RNA splicing

In molecular biology, splicing is the editing of the nascent pre-messenger RNA (pre-mRNA) transcript. After splicing introns are removed and exons are joined together (ligated). For nuclear-encoded genes, splicing takes place within the nucleus either co-transcriptionally or immediately after transcription. For those eukaryotic genes that contain introns, splicing is usually required in order to create an mRNA molecule that can be translated into protein. For many eukaryotic introns, splicing is carried out in a series of reactions which are catalyzed by the spliceosome, a complex of small nuclear ribonucleoproteins (snRNPs). Self-splicing introns, or ribozymes capable of catalyzing their own excision from their parent RNA molecule, also exist.

Splicing pathways

Several methods of RNA splicing occur in nature; the type of splicing depends on the structure of the spliced intron and the catalysts required for splicing to occur.

Spliceosomal

Introns

The word intron is derived from the term intragenic region, that is, a region inside a gene. The term intron refers to both the DNA sequence within a gene and the corresponding sequence in the unprocessed RNA transcript. As part of the RNA processing pathway, introns are removed by RNA splicing either shortly after or concurrent with transcription.[1] Introns are found in the genes of most organisms and many viruses. They can be located in a wide range of genes, including those that generate proteins, ribosomal RNA (rRNA), and transfer RNA (tRNA).[2]

Spliceosomal introns often reside within the sequence of eukaryotic protein-coding genes. Within the intron, a donor site (5' end of the intron), a branch site (near the 3' end of the intron) and an acceptor site (3' end of the intron) are required for splicing. The splice donor site includes an almost invariant sequence GU at the 5' end of the intron, within a larger, less highly conserved region. The splice acceptor site at the 3' end of the intron terminates the intron with an almost invariant AG sequence. Upstream (5'-ward) from the AG there is a region high in pyrimidines (C and U), or polypyrimidine tract. Further upstream from the polypyrimidine tract is the branchpoint, which includes an adenine nucleotide involved in lariat formation.[3][4] The consensus sequence for an intron (in IUPAC nucleic acid notation) is: G-G-[cut]-G-U-R-A-G-U (donor site) ... intron sequence ... Y-U-R-A-C (branch sequence 20-50 nucleotides upstream of acceptor site) ... Y-rich-N-C-A-G-[cut]-G (acceptor site).[5] However, it is noted that the specific sequence of intronic splicing elements and the number of nucleotides between the branchpoint and the nearest 3’ acceptor site affect splice site selection.[6][7] Also, point mutations in the underlying DNA or errors during transcription can activate a cryptic splice site in part of the transcript that usually is not spliced. This results in a mature messenger RNA with a missing section of an exon. In this way, a point mutation, which might otherwise only affect a single amino acid, can manifest as a deletion or truncation in the final protein.

Simple illustration of exons and introns in pre-mRNA

Formation and activity

Splicing is catalyzed by the spliceosome, a large RNA-protein complex composed of five small nuclear ribonucleoproteins (snRNPs, pronounced 'snurps'). Assembly and activity of the spliceosome occurs during transcription of the pre-mRNA. The RNA components of snRNPs interact with the intron and are involved in catalysis. Two types of spliceosomes have been identified (major and minor) which contain different snRNPs.

