4. A novel component of the SMN complex that is found in both gems and nucleoli.''; PubMed Europe PMC Scholia
  5. Friesen WJ, Dreyfuss G.; ''Specific sequences of the Sm and Sm-like (Lsm) proteins mediate their interaction with the spinal muscular atrophy disease gene product (SMN).''; PubMed Europe PMC Scholia
  6. Suntharalingam M, Wente SR.; ''Peering through the pore: nuclear pore complex structure, assembly, and function.''; PubMed Europe PMC Scholia
  7. Brahms H, Meheus L, de Brabandere V, Fischer U, Lührmann R.; ''Symmetrical dimethylation of arginine residues in spliceosomal Sm protein B/B' and the Sm-like protein LSm4, and their interaction with the SMN protein.''; PubMed Europe PMC Scholia
  8. Baccon J, Pellizzoni L, Rappsilber J, Mann M, Dreyfuss G.; ''Identification and characterization of Gemin7, a novel component of the survival of motor neuron complex.''; PubMed Europe PMC Scholia
  9. Bühler D, Raker V, Lührmann R, Fischer U.; ''Essential role for the tudor domain of SMN in spliceosomal U snRNP assembly: implications for spinal muscular atrophy.''; PubMed Europe PMC Scholia
  10. Ori A, Banterle N, Iskar M, Iskar M, Andrés-Pons A, Escher C, Khanh Bui H, Sparks L, Solis-Mezarino V, Rinner O, Bork P, Lemke EA, Beck M.; ''Cell type-specific nuclear pores: a case in point for context-dependent stoichiometry of molecular machines.''; PubMed Europe PMC Scholia
  11. Gubitz AK, Mourelatos Z, Abel L, Rappsilber J, Mann M, Dreyfuss G.; ''Gemin5, a novel WD repeat protein component of the SMN complex that binds Sm proteins.''; PubMed Europe PMC Scholia
  12. Narayanan U, Ospina JK, Frey MR, Hebert MD, Matera AG.; ''SMN, the spinal muscular atrophy protein, forms a pre-import snRNP complex with snurportin1 and importin beta.''; PubMed Europe PMC Scholia
  13. Pellizzoni L, Baccon J, Rappsilber J, Mann M, Dreyfuss G.; ''Purification of native survival of motor neurons complexes and identification of Gemin6 as a novel component.''; PubMed Europe PMC Scholia
  14. Sleeman JE, Lamond AI.; ''Newly assembled snRNPs associate with coiled bodies before speckles, suggesting a nuclear snRNP maturation pathway.''; PubMed Europe PMC Scholia
  15. Meister G, Eggert C, Fischer U.; ''SMN-mediated assembly of RNPs: a complex story.''; PubMed Europe PMC Scholia
  16. Segref A, Mattaj IW, Ohno M.; ''The evolutionarily conserved region of the U snRNA export mediator PHAX is a novel RNA-binding domain that is essential for U snRNA export.''; PubMed Europe PMC Scholia
  17. Carissimi C, Saieva L, Gabanella F, Pellizzoni L.; ''Gemin8 is required for the architecture and function of the survival motor neuron complex.''; PubMed Europe PMC Scholia
  18. Pellizzoni L, Kataoka N, Charroux B, Dreyfuss G.; ''A novel function for SMN, the spinal muscular atrophy disease gene product, in pre-mRNA splicing.''; PubMed Europe PMC Scholia
  19. Rabut G, Doye V, Ellenberg J.; ''Mapping the dynamic organization of the nuclear pore complex inside single living cells.''; PubMed Europe PMC Scholia
  20. Neuenkirchen N, Englbrecht C, Ohmer J, Ziegenhals T, Chari A, Fischer U.; ''Reconstitution of the human U snRNP assembly machinery reveals stepwise Sm protein organization.''; PubMed Europe PMC Scholia
  21. Mouaikel J, Narayanan U, Verheggen C, Matera AG, Bertrand E, Tazi J, Bordonné R.; ''Interaction between the small-nuclear-RNA cap hypermethylase and the spinal muscular atrophy protein, survival of motor neuron.''; PubMed Europe PMC Scholia
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History

