mRNA processing (Caenorhabditis elegans)

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U6 snRNPmRNA splice site selectionPoly(A) polymerase alphaU2AFexon 1iPo3U5hnRNP regulatorsFormation of the active Spliceosomal C complexSR-proteinsRNA helicaseU2 snRNP65snRNP Sm core complexSR protein kinasessnRNP Sm core complex5U2AGsplicing factor SF3APiU2AF5AGAexon 2Additional SR proteinsInternal methylation of mRNAYYYYmRNA cappingsplicing factor SF3B5Formation of the Spliceosomal E complexAGAlternative SplicingUGexon 1mRNA Cappingheterogeneous nuclear ribonucleoproteins3Formation of pre-mRNPsU1 snRNPSerine/Argenine Rich Proteins(SR)CF IIYYYYintronFormation of the Spliceosomal C complexA33P-3U15YYYYU2 snRNPsProcessing of Intron-Containing Pre-mRNAexon 2YYYYdegraded5Polr2aAGCFIFormation of pre-mRNPs5AMethylation of mRNAPoly(A)pb IIU6exon 1U4 snRNPmRNA splicing (major pathway)AGRnmt (methyltransferase)GUSpt5U2 snRNPCstFexon 1Primary RNA transcript3UGSR-proteinsFormation of the Spliceosomal A complexInternal methylation of mRNASR-binding sitesU5 snRNPFormation of the Spliceosomal A complexU4U4:U5:U6 tri-snRNP complex5AFormation of the Spliceosomal B complexU4/U65snRNP Sm core complexCF IAdditional FactorsCF II5 G capFormation of the Spliceosomal E complexexon 23U5SR-binding sites5GMPhnRNPs35exon 2pre-mRNAAdditional FactorsPoly(A)-binding protein IIYYYYRegulation ofPutative Alternative SplicingRNAi pathwayAAAAAAA3APoly(A) pol5exon 2exon 2Cap Binding3AGU1 snRNPSF3b14b3Formation of the Spliceosomal B complexARegulatorsexon 1Note: New participating members shown at each stepexon 1YYYYAccessory ProteinsRNA helicase AY67H2A.1nxf-1lsm-7rnp-3CUGBP2SFRS3rha-1sap-1F58B3.7prp-17C44B7.2HNRPKSSFA1F11A10.2SSFA1T08A11.2uaf-1gut-2C25A1.4prp-8prp-17SFRS5HNRPCsnr-5CLK3NSEP1SNRPBmog-1rnp-2F08G12.2M03C11.7RNU2HNRPH2rsp-2tag-172rsp-3gut-2prp-21F28C1.1CLK4PCBP2hrp-2cpf-2F47G9.1etr-1NCBP2CLK1Rnu6F59A2.4prp-8SF4tag-203him-1snr-3HRMT1L1snr-6F37E3.1dcr-1HNRPA1dnj-30FNBP3rsp-7mog-4teg-1HNRPABSF3B4phf-5mog-5Y48B6A.3rsr-1C27H5.3Y73B6BL.33suf-1FUSIP1unc-75U4 snRNASFRS14SNRPNHNRPA3P1Y59A8B.6F43G6.5Y76B12C.7F11A10.8W03F9.10eft-1tag-72SFRS9prp-4ptb-1cpf-1ama-1DDX20NONObath-43F56D2.6U5 snRNAPTBP2RBMXC36B1.5snr-7F43G9.5HNRPDSNRPNY113G7B.17rsp-4F09G2.4rsp-6T08B2.5TXNL4AU1 snRNApab-3METTL3SFRS10CSTF2cel-1spt-5Y55F3AM.3T13H5.4C36B1.5rnp-7snr-1HNRPA2B1snr-4Y55F3BR.1SF3B5rsp-1


Description

This process describes the conversion of precursor messenger RNA into mature messenger RNA (mRNA). The pre-mRNA molecule undergoes three main modifications. These modifications are 5' capping, 3' polyadenylation, and RNA splicing, which occur in the cell nucleus before the RNA is translated.

5' Capping: Capping of the pre-mRNA involves the addition of 7-methylguanosine (m7G) to the 5' end. The cap protects the 5' end of the primary RNA transcript from attack by ribonucleases that have specificity to the 3'5' phosphodiester bonds.

3' Processing: The pre-mRNA processing at the 3' end of the RNA molecule involves cleavage of its 3' end and then the addition of about 200 adenine residues to form a poly(A) tail. As the poly(A) tails is synthesised, it binds multiple copies of poly(A) binding protein, which protects the 3'end from ribonuclease digestion.

Splicing: RNA splicing is the process by which introns, regions of RNA that do not code for protein, are removed from the pre-mRNA and the remaining exons connected to re-form a single continuous molecule.

Description adapted from Wikipedia: http://en.wikipedia.org/wiki/Post-transcriptional_modification

Comments

GenMAPP notes 
Gene lists from obtained from InterPro 9-23-2003: Mm_RNA-binding region RNP-1 (RNA recognition motif)
GenMAPP remarks 
Adapted from http://www.reactome.org.