  • Complex E
    • The U1 snRNP binds to the GU sequence at the 5' splice site of an intron;
    • Splicing factor 1 binds to the intron branch point sequence;
    • U2AF1 binds at the 3' splice site of the intron;
    • U2AF2 binds to the polypyrimidine tract;[11]
  • Complex A (pre-spliceosome)
    • The U2 snRNP displaces SF1 and binds to the branch point sequence and ATP is hydrolyzed;
  • Complex B (pre-catalytic spliceosome)
    • The U5/U4/U6 snRNP trimer binds, and the U5 snRNP binds exons at the 5' site, with U6 binding to U2;
  • Complex B*
    • The U1 snRNP is released, U5 shifts from exon to intron, and the U6 binds at the 5' splice site;
  • Complex C (catalytic spliceosome)
    • U4 is released, U6/U2 catalyzes transesterification, making the 5'-end of the intron ligate to the A on intron and form a lariat, U5 binds exon at 3' splice site, and the 5' site is cleaved, resulting in the formation of the lariat;
  • Complex C* (post-spliceosomal complex)
    • U2/U5/U6 remain bound to the lariat, and the 3' site is cleaved and exons are ligated using ATP hydrolysis. The spliced RNA is released, the lariat is released and degraded,[12] and the snRNPs are recycled.
This type of splicing is termed canonical splicing or termed the lariat pathway, which accounts for more than 99% of splicing. By contrast, when the intronic flanking sequences do not follow the GU-AG rule, noncanonical splicing is said to occur (see "minor spliceosome" below).[13]

Self-splicing

Self-splicing occurs for rare introns that form a ribozyme, performing the functions of the spliceosome by RNA alone. There are three kinds of self-splicing introns, Group I, Group II and Group III. Group I and II introns perform splicing similar to the spliceosome without requiring any protein. This similarity suggests that Group I and II introns may be evolutionarily related to the spliceosome. Self-splicing may also be very ancient, and may have existed in an RNA world present before protein.

Two transesterifications characterize the mechanism in which group I introns are spliced:

  1. 3'OH of a free guanine nucleoside (or one located in the intron) or a nucleotide cofactor (GMP, GDP, GTP) attacks phosphate at the 5' splice site.
  2. 3'OH of the 5' exon becomes a nucleophile and the second transesterification results in the joining of the two exons.

The mechanism in which group II introns are spliced (two transesterification reaction like group I introns) is as follows:

  1. The 2'OH of a specific adenosine in the intron attacks the 5' splice site, thereby forming the lariat
  2. The 3'OH of the 5' exon triggers the second transesterification at the 3' splice site, thereby joining the exons together.

tRNA splicing

tRNA (also tRNA-like) splicing is another rare form of splicing that usually occurs in tRNA. The splicing reaction involves a different biochemistry than the spliceosomal and self-splicing pathways.

In the yeast Saccharomyces cerevisiae, a yeast tRNA splicing endonuclease heterotetramer, composed of TSEN54, TSEN2, TSEN34, and TSEN15, cleaves pre-tRNA at two sites in the acceptor loop to form a 5'-half tRNA, terminating at a 2',3'-cyclic phosphodiester group, and a 3'-half tRNA, terminating at a 5'-hydroxyl group, along with a discarded intron.[17] Yeast tRNA kinase then phosphorylates the 5'-hydroxyl group using adenosine triphosphate. Yeast tRNA cyclic phosphodiesterase cleaves the cyclic phosphodiester group to form a 2'-phosphorylated 3' end. Yeast tRNA ligase adds an adenosine monophosphate group to the 5' end of the 3'-half and joins the two halves together.[18] NAD-dependent 2'-phosphotransferase then removes the 2'-phosphate group.[19][20]

Evolution

Splicing occurs in all the kingdoms or domains of life, however, the extent and types of splicing can be very different between the major divisions. Eukaryotes splice many protein-coding messenger RNAs and some non-coding RNAs. Prokaryotes, on the other hand, splice rarely and mostly non-coding RNAs. Another important difference between these two groups of organisms is that prokaryotes completely lack the spliceosomal pathway.

Because spliceosomal introns are not conserved in all species, there is debate concerning when spliceosomal splicing evolved. Two models have been proposed: the intron late and intron early models (see intron evolution).