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CompareRevisionActionTimeUserComment
101423view11:30, 1 November 2018ReactomeTeamreactome version 66
100961view21:07, 31 October 2018ReactomeTeamreactome version 65
100498view19:41, 31 October 2018ReactomeTeamreactome version 64
100044view16:25, 31 October 2018ReactomeTeamreactome version 63
99596view14:58, 31 October 2018ReactomeTeamreactome version 62 (2nd attempt)
99214view12:43, 31 October 2018ReactomeTeamreactome version 62
94040view13:53, 16 August 2017ReactomeTeamreactome version 61
93664view11:30, 9 August 2017ReactomeTeamreactome version 61
86970view13:51, 15 July 2016MkutmonOntology Term : 'non-coding RNA pathway' added !
86786view09:26, 11 July 2016ReactomeTeamreactome version 56
83121view10:02, 18 November 2015ReactomeTeamVersion54
81460view12:59, 21 August 2015ReactomeTeamVersion53
76932view08:20, 17 July 2014ReactomeTeamFixed remaining interactions
76637view12:01, 16 July 2014ReactomeTeamFixed remaining interactions
75967view10:02, 11 June 2014ReactomeTeamRe-fixing comment source
75670view10:58, 10 June 2014ReactomeTeamReactome 48 Update
75025view13:53, 8 May 2014AnweshaFixing comment source for displaying WikiPathways description
74669view08:44, 30 April 2014ReactomeTeamNew pathway

