In genetics, splicing is a modification of genetic information after transcription, in which introns of precursor messenger RNA (pre-mRNA) are removed and exons of it are joined. Since introns do not exist in prokaryotic genomes, splicing naturally only occurs in eukaryotes. The splicing prepares the pre-mRNA to produce the mature messenger RNA (mRNA), which then undergoes translation as part of the protein synthesis to produce proteins. Splicing includes a series of biochemical reactions, which are catalyzed by the spliceosome, a complex of small nuclear ribonucleoproteins (snRNPs). This article is about the general scientific term. ... A micrograph of ongoing gene transcription of ribosomal RNA illustrating the growing primary transcripts. ... Diagram of the location of introns and exons within a gene. ... Precursor mRNA, more commonly termed pre-mRNA, is an incompletely processed single strand of ribonucleic acid (RNA), synthesized from a DNA template in the nucleus of a cell by transcription. ... The exon portion of a DNA strand encodes a specific portion of a protein. ... Prokaryotic bacteria cell structure Prokaryotes (IPA: //) are a group of organisms that lack a cell nucleus (= karyon), or any other membrane-bound organelles. ... Kingdoms Animalia - Animals Fungi Plantae - Plants Chromalveolata Protista Alternative phylogeny Unikonta Opisthokonta Metazoa Choanozoa Eumycota Amoebozoa Bikonta Apusozoa Cabozoa Rhizaria Excavata Corticata Archaeplastida Chromalveolata Animals, plants, fungi, and protists are eukaryotes (IPA: ), organisms whose cells are organized into complex structures by internal membranes and a cytoskeleton. ... Mature messenger RNA, often abbreviated as mature mRNA is a eukaryotic RNA transcript that has been spliced and processed and is ready for translation in the course of protein synthesis. ... The life cycle of an mRNA in a eukaryotic cell. ... Translation is the second stage of protein biosynthesis (part of the overall process of gene expression). ... Protein biosynthesis (synthesis) is the process in which cells build proteins. ... A representation of the 3D structure of myoglobin showing coloured alpha helices. ... Biochemistry (from Greek: , bios, life and Egyptian kēme, earth[1]) is the study of the chemical processes in living organisms. ... For other uses, see Chemical reaction (disambiguation). ... Catalyst redirects here. ... A spliceosome is a complex of RNA and many protein subunits called snRNPs, that removes the non-coding introns from unprocessed mRNA. Spliceosomes are unique to eukaryotic mRNA as the mRNA of prokaryotes lack introns. ... SnRNPs (pronounced snurps), or small nuclear ribonucleoproteins, are particles which combine with pre-mRNA and various proteins to form spliceosomes (a type of large molecular complex). ...

Simple illustration of exons and introns in pre-mRNA. The mature mRNA is formed by splicing.

Image File history File links Download high resolution version (1547x264, 11 KB) Summary Drawing of pre-mRNA to mRNA made by myself Licensing I, the creator of this work, hereby grant the permission to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License... Image File history File links Download high resolution version (1547x264, 11 KB) Summary Drawing of pre-mRNA to mRNA made by myself Licensing I, the creator of this work, hereby grant the permission to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License...

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. However, regardless of which pathway is used, the excised introns are discarded. It has been suggested that this article or section be merged into Catalysis. ...

Spliceosomal introns

Spliceosomal introns often reside in eukaryotic protein-coding genes. Within the intron, a 3' splice site, 5' splice site, and branch site are required for splicing. Splicing is catalyzed by the spliceosome which is a large RNA-protein complex composed of five small nuclear ribonucleoproteins (snRNPs, pronounced 'snurps' ). The RNA components of snRNPs interact with the intron and may be involved in catalysis. Two types of spliceosomes have been identified (the major and minor) which contain different snRNPs. Kingdoms Eukaryotes are organisms with complex cells, in which the genetic material is organized into membrane-bound nuclei. ... A spliceosome is a complex of RNA and many protein subunits called snRNPs, that removes the non-coding introns from unprocessed mRNA. Spliceosomes are unique to eukaryotic mRNA as the mRNA of prokaryotes lack introns. ... SnRNPs (pronounced snurps), or small nuclear ribonucleoproteins, are particles which combine with pre-mRNA and various proteins to form spliceosomes (a type of large molecular complex). ... SnRNPs (pronounced snurps), or small nuclear ribonucleoproteins, are particles which combine with pre-mRNA and various proteins to form spliceosomes (a type of large molecular complex). ...

