Metabolism of non-coding RNA (Homo sapiens)

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2, 11, 143, 151, 4-7, 13161815, 19cytosolnucleoplasmGEMIN6 POM121 NUP155 GEMIN6 NUP35 SNRPE NUP50 NUPL1-2 GEMIN2 SNRPENUP37 GEMIN2 U5 snRNA Nuclear Pore Complex(NPC)GEMIN7 GEMIN4 NUP62 TPR U4 snRNA SNRPFSNRPE SMN1 7-methylguanosine cap POM121C GEMIN7 2xMe-SNRPD1 SNRPG AAAS GEMIN2 NUP93 U5 snRNA GEMIN6 SNRPF GEMIN5 GEMIN7 NUP88 NUP98-5 DDX20 SMN complexSNRPF U4 snRNA 3-methylguanosine cap U4 snRNA NUP54 Cap Binding Complex(CBC)SNRPD1SNRPE SNRPG NDC1 SNRPF SNRPG Spliceosomal m3Gcapped snRNAs withSMN:SM proteincomplex boundSNRPF SMN1 NUP205 2xMe-SNRPB GEMIN7 NUPL2 U4 snRNA DDX20 GEMIN5 NUP214 SMN:SM proteincomplexU6 snRNA U2 snRNA Nup45 U6 snRNA 2xMe-SNRPB 2xMe-SNRPD1 GEMIN5 U5 snRNA U5 snRNA NCBP1 NUP160 7-methylguanosine cap GEMIN6 SNUPNSNRPBNUP85 SNRPE U2 snRNA SNRPD2 GEMIN4 SMN1 SNRPG WDR77 U6 snRNA 2xMe-SNRPD3 SNRPD2 2xMe-SNRPD3 GEMIN2 SEH1L-2 Spliceosomal m3Gcapped snRNA loadedwith the SM complexSMN1 GEMIN6 NUP188 PRMT5 U6 snRNA GEMIN2 NUP153 NUP210 PHAXPHAX RAE1 NCBP2 SNRPD2 GEMIN4 GEMIN6 2xMe-SNRPD1 SMN1 Spliceosomal m7Gcapped snRNAs withSMN:SM proteincomplex boundNUP133 U2 snRNA GEMIN7 SMN1 SNRPG GEMIN5 GEMIN4 U1 snRNA SNRPD2SNRPGDDX20 RANBP2 2xMe-SNRPB GEMIN4 Methylosome2xMe-SNRPB DDX20 U2 snRNA 2xMe-SNRPD1 2xMe-SNRPD1 U1 snRNA SNRPD2 U2 snRNA U4 snRNA GEMIN5 U1 snRNA NCBP2 NUP43 U1 snRNA 3-methylguanosine cap AdoMet2xMe-SNRPD3 NUP98-4 GEMIN7 DDX20 GEMIN2 GEMIN5 2xMe-SNRPD3 2xMe-SNRPB 7-methylguanosine cap NUP98-3 GEMIN4 CLNS1A 2xMe-SNRPD3 SNUPN NUP107 U1 snRNA Spliceosomalm3GcappedsnRNA:SMN:SM:Snurportin complexDDX20 NCBP1 U6 snRNA SNRPF TGS1SMN complexSNRPE 2xMe-SNRPD3m7G cappedsnRNA:CBC:PHAXcomplexSNRPD2 3-methylguanosine cap 3-methylguanosine cap U5 snRNA m7G cappedSpliceosomal snRNA128-10, 17


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. View original pathway at:Reactome.