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Bibliography

  1. Zahler, A. M.; ''Pre-mRNA splicing and its regulation in Caenorhabditis elegans''; WormBook, ed. The C. elegans Research Community, WormBook, doi/10.1895/wormbook.1.31.2, 2012 DOI Scholia

History

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CompareRevisionActionTimeUserComment
125266view13:03, 31 January 2023LarsgwAdd DOI to publication
122783view23:27, 17 May 2022AlexanderPicocleaning up broken comments
118541view11:23, 28 May 2021DeSlAdded lit. ref.
118426view14:25, 27 May 2021Fehrhartconverted graphical lines
118419view14:20, 27 May 2021Fehrhartconverted graphical lines
71848view20:09, 18 October 2013MaintBotremoved data source from nodes without identifier
69960view20:58, 11 July 2013MaintBotupdating to 2013 schema
67495view11:09, 26 June 2013DdiglesOntology Term : 'spliceosome pathway' added !
40645view19:58, 1 March 2011MaintBotRemoved redundant pathway information and comments
35240view19:45, 11 February 2010KhanspersModified description
20941view11:30, 14 November 2008MaintBot[[Pathway:Caenorhabditis elegans:mRNA processing Reactome]] moved to [[Pathway:WP123]]: Moved to stable identifier
8507view14:01, 7 January 2008MaintBotAdded to category $category
8505view14:01, 7 January 2008NsalomonisUploaded new pathway

External references

DataNodes

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NameTypeDatabase referenceComment
C25A1.4GeneProduct172881 (Entrez Gene)
C27H5.3GeneProduct174175 (Entrez Gene)
C36B1.5GeneProduct183250 (Entrez Gene)
C44B7.2GeneProduct3565706 (Entrez Gene)
CLK1GeneProductPMID: 15010457: Inhibitor John C. Bell, PhD

Professor, Depts. of Medicine and Biochemistry, Microbiology & Immunology University of Ottawa Career Scientist, Ottawa Regional Cancer Centre Associate Scientist, The Ottawa Hospital Research Institute Telephone: 613-737-7700 ext 6893 Fax: 613-247-3524 Email: [email protected] The control of pre-mRNA splicing by the Clk kinase family