Splicing diversity
Eukaryotes Prokaryotes
Spliceosomal + −
Self-splicing + +
tRNA + +

Biochemical mechanism

Diagram illustrating the two-step biochemistry of splicing

Spliceosomal splicing and self-splicing involve a two-step biochemical process. Both steps involve transesterification reactions that occur between RNA nucleotides. tRNA splicing, however, is an exception and does not occur by transesterification.[21]

Spliceosomal and self-splicing transesterification reactions occur via two sequential transesterification reactions. First, the 2'OH of a specific branchpoint nucleotide within the intron, defined during spliceosome assembly, performs a nucleophilic attack on the first nucleotide of the intron at the 5' splice site, forming the lariat intermediate. Second, the 3'OH of the released 5' exon then performs a nucleophilic attack at the last nucleotide of the intron at the 3' splice site, thus joining the exons and releasing the intron lariat.[22]

Alternative splicing

Main article: Alternative splicing

In many cases, the splicing process can create a range of unique proteins by varying the exon composition of the same mRNA. This phenomenon is then called alternative splicing. Alternative splicing can occur in many ways. Exons can be extended or skipped, or introns can be retained. It is estimated that 95% of transcripts from multiexon genes undergo alternative splicing, some instances of which occur in a tissue-specific manner and/or under specific cellular conditions.[23] Development of high throughput mRNA sequencing technology can help quantify the expression levels of alternatively spliced isoforms. Differential expression levels across tissues and cell lineages allowed computational approaches to be developed to predict the functions of these isoforms.[24][25] Given this complexity, alternative splicing of pre-mRNA transcripts is regulated by a system of trans-acting proteins (activators and repressors) that bind to cis-acting sites or "elements" (enhancers and silencers) on the pre-mRNA transcript itself. These proteins and their respective binding elements promote or reduce the usage of a particular splice site. The binding specificity comes from the sequence and structure of the cis-elements e.g in HIV-1 there are many donor and acceptor splice sites. Among the various splice sites ssA7 which is 3' acceptor site folds into three stem loop structure i.e. Intronic splicing silencer (ISS), Exonic splicing enhancer (ESE) and Exonic splicing silencer (ESSE3). Solution structure of Intronic splicing silencer and its interaction to host protein hnRNPA1 give insight into specific recognition.[26] However, adding to the complexity of alternative splicing, it is noted that the effects of regulatory factors are many times position-dependent. For example, a splicing factor that serves as a splicing activator when bound to an intronic enhancer element may serve as a repressor when bound to its splicing element in the context of an exon, and vice versa.[27] In addition to the position-dependent effects of enhancer and silencer elements, the location of the branchpoint (i.e., distance upstream of the nearest 3’ acceptor site) also affects splicing.[6] The secondary structure of the pre-mRNA transcript also plays a role in regulating splicing, such as by bringing together splicing elements or by masking a sequence that would otherwise serve as a binding element for a splicing factor.[28][29]

Experimental manipulation of splicing

Splicing events can be experimentally altered[30][31] by binding steric-blocking antisense oligos such as Morpholinos or Peptide nucleic acids to snRNP binding sites, to the branchpoint nucleotide that closes the lariat,[32] or to splice-regulatory element binding sites.[33]

Splicing errors and variation

It has been suggested that one third of all disease-causing mutations impact on splicing.[27] Common errors include:

Although many splicing errors are safeguarded by a cellular quality control mechanism termed nonsense-mediated mRNA decay (NMD),[34] a number of splicing-related diseases also exist, as suggested above.[35]

Allelic differences in mRNA splicing are likely to be a common and important source of phenotypic diversity at the molecular level, in addition to their contribution to genetic disease susceptibility. Indeed, genome-wide studies in humans have identified a range of genes that are subject to allele-specific splicing.

Protein splicing

Main article: Protein splicing

In addition to RNA, proteins can undergo splicing. Although the biomolecular mechanisms are different, the principle is the same: parts of the protein, called inteins instead of introns, are removed. The remaining parts, called exteins instead of exons, are fused together. Protein splicing has been observed in a wide range of organisms, including bacteria, archaea, plants, yeast and humans.[36]

See also

Wikimedia Commons has media related to Splicing.