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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
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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 (CBC)ComplexR-HSA-162460 (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)
MethylosomeComplexR-HSA-191849 (Reactome)
NCBP1 ProteinQ09161 (Uniprot-TrEMBL)
NCBP2 ProteinP52298 (Uniprot-TrEMBL)
NDC1 ProteinQ9BTX1 (Uniprot-TrEMBL)
NUP107 ProteinP57740 (Uniprot-TrEMBL)
NUP133 ProteinQ8WUM0 (Uniprot-TrEMBL)
NUP153 ProteinP49790 (Uniprot-TrEMBL)
NUP155 ProteinO75694 (Uniprot-TrEMBL)
NUP160 ProteinQ12769 (Uniprot-TrEMBL)
NUP188 ProteinQ5SRE5 (Uniprot-TrEMBL)
NUP205 ProteinQ92621 (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)
NUP98-3 ProteinP52948-3 (Uniprot-TrEMBL)
NUP98-4 ProteinP52948-4 (Uniprot-TrEMBL)
NUP98-5 ProteinP52948-5 (Uniprot-TrEMBL)
NUPL1-2 ProteinQ9BVL2-1 (Uniprot-TrEMBL)
NUPL2 ProteinO15504 (Uniprot-TrEMBL)
Nuclear Pore Complex (NPC)ComplexR-HSA-157689 (Reactome)
Nup45 ProteinQ9BVL2-2 (Uniprot-TrEMBL)
PHAX ProteinQ9H814 (Uniprot-TrEMBL)
PHAXProteinQ9H814 (Uniprot-TrEMBL)
POM121 ProteinQ96HA1 (Uniprot-TrEMBL)
POM121C ProteinA8CG34 (Uniprot-TrEMBL)
PRMT5 ProteinO14744 (Uniprot-TrEMBL)
RAE1 ProteinP78406 (Uniprot-TrEMBL)
RANBP2 ProteinP49792 (Uniprot-TrEMBL)
SEH1L-2 ProteinQ96EE3-2 (Uniprot-TrEMBL)
SMN complexComplexR-HSA-191762 (Reactome)
SMN complexComplexR-HSA-191881 (Reactome)
SMN1 ProteinQ16637 (Uniprot-TrEMBL)
SMN:SM protein complexComplexR-HSA-191791 (Reactome)
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
ComplexR-HSA-191778 (Reactome)
Spliceosomal m3G

capped snRNA loaded

with the SM complex
ComplexR-HSA-191870 (Reactome)
Spliceosomal m3G

capped snRNAs with SMN:SM protein

complex bound
ComplexR-HSA-191891 (Reactome)
Spliceosomal m7G

capped snRNAs with SMN:SM protein

complex bound
ComplexR-HSA-191813 (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 snRNAComplexR-HSA-191853 (Reactome)
m7G capped

snRNA:CBC:PHAX

complex
ComplexR-HSA-191887 (Reactome)

Annotated Interactions

View all...
SourceTargetTypeDatabase referenceComment
2xMe-SNRPD3R-HSA-191790 (Reactome)
AdoMetR-HSA-191790 (Reactome)
Cap Binding Complex (CBC)ArrowR-HSA-191825 (Reactome)
Methylosomemim-catalysisR-HSA-191790 (Reactome)
Nuclear Pore Complex (NPC)ArrowR-HSA-191825 (Reactome)
Nuclear Pore Complex (NPC)ArrowR-HSA-191830 (Reactome)
PHAXArrowR-HSA-191825 (Reactome)
R-HSA-191763 (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.
R-HSA-191784 (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).
R-HSA-191786 (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.
R-HSA-191790 (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.
R-HSA-191825 (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.
R-HSA-191830 (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.
SMN complexArrowR-HSA-191830 (Reactome)
SMN complexR-HSA-191790 (Reactome)
SMN:SM protein complexArrowR-HSA-191790 (Reactome)
SMN:SM protein complexR-HSA-191786 (Reactome)
SNRPBR-HSA-191790 (Reactome)
SNRPD1R-HSA-191790 (Reactome)
SNRPD2R-HSA-191790 (Reactome)
SNRPER-HSA-191790 (Reactome)
SNRPFR-HSA-191790 (Reactome)
SNRPGR-HSA-191790 (Reactome)
SNUPNArrowR-HSA-191830 (Reactome)
SNUPNR-HSA-191763 (Reactome)
Spliceosomal

m3G capped

snRNA:SMN:SM:Snurportin complex
ArrowR-HSA-191763 (Reactome)
Spliceosomal

m3G capped

snRNA:SMN:SM:Snurportin complex
R-HSA-191830 (Reactome)
Spliceosomal m3G

capped snRNA loaded

with the SM complex
ArrowR-HSA-191830 (Reactome)
Spliceosomal m3G

capped snRNAs with SMN:SM protein

complex bound
ArrowR-HSA-191784 (Reactome)
Spliceosomal m3G

capped snRNAs with SMN:SM protein

complex bound
R-HSA-191763 (Reactome)
Spliceosomal m7G

capped snRNAs with SMN:SM protein

complex bound
ArrowR-HSA-191786 (Reactome)
Spliceosomal m7G

capped snRNAs with SMN:SM protein

complex bound
R-HSA-191784 (Reactome)
TGS1mim-catalysisR-HSA-191784 (Reactome)
m7G capped Spliceosomal snRNAArrowR-HSA-191825 (Reactome)
m7G capped Spliceosomal snRNAR-HSA-191786 (Reactome)
m7G capped

snRNA:CBC:PHAX

complex
R-HSA-191825 (Reactome)
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