• Major

The major spliceosome splices introns containing GU at the 5' splice site and AG at the 3' splice site. It is composed of the U1, U2, U4, U5, and U6 snRNPs and is active in the nucleus.

• E Complex-U1 binds to the GU sequence at the 5' splice site, along with accessory proteins/enzymes ASF/SF2, U2AF (binds at the Py-AG site), SF1/BBP (BBP=Branch Binding Protein);
  
• A Complex-U2 binds to the branch site, and ATP is hydrolyzed;
  
• B1 Complex-U5/U4/U6 trimer binds, and the U5 binds exons at the 5' site, with U6 binding to U2;
  
• B2 Complex-U1 is released, U5 shifts from exon to intron and the U6 binds at the 5' splice site;
  
• C1 Complex-U4 is released, U6/U2 catalyzes transesterification, U5 binds exon at 3' splice site, and the 5' site is cleaved, resulting in the formation of the lariat;
  
• C2 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 and the lariat debranches.
  

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). ^[1]

• Minor

The minor spliceosome is very similar to the major spliceosome, however it splices out rare introns with different splice site sequences and is active in the cytosol ^[2]. While the minor and major spliceosomes contain the same U5 snRNP, the minor spliceosome has different, but functionally analogous snRNPs for U1, U2, U4, and U6, which are respectively called U11, U12, U4atac, and U6atac. ^[3]

• Trans-splicing

Trans-splicing is a form of splicing that joins two exons that are not within the same RNA transcript.

SnRNPs (pronounced snurps), or small nuclear ribonucleoproteins, are particles which combine with pre-mRNA and various proteins to form spliceosomes (a type of large molecular complex). ... The minor spliceosome is a ribonucleoprotein complex that catalyses the removal of an atypical class of spliceosomal introns (U12-type) from eukaryotic messenger RNAs in plant, insects, vertebrates and some fungi (Rhizopus oryzae). ... SnRNPs (pronounced snurps), or small nuclear ribonucleoproteins, are particles which combine with pre-mRNA and various proteins to form spliceosomes (a type of large molecular complex). ... Trans-splicing is a special form of RNA processing in eukaryotes where exons from two RNA molecules are ligated in an intermolecular reaction. ...

Self-splicing

Self-splicing occurs for rare introns that form a ribozyme, performing the functions of the spliceosome by RNA alone. There are two kinds of self-splicing introns, Group I and Group II. 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 that was present before protein. Although the two splicing mechanisms described below do not require any proteins to occur, 5 additional RNA molecules and over 50 proteins are used and hydrolyzes many ATP molecules. The splicing mechanisms use ATP in order to accurately splice mRNA's. If the cell were to not use any ATP's, the process would be highly inaccurate and many mistakes would occur. Two transesterfications characterize the mechanism in which group I introns are sliced: 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'OH becomes a nucleophile and the second transesterfication results in the joining of the two exons. The mechanism in which group II introns are spliced (two transesterfication 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 transesterfication at the 3' splice site thereby joining the exons together. This article is about the chemical. ... Group I catalytic introns are large self-splicing ribozymes. ... Group II intron is a class of intron found in rRNA, tRNA, mRNA of organelles in fungi, plants, protists, and mRNA in bacteria. ... The RNA world hypothesis proposes that RNA was, before the emergence of the first cell, the dominant, and probably the only, form of life. ...