References

  1. ↑ Tilgner, Hagen; Knowles, David G.; Johnson, Rory; Davis, Carrie A.; Chakrabortty, udipto; Djebali, Sarah; Curado, João; Snyder, Michael; Gingeras, Thomas R.; Guigó, Roderic (2012). "Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs". Genome Research 22 (9): 1616–25. doi:10.1101/gr.134445.111. PMC 3431479. PMID 22955974.
  2. ↑ William Roy, Scott; Gilbert, Walter (2006). "The evolution of spliceosomal introns: Patterns, puzzles and progress". Nature Reviews Genetics 7 (3): 211–21. doi:10.1038/nrg1807. PMID 16485020.
  3. ↑ Clancy, Suzanne (2008). "RNA Splicing: Introns, Exons and Spliceosome". Nature Education 1 (1): 31. Retrieved 31 March 2011.
  4. 1 2 Black, Douglas L. (June 2003). "Mechanisms of Alternative Pre-Messenger RNA Splicing". Annual Review of Biochemistry 72 (1): 291–336. doi:10.1146/annurev.biochem.72.121801.161720. PMID 12626338.
  5. ↑ "Molecular Biology of the Cell". 2012 Journal Citation Reports. Web of Science (Science ed.). Thomson Reuters. 2013.
  6. 1 2 Taggart, Allison J; Desimone, Alec M; Shih, Janice S; Filloux, Madeleine E; Fairbrother, William G (2012). "Large-scale mapping of branchpoints in human pre-mRNA transcripts in vivo". Nature Structural & Molecular Biology 19 (7): 719–21. doi:10.1038/nsmb.2327. PMC 3465671. PMID 22705790.
  7. ↑ Corvelo, André; Hallegger, Martina; Smith, Christopher W. J.; Eyras, Eduardo (2010). Meyer, Irmtraud M, ed. "Genome-Wide Association between Branch Point Properties and Alternative Splicing". PLoS Computational Biology 6 (11): e1001016. doi:10.1371/journal.pcbi.1001016. PMC 2991248. PMID 21124863.
  8. ↑ Graveley, Brenton R; Hertel, Klemens J; Maniatis, Tom (June 2001). "The role of U2AF35 and U2AF65 in enhancer-dependent splicing". RNA 7 (6): 806–818. doi:10.1017/s1355838201010317. PMC 1370132. PMID 11421359. Retrieved 17 December 2014.
  9. ↑ Matlin, Arianne J.; Clark, Francis; Smith, Christopher W. J. (2005). "Understanding alternative splicing: Towards a cellular code". Nature Reviews Molecular Cell Biology 6 (5): 386–98. doi:10.1038/nrm1645. PMID 15956978.
  10. ↑ Matera, A. Gregory; Wang, Zefeng (23 January 2014). "A day in the life of the spliceosome". Nature Reviews Molecular Cell Biology 15 (2): 108–121. doi:10.1038/nrm3742. Retrieved 12 December 2014.
  11. ↑ Guth, Sabine; Valcárcel, Juan (1 December 2000). "Kinetic role for mammalian SF1/BBP in spliceosome assembly and function after polypyrimidine tract recognition by U2AF". Journal of Biological Chemistry 275 (48): 38059–66. doi:10.1074/jbc.M001483200. PMID 10954700. Retrieved 12 December 2014.
  12. ↑ Cheng, Zhi; Menees, Thomas M. (8 November 2011). "RNA splicing and debranching viewed through analysis of RNA lariats". Molecular Genetics and Genomics 286 (5-6): 395–410. doi:10.1007/s00438-011-0635-y. Retrieved 12 December 2014.
  13. ↑ Ng, Bernard; Yang, Fan; Huston, David P.; Yan, Yan; Yang, Yu; Xiong, Zeyu; Peterson, Leif E.; Wang, Hong; Yang, Xiao-Feng (2004). "Increased noncanonical splicing of autoantigen transcripts provides the structural basis for expression of untolerized epitopes". Journal of Allergy and Clinical Immunology 114 (6): 1463–70. doi:10.1016/j.jaci.2004.09.006. PMID 15577853.
