Exon

An exon is any part of a gene that will encode a part of the final mature RNA produced by that gene after introns have been removed by RNA splicing. The term exon refers to both the DNA sequence within a gene and to the corresponding sequence in RNA transcripts. In RNA splicing, introns are removed and exons are covalently joined to one another as part of generating the mature messenger RNA. Just as the entire set of genes for a species constitutes the genome, the entire set of exons constitutes the exome.

Not to be confused with axon, the projection of a neuron, or Exxon, a brand of fuel sold by ExxonMobil, or hexon, a viral protein.
For other uses, see Exon (disambiguation).
Introns are removed and exons joined together in the process of RNA splicing.

History

The term exon derives from the expressed region and was coined by American biochemist Walter Gilbert in 1978: "The notion of the cistron… must be replaced by that of a transcription unit containing regions which will be lost from the mature messenger – which I suggest we call introns (for intragenic regions) – alternating with regions which will be expressed – exons."[1]

This definition was originally made for protein-coding transcripts that are spliced before being translated. The term later came to include sequences removed from rRNA[2] and tRNA,[3] and it also was used later for RNA molecules originating from different parts of the genome that are then ligated by trans-splicing.[4]

Contribution to genomes and size distribution

Although unicellular eukaryotes such as yeast have either no introns or very few, metazoans and especially vertebrate genomes have a large fraction of non-coding DNA. For instance, in the human genome only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA.[5] This can provide a practical advantage in omics-aided health care (such as precision medicine) because it makes commercialized whole exome sequencing a smaller and less expensive challenge than commercialized whole genome sequencing. The large variation in genome size and C-value across life forms has posed an interesting challenge called the C-value enigma.

Across all eukaryotic genes in GenBank, there were (in 2002), on average, 5.48 exons per gene. The average exon encoded 30-36 amino acids.[6] While the longest exon in the human genome is 11555 bp long, several exons have been found to be only 2 bp long.[7] A single-nucleotide exon has been reported from the Arabidopsis genome.[8]

Structure and function
Exons in a messenger RNA precursor (pre-mRNA). Exons can include both sequences that code for amino acids (red) and untranslated sequences (grey). Introns — those parts of the pre-mRNA that are not in the mRNA — (blue) are removed, and the exons are joined together (spliced) to form the final functional mRNA. The 5′ and 3′ ends of the mRNA are marked to differentiate the two untranslated regions (grey).

In protein-coding genes, the exons include both the protein-coding sequence and the 5′- and 3′-untranslated regions (UTR). Often the first exon includes both the 5′-UTR and the first part of the coding sequence, but exons containing only regions of 5′-UTR or (more rarely) 3′-UTR occur in some genes, i.e. the UTRs may contain introns.[9] Some non-coding RNA transcripts also have exons and introns.

Mature mRNAs originating from the same gene need not include the same exons, since different introns in the pre-mRNA can be removed by the process of alternative splicing.

Exonization is the creation of a new exon, as a result of mutations in introns.[10]

Experimental approaches using exons

Exon trapping or 'gene trapping' is a molecular biology technique that exploits the existence of the intron-exon splicing to find new genes.[11] The first exon of a 'trapped' gene splices into the exon that is contained in the insertional DNA. This new exon contains the ORF for a reporter gene that can now be expressed using the enhancers that control the target gene. A scientist knows that a new gene has been trapped when the reporter gene is expressed.

Splicing can be experimentally modified so that targeted exons are excluded from mature mRNA transcripts by blocking the access of splice-directing small nuclear ribonucleoprotein particles (snRNPs) to pre-mRNA using Morpholino antisense oligos.[12] This has become a standard technique in developmental biology. Morpholino oligos can also be targeted to prevent molecules that regulate splicing (e.g. splice enhancers, splice suppressors) from binding to pre-mRNA, altering patterns of splicing.