External references

DataNodes

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NameTypeDatabase referenceComment
2xMe-SNRPB ProteinP14678 (Uniprot-TrEMBL)
2xMe-SNRPD1 ProteinP62314 (Uniprot-TrEMBL)
2xMe-SNRPD3 ProteinP62318 (Uniprot-TrEMBL)
2xMe-SNRPD3ProteinP62318 (Uniprot-TrEMBL)
3-methylguanosine cap MetaboliteCHEBI:1604 (ChEBI)
7-methylguanosine cap MetaboliteCHEBI:17825 (ChEBI)
7-methylguanosine cap MetaboliteCHEBI:2274 (ChEBI)
AAAS ProteinQ9NRG9 (Uniprot-TrEMBL)
AdoMetMetaboliteCHEBI:15414 (ChEBI)
CLNS1A ProteinP54105 (Uniprot-TrEMBL)
Cap Binding Complex ComplexREACT_3506 (Reactome)
DDX20 ProteinQ9UHI6 (Uniprot-TrEMBL)
GEMIN2 ProteinO14893 (Uniprot-TrEMBL)
GEMIN4 ProteinP57678 (Uniprot-TrEMBL)
GEMIN5 ProteinQ8TEQ6 (Uniprot-TrEMBL)
GEMIN6 ProteinQ8WXD5 (Uniprot-TrEMBL)
GEMIN7 ProteinQ9H840 (Uniprot-TrEMBL)
MethylosomeComplexREACT_10865 (Reactome)
NCBP1 ProteinQ09161 (Uniprot-TrEMBL)
NCBP2 ProteinP52298 (Uniprot-TrEMBL)
NUP107 ProteinP57740 (Uniprot-TrEMBL)
NUP133 ProteinQ8WUM0 (Uniprot-TrEMBL)
NUP153 ProteinP49790 (Uniprot-TrEMBL)
NUP155 ProteinO75694 (Uniprot-TrEMBL)
NUP160 ProteinQ12769 (Uniprot-TrEMBL)
NUP188ProteinQ5SRE5 (Uniprot-TrEMBL)
NUP205ProteinQ92621 (Uniprot-TrEMBL)
NUP210 ProteinQ8TEM1 (Uniprot-TrEMBL)
NUP214 ProteinP35658 (Uniprot-TrEMBL)
NUP35 ProteinQ8NFH5 (Uniprot-TrEMBL)
NUP37 ProteinQ8NFH4 (Uniprot-TrEMBL)
NUP43 ProteinQ8NFH3 (Uniprot-TrEMBL)
NUP50 ProteinQ9UKX7 (Uniprot-TrEMBL)
NUP54 ProteinQ7Z3B4 (Uniprot-TrEMBL)
NUP62 ProteinP37198 (Uniprot-TrEMBL)
NUP85 ProteinQ9BW27 (Uniprot-TrEMBL)
NUP88 ProteinQ99567 (Uniprot-TrEMBL)
NUP93 ProteinQ8N1F7 (Uniprot-TrEMBL)
NUP98-5 ProteinP52948-5 (Uniprot-TrEMBL)
NUPL1-2 ProteinQ9BVL2-1 (Uniprot-TrEMBL)
NUPL2 ProteinO15504 (Uniprot-TrEMBL)
Nuclear Pore Complex ComplexREACT_5542 (Reactome)
Nup45 ProteinQ9BVL2-2 (Uniprot-TrEMBL)
PHAXProteinQ9H814 (Uniprot-TrEMBL)
POM121 ProteinQ96HA1 (Uniprot-TrEMBL)
PRMT5ProteinO14744 (Uniprot-TrEMBL)
RAE1 ProteinP78406 (Uniprot-TrEMBL)
RANBP2 ProteinP49792 (Uniprot-TrEMBL)
SEH1L-2 ProteinQ96EE3-2 (Uniprot-TrEMBL)
SMN SM protein complexComplexREACT_10415 (Reactome)
SMN complexComplexREACT_10606 (Reactome)
SMN complexComplexREACT_10714 (Reactome)
SMN1 ProteinQ16637 (Uniprot-TrEMBL)
SNRPBProteinP14678 (Uniprot-TrEMBL)
SNRPD1ProteinP62314 (Uniprot-TrEMBL)
SNRPD2 ProteinP62316 (Uniprot-TrEMBL)
SNRPD2ProteinP62316 (Uniprot-TrEMBL)
SNRPE ProteinP62304 (Uniprot-TrEMBL)
SNRPEProteinP62304 (Uniprot-TrEMBL)
SNRPF ProteinP62306 (Uniprot-TrEMBL)
SNRPFProteinP62306 (Uniprot-TrEMBL)
SNRPG ProteinP62308 (Uniprot-TrEMBL)
SNRPGProteinP62308 (Uniprot-TrEMBL)
SNUPN ProteinO95149 (Uniprot-TrEMBL)
SNUPNProteinO95149 (Uniprot-TrEMBL)
Spliceosomal m3G capped snRNA

SMN SM

Snurportin complex
ComplexREACT_10792 (Reactome)
Spliceosomal m3G capped snRNA loaded with the SM complexComplexREACT_10264 (Reactome)
Spliceosomal m3G capped snRNAs with SMN SM protein complex boundComplexREACT_10845 (Reactome)
Spliceosomal m7G capped snRNAs with SMN SM protein complex boundComplexREACT_10860 (Reactome)
TGS1ProteinQ96RS0 (Uniprot-TrEMBL)
TPR ProteinP12270 (Uniprot-TrEMBL)
U1 snRNA ProteinV00590 (EMBL)
U2 snRNA ProteinX59360 (EMBL)
U4 snRNA ProteinX59361 (EMBL)
U5 snRNA ProteinX04293 (EMBL)
U6 snRNA ProteinX59362 (EMBL)
WDR77 ProteinQ9BQA1 (Uniprot-TrEMBL)
m7G capped Spliceosomal snRNAComplexREACT_10232 (Reactome)
m7G capped snRNA

CBC

PHAX complex
ComplexREACT_10849 (Reactome)