  14. ↑ Patel, Abhijit A.; Steitz, Joan A. (2003). "Splicing double: Insights from the second spliceosome". Nature Reviews Molecular Cell Biology 4 (12): 960–70. doi:10.1038/nrm1259. PMID 14685174.
  15. ↑ König, Harald; Matter, Nathalie; Bader, Rüdiger; Thiele, Wilko; Müller, Ferenc (2007). "Splicing Segregation: The Minor Spliceosome Acts outside the Nucleus and Controls Cell Proliferation". Cell 131 (4): 718–29. doi:10.1016/j.cell.2007.09.043. PMID 18022366.
  16. ↑ Di Segni, Gianfranco; Gastaldi, Serena; Tocchini-Valentini, Glauco P. (2008). "Cis- and trans-splicing of mRNAs mediated by tRNA sequences in eukaryotic cells". Proceedings of the National Academy of Sciences 105 (19): 6864–9. Bibcode:2008PNAS..105.6864D. doi:10.1073/pnas.0800420105. JSTOR 25461891. PMC 2383978. PMID 18458335.
  17. ↑ Trotta, Christopher R; Miao, Feng; Arn, Eric A; Stevens, Scott W; Ho, Calvin K; Rauhut, Reinhard; Abelson, John N (June 1997). "The Yeast tRNA Splicing Endonuclease: A Tetrameric Enzyme with Two Active Site Subunits Homologous to the Archaeal tRNA Endonucleases". Cell 89 (6): 849–858. doi:10.1016/S0092-8674(00)80270-6. Retrieved 17 December 2014.
  18. ↑ Westaway, Shawn K; Phizicky, Eric M; Abelson, John (5 March 1988). "Structure and function of the yeast tRNA ligase gene.". The Journal of Biological Chemistry 263 (7): 3171–6. PMID 3277966. Retrieved 17 December 2014.
  19. ↑ Paushkin, Sergey V; Patel, Meenal; Furia, Bansri S; Peltz, Stuart W; Trotta, Christopher R (April 2004). "Identification of a Human Endonuclease Complex Reveals a Link between tRNA Splicing and Pre-mRNA 3′ End Formation". Cell 117 (3): 311–321. doi:10.1016/S0092-8674(04)00342-3. PMID 15109492. Retrieved 17 December 2014.
  20. ↑ Soma, Akiko (1 April 2014). "Circularly permuted tRNA genes: their expression and implications for their physiological relevance and development". Frontiers in Genetics 5. doi:10.3389/fgene.2014.00063. Retrieved 17 December 2014.
  21. ↑ Abelson, John; Trotta, Christopher R; Li, Hong (22 May 1998). "tRNA Splicing". Journal of Biological Chemistry 273 (21): 12685–12688. doi:10.1074/jbc.273.21.12685. PMID 9582290. Retrieved 17 December 2014.
  22. ↑ Fica, Sebastian M.; Tuttle, Nicole; Novak, Thaddeus; Li, Nan-Sheng; Lu, Jun; Koodathingal, Prakash; Dai, Qing; Staley, Jonathan P.; Piccirilli, Joseph A. (6 November 2013). "RNA catalyses nuclear pre-mRNA splicing". Nature 503 (7475): 229–234. doi:10.1038/nature12734. PMID 24196718. Retrieved 17 December 2014.
  23. ↑ Pan, Qun; Shai, Ofer; Lee, Leo J; Frey, Brendan J; Blencowe, Benjamin J (2008). "Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing". Nature Genetics 40 (12): 1413–5. doi:10.1038/ng.259. PMID 18978789.
  24. ↑ Eksi, R; Li, HD; Menon, R; Wen, Y; Omenn, GS; Kretzler, M; Guan, Y (Nov 2013). "Systematically differentiating functions for alternatively spliced isoforms through integrating RNA-seq data.". PLOS Computational Biology 9 (11): e1003314. doi:10.1371/journal.pcbi.1003314. PMC 3820534. PMID 24244129.