We are studying a family of kinases which we believe provide an interface between intracellular signaling networks and the post-transcriptional mechanism of mRNA splicing. We are performing a structure:function analysis of the three Clk family members to identify domains in the three proteins which are involved in regulating splicing. Using homologous recombination we are generating null strains of mice which are lacking one, two or all three Clk genes. The Clk kinases all possess dual specificity kinase activity and yeast expression systems are being used to produce large amounts of the kinase to perform a detailed analysis of the sites of serine, threonine and tyrosine autophosphorylation within the kinase.
CLK3GeneProduct
CLK4GeneProduct
CSTF2GeneProduct
CUGBP2GeneProduct
DDX20GeneProduct
F08G12.2GeneProduct181319 (Entrez Gene)
F09G2.4GeneProduct179103 (Entrez Gene)
F11A10.2GeneProduct178147 (Entrez Gene)
F11A10.8GeneProduct178151 (Entrez Gene)
F28C1.1GeneProduct179705 (Entrez Gene)
F37E3.1GeneProduct172345 (Entrez Gene)
F43G6.5GeneProduct174816 (Entrez Gene)
F43G9.5GeneProduct172657 (Entrez Gene)
F47G9.1GeneProduct179567 (Entrez Gene)
F56D2.6GeneProduct175771 (Entrez Gene)
F58B3.7GeneProduct178091 (Entrez Gene)
F59A2.4GeneProduct175442 (Entrez Gene)
FNBP3GeneProduct
FUSIP1GeneProduct
HNRPA1GeneProduct
HNRPA2B1GeneProduct
HNRPA3P1GeneProduct
HNRPABGeneProduct
HNRPCGeneProduct
HNRPDGeneProduct
HNRPH2GeneProduct
HNRPKGeneProduct
HRMT1L1GeneProduct
M03C11.7GeneProduct176461 (Entrez Gene)
METTL3GeneProduct
NCBP2GeneProduct
NONOGeneProduct
NSEP1GeneProduct
PCBP2GeneProduct
PTBP2GeneProduct
RBMXGeneProduct
RNU2GeneProductGenBank sequence: K00027
Rnu6GeneProductGenBank sequence: M10329
SF3B4GeneProduct
SF3B5GeneProduct
SF4GeneProductinferred from: SURP 2, G patch protein, UniProt:O60378
SFRS10GeneProduct
SFRS14GeneProduct
SFRS3GeneProduct
SFRS5GeneProduct
SFRS9GeneProductPMID: 12738786, PMID: 12024014 (associated with hnRNP A1 splicing)
SNRPBGeneProduct
SNRPNGeneProduct
SSFA1GeneProduct
T08A11.2GeneProduct175549 (Entrez Gene)
T08B2.5GeneProduct172312 (Entrez Gene)
T13H5.4GeneProduct174364 (Entrez Gene)
TXNL4AGeneProduct
U1 snRNAGeneProductGenBank sequence: J00645
U4 snRNAGeneProductGenBank sequence: M10328, M18004
U5 snRNAGeneProductGenBank sequence: AB021173
W03F9.10GeneProduct178542 (Entrez Gene)
Y113G7B.17GeneProduct180326 (Entrez Gene)
Y48B6A.3GeneProduct175071 (Entrez Gene)
Y55F3AM.3GeneProduct176922 (Entrez Gene)
Y55F3BR.1GeneProduct176913 (Entrez Gene)
Y59A8B.6GeneProduct180180 (Entrez Gene)
Y67H2A.1GeneProduct178285 (Entrez Gene)
Y73B6BL.33GeneProduct177398 (Entrez Gene)
Y76B12C.7GeneProduct177003 (Entrez Gene)
ama-1GeneProduct177190 (Entrez Gene)
bath-43GeneProduct176422 (Entrez Gene)
cel-1GeneProduct172814 (Entrez Gene)
cpf-1GeneProduct174378 (Entrez Gene)
cpf-2GeneProduct176742 (Entrez Gene)
dcr-1GeneProduct176138 (Entrez Gene)
dnj-30GeneProduct171833 (Entrez Gene)
eft-1GeneProduct175851 (Entrez Gene)
etr-1GeneProduct173401 (Entrez Gene)
gut-2GeneProduct179833 (Entrez Gene)
him-1GeneProduct172116 (Entrez Gene)
hrp-2GeneProduct173086 (Entrez Gene)
lsm-7GeneProduct177988 (Entrez Gene)
mog-1GeneProduct176409 (Entrez Gene)
mog-4GeneProduct175117 (Entrez Gene)
mog-5GeneProduct173920 (Entrez Gene)
nxf-1GeneProduct191736 (Entrez Gene)
pab-3GeneProduct172768 (Entrez Gene)
phf-5GeneProduct3564851 (Entrez Gene)
prp-17GeneProduct172999 (Entrez Gene)
prp-21GeneProduct173440 (Entrez Gene)
prp-4GeneProduct172443 (Entrez Gene)
prp-8GeneProduct176153 (Entrez Gene)
ptb-1GeneProduct174647 (Entrez Gene)
rha-1GeneProduct174417 (Entrez Gene)
rnp-2GeneProduct177181 (Entrez Gene)
rnp-3GeneProduct177182 (Entrez Gene)
rnp-7GeneProduct176002 (Entrez Gene)
rsp-1GeneProduct174748 (Entrez Gene)
rsp-2GeneProduct174747 (Entrez Gene)
rsp-3GeneProduct176688 (Entrez Gene) Antagonist splicing factor
rsp-4GeneProduct173915 (Entrez Gene)
rsp-6GeneProduct177566 (Entrez Gene)
rsp-7GeneProduct174646 (Entrez Gene) PMID: 14559993. SRrp86 is a unique member of the SR protein superfamily containing one RNA recognition motif and two serine-arginine (SR)-rich domains separated by an unusual glutamic acid-lysine (EK)-rich region. Previously, we showed that SRrp86 could regulate alternative splicing by both positively and negatively modulating the activity of other SR proteins and that the unique EK domain could inhibit both constitutive and alternative splicing. These functions were most consistent with the model in which SRrp86 functions by interacting with and thereby modulating the activity of target proteins. To identify the specific proteins that interact with SRrp86, we used a yeast two-hybrid library screen and immunoprecipitation coupled to mass spectrometry. We show that SRrp86 interacts with all of the core SR proteins, as well as a subset of other splicing regulatory proteins, including SAF-B, hnRNP G, YB-1, and p72. In contrast to previous results that showed activation of SRp20 by SRrp86, we now show that SAF-B, hnRNP G, and 9G8 all antagonize the activity of SRrp86. Overall, we conclude that not only does SRrp86 regulate SR protein activity but that it is, in turn, regulated by other splicing factors to control alternative splice site selection.
rsr-1GeneProduct173013 (Entrez Gene)
sap-1GeneProduct173767 (Entrez Gene)
snr-1GeneProduct178483 (Entrez Gene)
snr-3GeneProduct174072 (Entrez Gene)
snr-4GeneProduct179639 (Entrez Gene)
snr-5GeneProduct176103 (Entrez Gene)
snr-6GeneProduct176668 (Entrez Gene)
snr-7GeneProduct171834 (Entrez Gene)
spt-5GeneProduct178143 (Entrez Gene)
suf-1GeneProduct174380 (Entrez Gene)
tag-172GeneProduct3565068 (Entrez Gene)
tag-203GeneProduct172406 (Entrez Gene)
tag-72GeneProduct182875 (Entrez Gene)
teg-1GeneProduct176561 (Entrez Gene)
uaf-1GeneProduct175270 (Entrez Gene)
unc-75GeneProduct182722 (Entrez Gene)

Annotated Interactions

No annotated interactions
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