Annotated Interactions

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SourceTargetTypeDatabase referenceComment
2xMe-SNRPD3REACT_10041 (Reactome)
AdoMetREACT_10041 (Reactome)
Cap Binding Complex ArrowREACT_10069 (Reactome)
Methylosomemim-catalysisREACT_10041 (Reactome)
Nuclear Pore Complex ArrowREACT_10010 (Reactome)
Nuclear Pore Complex ArrowREACT_10069 (Reactome)
PHAXArrowREACT_10069 (Reactome)
REACT_10002 (Reactome) The snRNA:SMN:SM protein complex is engaged by a hypermethylase that hypermethylates the snRNA cap from m7G (7-methylguanosine) to m3G (2,2,7-trimethylguanosine).
REACT_10010 (Reactome) A properly assembled Sm core and the m3G cap structure are prerequisites for small nuclear ribonucleoprotein (snRNP) import into the nucleus. Once imported into the nucleus, the snRNPs are initially concentrated in Cajal bodies (CBs), where there is further processing of the snRNAs plus binding of additional proteins, from CRBs they transit to "speckles", from where they are engaged for pre-mRNA splicing. The SMN complexes in the nucleus are found throughout the nucleoplasm but are particularly concentrated in Gems, the "twins" of the snRNP-rich CBs.
REACT_10041 (Reactome) The survival of motor neurons (SMN) complex binds to Sm proteins and small nuclear RNAs (snRNAs) in the cytoplasm. Sm is part the SMN multiprotein complex that contains Gemins 2 – 7, including the DEAD-box RNA helicase Gemin3. The binding of the SMN complex to the snRNAs depends on the presence of specific, high-affinity (nanomolar) binding domains in the snRNAs. The SMN complex binds the Sm proteins through the Sm domains interaction with the Gemins, the TUDOR domain, and through unique arginine- and glycine-rich (RG) domains found in three of these, SmB, SmD1 and SmD3. The association with RG domains is strongly enhanced by the post-translational symmetric dimethylation of specific arginines in these domains, a process that is carried out by the methylosome (JBP1 or PRMT5) complex.
REACT_10069 (Reactome) The snRNAs, except U6 snRNA, are transcribed by RNA polymerase II, co-transcriptionally capped and exported rapidly to the cytoplasm in association with a cap-binding complex and the export factor PHAX.
REACT_9946 (Reactome) The nuclear import signal has two parts; Cap hypermethylation triggers nuclear import via snurportin1 binding and by receptor recognition of the Sm proteins. Snurportin1 (SPN) is an adaptor that links the assembled snRNP to the nuclear transport machinery, recruiting importin beta for nuclear import. The import receptor that recognizes the Sm proteins is not yet known.
REACT_9957 (Reactome) To facilitate snRNP assembly, the SMN complex must bring together the Sm proteins and an Sm-site-containing snRNA. The SMN:Sm protein complex binds to the m7G capped snRNAs in the cytoplasm.
SMN SM protein complexREACT_9957 (Reactome)
SMN complexArrowREACT_10010 (Reactome)
SMN complexREACT_10041 (Reactome)
SNRPBREACT_10041 (Reactome)
SNRPD1REACT_10041 (Reactome)
SNRPD2REACT_10041 (Reactome)
SNRPEREACT_10041 (Reactome)
SNRPFREACT_10041 (Reactome)
SNRPGREACT_10041 (Reactome)
SNUPNArrowREACT_10010 (Reactome)
SNUPNREACT_9946 (Reactome)
Spliceosomal m3G capped snRNA loaded with the SM complexArrowREACT_10010 (Reactome)
Spliceosomal m3G capped snRNAs with SMN SM protein complex boundREACT_9946 (Reactome)
TGS1mim-catalysisREACT_10002 (Reactome)
m7G capped Spliceosomal snRNAArrowREACT_10069 (Reactome)
m7G capped Spliceosomal snRNAREACT_9957 (Reactome)
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