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 spliceomsomal and self-splicing pathways. Ribonucleases cleave the RNA and ligases join the exons together. This form of splicing does also not require any RNA components for catalysis. Transfer RNA (abbreviated tRNA) is a small RNA chain (74-93 nucleotides) that transfers a specific amino acid to a growing polypeptide chain at the ribosomal site of protein synthesis during translation. ... Ribonuclease (RNase) is an enzyme that catalyzes the breakdown of RNA into smaller components. ... In biochemistry, a ligase is an enzyme that can catalyse the joining of two molecules (ligation or glue together) by forming a new chemical bond, with concomitant hydrolysis of ATP or other similar molecules. ...

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, but mostly non-coding RNAs. Another important difference between these two groups of organisms is that prokaryotes completely lack the spliceosomal pathway. The hierarchy of scientific classifications major eight taxonomic ranks. ... The hierarchy of scientific classifications major eight taxonomic ranks. ... Kingdoms Animalia - Animals Fungi Plantae - Plants Chromalveolata Protista Alternative phylogeny Unikonta Opisthokonta Metazoa Choanozoa Eumycota Amoebozoa Bikonta Apusozoa Cabozoa Rhizaria Excavata Corticata Archaeplastida Chromalveolata Animals, plants, fungi, and protists are eukaryotes (IPA: ), organisms whose cells are organized into complex structures by internal membranes and a cytoskeleton. ... The interaction of mRNA in a eukaryote cell. ... A non-coding RNA (ncRNA) is any RNA molecule that is not translated into a protein. ... Prokaryotic bacteria cell structure Prokaryotes (IPA: //) are a group of organisms that lack a cell nucleus (= karyon), or any other membrane-bound organelles. ...

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). Diagram of the location of introns and exons within a gene. ...

Biochemical mechanism

Diagram illustrating the two-step biochemistry of splicing

Spliceosomal splicing and self-splicing involves 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. Image File history File links Download high resolution version (1418x1002, 34 KB)Cartoon illustrating the two-step chemistry of mRNA splicing. ... Image File history File links Download high resolution version (1418x1002, 34 KB)Cartoon illustrating the two-step chemistry of mRNA splicing. ... In organic chemistry, transesterification is the process of exchanging the alkoxy group of an ester compound by another alcohol. ...

Spliceosomal and self-splicing transesterification reactions occur via two sequential transesterification reactions. First, the 2'OH of a specific branch-point nucleotide within the intron that is 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.

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 messenger RNA. This phenomenon is then called alternative splicing. Various modes of alternative splicing Alternative splicing is the process that occurs in eukaryotes in which the splicing process of a pre-mRNA transcribed from one gene can lead to different mature mRNA molecules and therefore to different proteins. ... Various modes of alternative splicing Alternative splicing is the process that occurs in eukaryotes in which the splicing process of a pre-mRNA transcribed from one gene can lead to different mature mRNA molecules and therefore to different proteins. ...

Experimental manipulation of splicing

Splicing events can be experimentally altered^[4] 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,^[5] or to splice-regulatory element binding sites.^[6] Segment of a Morpholino-RNA heteroduplex, 8-mer shown In molecular biology, a Morpholino is a kind of molecule used to modify gene expression. ... PNA can also refer to the Palestinian National Authority or Pakistan National Alliance. ...

Splicing errors

Mutations in the introns or exons can prevent splicing and thus may prevent protein biosynthesis. Protein biosynthesis (synthesis) is the process in which cells build proteins. ...

Common errors:

• Mutation of a splice site resulting in loss of function of that site. Results in exposure of a premature stop codon, loss of an exon, or inclusion of an intron.
• Mutation of a splice site reducing specificity. May result in variation in the splice location, causing insertion or deletion of amino acids, or most likely, a loss of the reading frame.
• Transposition of a splice site, resulting in inclusion or exclusion of more DNA than expected. Results in longer or shorter exons.

Protein splicing

Main article: Protein splicing

Not only pre-mRNA but also proteins can undergo splicing. Although the biomolecular mechanisms are different, the principle is the same, that 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 lower organisms, yeast, plants and animals, including in humans.^[7] Protein splicing is an intramolecular reaction of a particular protein in which an internal protein segment (called an intein) is removed from a precursor protein with a ligation of C-terminal and N-terminal external proteins (called exteins) on both sides. ... An intein is a segment of a protein that is able to excise itself and rejoin the remaining portions (the exteins) with a peptide bond. ...

