Reactome | mRNA Splicing

mRNA Splicing - Major Pathway

Stable Identifier

R-HSA-72163

DOI

10.3180/R-HSA-72163.3

Type

Pathway

Species

Homo sapiens

Compartment

nucleoplasm

Synonyms

pre-mRNA splicing, U2 Dependent Splicing

ReviewStatus

5/5

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Eukaryotic genes are transcribed to yield pre-mRNAs that are processed to add methyl guanosine cap structures and polyadenylate tails and to splice together segments of a pre-mRNA termed exons, thereby removing segments termed introns. More than 90% of human genes contain introns, with an average of 4.0 introns per gene and 3413 nucleotides per intron compared with 5.0 exons per gene and 50.9 nucleotides per exon (Deutsch and Long 1999). (Notable exceptions are the histone genes, which are intronless.)
Pre-mRNA splicing is performed by a large ribonucleoprotein complex, the spliceosome, which contains 5 small nuclear RNAs (snRNAs) and more than 150 proteins (reviewed in Will and Luhrmann 2011, Kastner et al. 2019, Yan et al. 2019, Fica et al. 2020, Wan et al. 2020, Wilkinson et al. 2020). The catalyst in the spliceosome comprises magnesium ions coordinated by the U6 snRNA that catalyze transesterification reactions between hydroxyl groups and phosphate groups from the pre-mRNA. The role of the U6 snRNA demonstrates that the spliceosome is a ribozyme hints at the origin of the spliceosome as a self-splicing group II intron.
The spliceosome is initially assembled cotranscriptionally on the pre-mRNA as the Spliceosomal E (Early) complex and then remodelled sequentially by association and dissociation of proteins and snRNAs to catalyze of the two reactions of splicing. First, a nucleophilic attack by the 2' hydroxyl group of a conserved adenine residue, the branch point, within the intron on the phosphate group of the 5' residue of the intron yields a lariat (looped) structure in the intron joined to the downstream (3') exon and a free upstream exon with a 3' hydroxyl group. Second, a nucleophilic attack by the 3' hydroxyl group of the upstream exon on the phosphate of the 5' residue of the downstream exon yields a spliced mRNA containing the upstream exon ligated to the downstream exon and a free intron containing a lariat structure.
The Spliceosomal E complex contains the U1 snRNP bound to the 5' splice site, SF1 bound to the branch point, and the U2AF complex bound to the polypyrimidine tract of the intron and the 3' splice site of the pre-mRNA (Zhuang and Weiner 1986, Hong et al. 1997, Das et al. 2000, Hartmuth et al. 2002, Rappsilber et al. 2002, Hegele et al. 2012, Makarov et al. 2012, Crisci et al. 2015, Kondo et al. 2015, Tan et al. 2016). SF1 and U2AF are displaced on the pre-mRNA and the U2 snRNP binds the branch region to yield the Spliceosomal A complex (Wu and Manley 1989, Fleckner et al. 1997, Neubauer et al. 1998, Hartmuth et al. 2002, Rappsilber et al. 2002, Xu et al. 2004, Behzadnia et al. 2007, Shen et al. 2008, Chen et al. 2017, Zhang