gollark: Or Great Information Transfer.
gollark: Git stands for GIT Is Tremendous.
gollark: The stages of git clone are: Receive a "pack" file of all the objects in the repo database Create an index file for the received pack Check out the head revision (for a non-bare repo, obviously)"Resolving deltas" is the message shown for the second stage, indexing the pack file ("git index-pack").Pack files do not have the actual object IDs in them, only the object content. So to determine what the object IDs are, git has to do a decompress+SHA1 of each object in the pack to produce the object ID, which is then written into the index file.An object in a pack file may be stored as a delta i.e. a sequence of changes to make to some other object. In this case, git needs to retrieve the base object, apply the commands and SHA1 the result. The base object itself might have to be derived by applying a sequence of delta commands. (Even though in the case of a clone, the base object will have been encountered already, there is a limit to how many manufactured objects are cached in memory).In summary, the "resolving deltas" stage involves decompressing and checksumming the entire repo database, which not surprisingly takes quite a long time. Presumably decompressing and calculating SHA1s actually takes more time than applying the delta commands.In the case of a subsequent fetch, the received pack file may contain references (as delta object bases) to other objects that the receiving git is expected to already have. In this case, the receiving git actually rewrites the received pack file to include any such referenced objects, so that any stored pack file is self-sufficient. This might be where the message "resolving deltas" originated.
gollark: UPDATE: this is wrong.
gollark: > Git uses delta encoding to store some of the objects in packfiles. However, you don't want to have to play back every single change ever on a given file in order to get the current version, so Git also has occasional snapshots of the file contents stored as well. "Resolving deltas" is the step that deals with making sure all of that stays consistent.

See also

References
  1. Gilbert W (February 1978). "Why genes in pieces?". Nature. 271 (5645): 501. doi:10.1038/271501a0. PMID 622185.
  2. Kister KP, Eckert WA (March 1987). "Characterization of an authentic intermediate in the self-splicing process of ribosomal precursor RNA in macronuclei of Tetrahymena thermophila". Nucleic Acids Research. 15 (5): 1905–20. doi:10.1093/nar/15.5.1905. PMC 340607. PMID 3645543.
  3. Valenzuela P, Venegas A, Weinberg F, Bishop R, Rutter WJ (January 1978). "Structure of yeast phenylalanine-tRNA genes: an intervening DNA segment within the region coding for the tRNA". Proceedings of the National Academy of Sciences of the United States of America. 75 (1): 190–4. doi:10.1073/pnas.75.1.190. PMC 411211. PMID 343104.
  4. Liu AY, Van der Ploeg LH, Rijsewijk FA, Borst P (June 1983). "The transposition unit of variant surface glycoprotein gene 118 of Trypanosoma brucei. Presence of repeated elements at its border and absence of promoter-associated sequences". Journal of Molecular Biology. 167 (1): 57–75. doi:10.1016/S0022-2836(83)80034-5. PMID 6306255.
  5. Venter J.C.; et al. (2000). "The Sequence of the Human Genome". Science. 291 (5507): 1304–51. doi:10.1126/science.1058040. PMID 11181995.
  6. Sakharkar M, Passetti F, de Souza JE, Long M, de Souza SJ (2002). "ExInt: an Exon Intron Database". Nucleic Acids Res. 30 (1): 191–4. doi:10.1093/nar/30.1.191. PMC 99089. PMID 11752290.
  7. Sakharkar M.K.; Chow VT; Kangueane P. (2004). "Distributions of exons and introns in the human genome". In Silico Biol. 4 (4): 387–93. PMID 15217358.
  8. Guo Lei, Liu Chun-Ming (2015). "A single-nucleotide exon found in Arabidopsis". Scientific Reports. 5: 18087. doi:10.1038/srep18087. PMC 4674806. PMID 26657562.
  9. Bicknell, AA (December 2012). "Introns in UTRs: Why we should stop ignoring them". BioEssays. 34 (12): 1025–1034. doi:10.1002/bies.201200073. PMID 23108796. S2CID 5808466.
  10. Sorek R (October 2007). "The birth of new exons: mechanisms and evolutionary consequences". RNA. 13 (10): 1603–8. doi:10.1261/rna.682507. PMC 1986822. PMID 17709368.
  11. Duyk G. M; Kim S. W.; Myers R. M; Cox D. R (1990). "Exon Trapping: a Genetic Screen to Identify Candidate Transcribed Sequences in Cloned Mammalian Genomic DNA". Proceedings of the National Academy of Sciences. 87 (22): 8995–8999. doi:10.1073/pnas.87.22.8995. PMC 55087. PMID 2247475.
  12. Morcos PA (June 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.

General references
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