References

1. ^ Ng B, Yang F, Huston DP, et al (Dec 2004). "Increased noncanonical splicing of autoantigen transcripts provides the structural basis for expression of untolerized epitopes". J. Allergy Clin. Immunol. 114 (6): 1463-70. doi:10.1016/j.jaci.2004.09.006. PMID 15577853. 
2. ^ König H, Matter N, Bader R, Thiele W, Müller F (Nov 16 2007). "Splicing segregation: the minor spliceosome acts outside the nucleus and controls cell proliferation". Cell. 131 (4): 1718-29. PMID 18022366. 
3. ^ Patel AA, Steitz JA (2003). "Splicing double: insights from the second spliceosome". Nat. Rev. Mol. Cell Biol. 4 (12): 960-70. doi:10.1038/nrm1259. PMID 14685174. 
4. ^ Draper BW, Morcos PA, Kimmel CB (2001). "Inhibition of zebrafish fgf8 pre-mRNA splicing with morpholino oligos: a quantifiable method for gene knockdown". Genesis 30 (3): 154-6. doi:10.1002/gene.1053. PMID 11477696. 
   Sazani P, Kang SH, Maier MA, et al (Oct 2001). "Nuclear antisense effects of neutral, anionic and cationic oligonucleotide analogs". Nucleic Acids Res. 29 (19): 3965-74. PMID 11574678. 
5. ^ Morcos, PA (2007). "Achieving targeted and quantifiable alteration of mRNA splicing with Morpholino oligos.". Biochem Biophys Res Commun 358 (2): 521-7. doi:10.1016/j.bbrc.2007.04.172. PMID 17493584. 
6. ^ Bruno IG, Jin W, Cote GJ (2004 Oct 15). "Correction of aberrant FGFR1 alternative RNA splicing through targeting of intronic regulatory elements". Hum. Mol. Genet. 13 (20): 2409-20. doi:10.1093/hmg/ddh272. PMID 15333583. (Epub August 27, 2004)
7. ^ Ken-ichi Hanada, James C. Yang (2005). "Increased Novel biochemistry: post-translational protein splicing and other lessons from the school of antigen processing". J Mol Med 83 (6): 420–428. doi:10.1007/s00109-005-0652-6 DOI 10.1007/s00109-005-0652-6. 

• Lodish, Harvey; Berk, Arnold; Zipursky, S. Lawrence; Matsudaira, Paul; Baltimore, David; Darnell, James E. (1999). Molecular Cell Biology. New York: W. H. Freeman & Co.. ISBN 0-7167-3706-X. 
• Hartl, Daniel L.; Elizabeth W. Jones (2005). Genetics: Analysis of Genes and Genomes. Jones & Bartlett Publishers. ISBN 0763715115. 

A digital object identifier (or DOI) is a standard for persistently identifying a piece of intellectual property on a digital network and associating it with related data, the metadata, in a structured extensible way. ... A digital object identifier (or DOI) is a standard for persistently identifying a piece of intellectual property on a digital network and associating it with related data, the metadata, in a structured extensible way. ... A digital object identifier (or DOI) is a standard for persistently identifying a piece of intellectual property on a digital network and associating it with related data, the metadata, in a structured extensible way. ... A digital object identifier (or DOI) is a standard for persistently identifying a piece of intellectual property on a digital network and associating it with related data, the metadata, in a structured extensible way. ... A digital object identifier (or DOI) is a standard for persistently identifying a piece of intellectual property on a digital network and associating it with related data, the metadata, in a structured extensible way. ... A digital object identifier (or DOI) is a standard for persistently identifying a piece of intellectual property on a digital network and associating it with related data, the metadata, in a structured extensible way. ...

See also

Wikimedia Commons has media related to:

Splicing

• cDNA
• Exon
• Intron
• Primary transcript
• Spliceosome
• Minor spliceosome