et al. 2020). The U4/U6.U5 tri-snRNP, containing the U4 snRNA base-paired with the U6 snRNA plus the U5 snRNP and accessory proteins, binds the Spliceosomal A complex to form the Spliceosomal Pre-B complex (Hausner et al. 1990, Kataoka and Dreyfuss 2004, Chi et al. 2013, Mohlmann et al. 2014, Boesler et al. 2016, Zhan et al. 2018, Charenton et al. 2019, Kastner et al. 2019, Townsend et al. 2020). The U1 snRNP is replaced at the 5' splice site by the U6 snRNA and the spliceosome is remodelled to yield the Spliceosomal B complex (Ismaïli et al. 2001, Deckert et al. 2006, Bessonov et al. 2008, Wolf et al. 2009, Bessonov et al. 2010, Schmidt et al. 2014, Boesler et al. 2016, Bertram et al. 2017, Zhang et al. 2018, Kastner et al. 2019). The Spliceosomal B complex is activated to form the Spliceosomal Bact complex by dissociation of the U4 snRNP and Lsm proteins from the U6 snRNA, freeing the U6 snRNA to form the active site of the spliceosome (Lamond et al. 1988, Laggerbauer et al. 1998, Ajuh et al. 2000, Bessonov et al. 2010, Agafonov et al. 2011, Haselbach et al. 2018, Zhang et al. 2018, Kastner et al. 2019, Busetto et al. 2020). Dissociation of the SF3A and SF3B subcomplexes of the U2 snRNP allows the intron branch point to dock near the 5' splice site, forming the B* Spliceosomal complex. Reaction of the branch point at the 5' splice site, yields the Spliceosomal C complex (Jurica et al. 2002, Makarov et al. 2002, Rappsilber et al. 2002, Reichert et al. 2002, Kataoka and Dreyfuss 2004, Bessonov et al. 2010, Gencheva et al. 2010, Agafonov et al. 2011, Alexandrov et al. 2012, Barbosa et al. 2012, Steckelberg et al. 2012, Schmidt et al. 2014, Zhan et al. 2018, Kastner et al. 2019, Busetto et al. 2020). The branch point is rotated to allow the 3' splice site to enter the active site, yielding the Spliceosomal C* complex (Ortlepp et al. 1998, Zhou and Reed 1998, Jurica et al. 2002, Makarov et al. 2002, Rappsilber et al. 2002, Ilagan et al. 2013, Bertram et al. 2017, Zhang et al. 2017, Kastner et al. 2019). Reaction of the 3' hydroxyl group of the upstream exon at the 3' splice site yields the Spliceosomal P (postcatalytic) complex (Zhou et al. 2000, Kataoka and Dreyfuss 2004, Tange et al. 2005, Zhang and Krainer 2007, Chi et al. 2013, Ilagan et al. 2013, Bertram et al. 2017, Zhang et al. 2017, Fica et al. 2019, Zhang et al. 2019). The Spliceosomal P complex then dissociates to yield an mRNP containing the spliced mRNA and associated proteins, including the exon junction complex (EJC) (Ohno and Shimura 1996, Merz et al. 2007, Yoshimoto et al. 2009, Zanini et al. 2017, Felisberto-Rodrigues et al. 2019, Zhang et al. 2019, EJC reviewed in Schlautmann and Gehring 2020), and the Intron Lariat Spliceosome (ILS), which contains the intron lariat. The ILS is then disassembled to free its components for further splicing reactions and the intron lariat is degraded (Wen et al. 2008, Yoshimoto et al. 2009, Yoshimoto et al. 2014, Zhang et al. 2019, Studer et al. 2020).