  25. ↑ Li, HD; Menon, R; Omenn, GS; Guan, Y (Jun 17, 2014). "The emerging era of genomic data integration for analyzing splice isoform function.". Trends in genetics : TIG 30 (8): 340–347. doi:10.1016/j.tig.2014.05.005. PMID 24951248.
  26. ↑ Jain, Niyati; Morgan, Christopher; Rife, Brittney; Salemi, Marco; Tolbert, Blanton (24 November 2015). "Solution Structure of the HIV-1 Intron Splicing Silencer and its Interactions with the UP1 Domain of hnRNP A1". Journal of Biological sciences.
  27. 1 2 Lim, Kian Huat; Ferraris, Luciana; Filloux, Madeleine E.; Raphael, Benjamin J.; Fairbrother, William G. (2011). "Using positional distribution to identify splicing elements and predict pre-mRNA processing defects in human genes". Proceedings of the National Academy of Sciences 108 (27): 11093–8. doi:10.1073/pnas.1101135108. PMC 3131313. PMID 21685335.
  28. ↑ Warf, M. Bryan; Berglund, J. Andrew (2010). "Role of RNA structure in regulating pre-mRNA splicing". Trends in Biochemical Sciences 35 (3): 169–78. doi:10.1016/j.tibs.2009.10.004. PMC 2834840. PMID 19959365.
  29. ↑ Reid, D. C.; Chang, B. L.; Gunderson, S. I.; Alpert, L.; Thompson, W. A.; Fairbrother, W. G. (2009). "Next-generation SELEX identifies sequence and structural determinants of splicing factor binding in human pre-mRNA sequence". RNA 15 (12): 2385–97. doi:10.1261/rna.1821809. PMC 2779669. PMID 19861426.
  30. ↑ Draper, Bruce W.; Morcos, Paul A.; Kimmel, Charles B. (2001). "Inhibition of zebrafishfgf8 pre-mRNA splicing with morpholino oligos: A quantifiable method for gene knockdown". Genesis 30 (3): 154–6. doi:10.1002/gene.1053. PMID 11477696.
  31. ↑ Sazani, Peter; Kang, Shin-Hong; Maier, Martin A.; Wei, Changfu; Dillman, Jennifer; Summerton, James; Manoharan, Muthiah; Kole, Ryszard (2001). "Nuclear antisense effects of neutral, anionic and cationic oligonucleotide analogs". Nucleic Acids Research 29 (19): 3965–74. doi:10.1093/nar/29.19.3965. PMC 60237. PMID 11574678.
  32. ↑ Morcos, Paul A. (2007). "Achieving targeted and quantifiable alteration of mRNA splicing with Morpholino oligos". Biochemical and Biophysical Research Communications 358 (2): 521–7. doi:10.1016/j.bbrc.2007.04.172. PMID 17493584.
  33. ↑ Bruno, I. G.; Jin, W; Cote, GJ (2004). "Correction of aberrant FGFR1 alternative RNA splicing through targeting of intronic regulatory elements". Human Molecular Genetics 13 (20): 2409–20. doi:10.1093/hmg/ddh272. PMID 15333583.
  34. ↑ Danckwardt, S.; Neu-Yilik, G; Thermann, R; Frede, U; Hentze, MW; Kulozik, AE (2002). "Abnormally spliced beta -globin mRNAs: A single point mutation generates transcripts sensitive and insensitive to nonsense-mediated mRNA decay". Blood 99 (5): 1811–6. doi:10.1182/blood.V99.5.1811. PMID 11861299.
  35. ↑ Ward, Amanda J; Cooper, Thomas A (2009). "The pathobiology of splicing". The Journal of Pathology 220 (2): 152–63. doi:10.1002/path.2649. PMC 2855871. PMID 19918805.
  36. ↑ Hanada, Ken-Ichi; Yang, James C. (2005). "Novel biochemistry: Post-translational protein splicing and other lessons from the school of antigen processing". Journal of Molecular Medicine 83 (6): 420–8. doi:10.1007/s00109-005-0652-6. PMID 15759099.

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