Literature References

PubMed ID	Title	Journal	Year
11014198	The protein Aly links pre-messenger-RNA splicing to nuclear export in metazoans Zhou, Z, Luo, MJ, Straesser, K, Katahira, J, Hurt, E, Reed, R	Nature	2000
20980672	Characterization of purified human Bact spliceosomal complexes reveals compositional and morphological changes during spliceosome activation and first step catalysis Bessonov, S, Anokhina, M, Krasauskas, A, Golas, MM, Sander, B, Will, CL, Urlaub, H, Stark, H, Lührmann, R	RNA	2010
10882114	Functional association of U2 snRNP with the ATP-independent spliceosomal complex E Das, R, Zhou, Z, Reed, R	Mol Cell	2000
12411573	Small nuclear ribonucleoprotein remodeling during catalytic activation of the spliceosome Makarov, EM, Makarova, OV, Urlaub, H, Gentzel, M, Will, CL, Wilm, M, Lührmann, R	Science	2002
29361316	Structure and Conformational Dynamics of the Human Spliceosomal B^act Complex Haselbach, D, Komarov, I, Agafonov, DE, Hartmuth, K, Graf, B, Dybkov, O, Urlaub, H, Kastner, B, Lührmann, R, Stark, H	Cell	2018
18322460	Isolation of an active step I spliceosome and composition of its RNP core Bessonov, S, Anokhina, M, Will, CL, Urlaub, H, Lührmann, R	Nature	2008
30765414	Structural Insights into Nuclear pre-mRNA Splicing in Higher Eukaryotes Kastner, B, Will, CL, Stark, H, Lührmann, R	Cold Spring Harb Perspect Biol	2019
32494006	Molecular architecture of the human 17S U2 snRNP Zhang, Z, Will, CL, Bertram, K, Dybkov, O, Hartmuth, K, Agafonov, DE, Hofele, R, Urlaub, H, Kastner, B, Lührmann, R, Stark, H	Nature	2020
29360106	Structure of the human activated spliceosome in three conformational states Zhang, X, Yan, C, Zhan, X, Li, L, Lei, J, Shi, Y	Cell Res	2018
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16809785	Protein composition and electron microscopy structure of affinity-purified human spliceosomal B complexes isolated under physiological conditions Deckert, J, Hartmuth, K, Boehringer, D, Behzadnia, N, Will, CL, Kastner, B, Stark, H, Urlaub, H, Lührmann, R	Mol. Cell. Biol.	2006
26420826	Mammalian splicing factor SF1 interacts with SURP domains of U2 snRNP-associated proteins Crisci, A, Raleff, F, Bagdiul, I, Raabe, M, Urlaub, H, Rain, JC, Krämer, A	Nucleic Acids Res.	2015
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25555158	Crystal structure of human U1 snRNP, a small nuclear ribonucleoprotein particle, reveals the mechanism of 5' splice site recognition Kondo, Y, Oubridge, C, van Roon, AM, Nagai, K	Elife	2015
3757028	A compensatory base change in U1 snRNA suppresses a 5' splice site mutation Zhuang, Y, Weiner, AM	Cell	1986
18593880	Distinct activities of the DExD/H-box splicing factor hUAP56 facilitate stepwise assembly of the spliceosome Shen, H, Zheng, X, Shen, J, Zhang, L, Zhao, R, Green, MR	Genes Dev	2008
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9539711	The human U5-200kD DEXH-box protein unwinds U4/U6 RNA duplices in vitro Laggerbauer, B, Achsel, T, Lührmann, R	Proc Natl Acad Sci U S A	1998
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8608946	A human RNA helicase-like protein, HRH1, facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome Ohno, M, Shimura, Y	Genes Dev	1996
9701291	The mammalian homologue of Prp16p is overexpressed in a cell line tolerant to Leflunomide, a new immunoregulatory drug effective against rheumatoid arthritis Ortlepp, D, Laggerbauer, B, Müllner, S, Achsel, T, Kirschbaum, B, Lührmann, R	RNA	1998
11233976	The 100-kda U5 snRNP protein (hPrp28p) contacts the 5' splice site through its ATPase site Ismaïli, N, Sha, M, Gustafson, EH, Konarska, MM	RNA	2001
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27683217	Stoichiometries of U2AF35, U2AF65 and U2 snRNP reveal new early spliceosome assembly pathways Chen, L, Weinmeister, R, Kralovicova, J, Eperon, LP, Vorechovsky, I, Hudson, AJ, Eperon, IC	Nucleic Acids Res	2017
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30315277	Structures of the human pre-catalytic spliceosome and its precursor spliceosome Zhan, X, Yan, C, Zhang, X, Lei, J, Shi, Y	Cell Res	2018
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22961380	Human CWC22 escorts the helicase eIF4AIII to spliceosomes and promotes exon junction complex assembly Barbosa, I, Haque, N, Fiorini, F, Barrandon, C, Tomasetto, C, Blanchette, M, Le Hir, H	Nat Struct Mol Biol	2012
19165350	TFIP11 interacts with mDEAH9, an RNA helicase involved in spliceosome disassembly Wen, X, Tannukit, S, Paine, ML	Int J Mol Sci	2008
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