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Exon

February 15, 2024

For other uses, see Exon (disambiguation). Not to be confused with Axon, Exxon, Hexon, or Nexon.

An exon is any part of a gene that will form 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 RNA. Just as the entire set of genes for a species constitutes the genome, the entire set of exons constitutes the exome.

Introns are removed and exons joined in the process of RNA splicing. RNAs could be mRNA or non-coding RNA

History edit

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This definition was originally made for protein-coding transcripts that are spliced before being translated.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 other ncRNA[4] and it also was used later for RNA molecules originating from different parts of the genome that are then ligated by trans-splicing.[5]

Contribution to genomes and size distribution edit

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.[6] 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 protein coding gene. The average exon encoded 30-36 amino acids.[7] While the longest exon in the human genome is 11555 bp long, several exons have been found to be only 2 bp long.[8] A single-nucleotide exon has been reported from the Arabidopsis genome.[9] In humans, like protein coding mRNA, most non-coding RNA also contain multiple exons[10]

Structure and function edit

 
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 (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.[11] 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.[12]

Experimental approaches using exons edit

Exon trapping or 'gene trapping' is a molecular biology technique that exploits the existence of the intron-exon splicing to find new genes.[13] 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.[14] 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.

Common misuse of the term edit

Common incorrect uses of the term exon are that 'exons code for protein', or 'exons code for amino-acids' or 'exons are translated'. However, these sorts of definitions only cover protein-coding genes, and omit those exons that become part of a non-coding RNA[15] or the untranslated region of an mRNA.[16][17] Such incorrect definitions still occur in overall reputable secondary sources.[18][19]

See also edit

References edit

  1. ^ Gilbert W (February 1978). "Why genes in pieces?". Nature. 271 (5645): 501. Bibcode:1978Natur.271..501G. 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. Bibcode:1978PNAS...75..190V. doi:10.1073/pnas.75.1.190. PMC 411211. PMID 343104.
  4. ^ Khan, MR; Wellinger, RJ; Laurent, B (August 2021). "Exploring the Alternative Splicing of Long Noncoding RNAs". Trends in Genetics. 37 (8): 695–698. doi:10.1016/j.tig.2021.03.010. PMID 33892960. S2CID 233382870.
  5. ^ 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.
  6. ^ Venter J.C.; et al. (2000). "The Sequence of the Human Genome". Science. 291 (5507): 1304–51. Bibcode:2001Sci...291.1304V. doi:10.1126/science.1058040. PMID 11181995.
  7. ^ 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.
  8. ^ 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.
  9. ^ Guo Lei, Liu Chun-Ming (2015). "A single-nucleotide exon found in Arabidopsis". Scientific Reports. 5: 18087. Bibcode:2015NatSR...518087G. doi:10.1038/srep18087. PMC 4674806. PMID 26657562.
  10. ^ Derrien, T; Johnson, R; Bussotti, G; Tanzer, A; Djebali, S; Tilgner, H; Guernec, G; Martin, D; Merkel, A; Knowles, DG; Lagarde, J; Veeravalli, L; Ruan, X; Ruan, Y; Lassmann, T; Carninci, P; Brown, JB; Lipovich, L; Gonzalez, JM; Thomas, M; Davis, CA; Shiekhattar, R; Gingeras, TR; Hubbard, TJ; Notredame, C; Harrow, J; Guigó, R (September 2012). "The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression". Genome Research. 22 (9): 1775–89. doi:10.1101/gr.132159.111. PMC 3431493. PMID 22955988.
  11. ^ 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.
  12. ^ 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.
  13. ^ 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. Bibcode:1990PNAS...87.8995D. doi:10.1073/pnas.87.22.8995. PMC 55087. PMID 2247475.
  14. ^ 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.
  15. ^ Khan, MR; Wellinger, RJ; Laurent, B (August 2021). "Exploring the Alternative Splicing of Long Noncoding RNAs". Trends in Genetics. 37 (8): 695–698. doi:10.1016/j.tig.2021.03.010. PMID 33892960. S2CID 233382870.
  16. ^ Lu, J; Williams, JA; Luke, J; Zhang, F; Chu, K; Kay, MA (January 2017). "A 5' Noncoding Exon Containing Engineered Intron Enhances Transgene Expression from Recombinant AAV Vectors in vivo". Human Gene Therapy. 28 (1): 125–134. doi:10.1089/hum.2016.140. PMC 5278795. PMID 27903072.
  17. ^ Chung, BY; Simons, C; Firth, AE; Brown, CM; Hellens, RP (19 May 2006). "Effect of 5'UTR introns on gene expression in Arabidopsis thaliana". BMC Genomics. 7: 120. doi:10.1186/1471-2164-7-120. PMC 1482700. PMID 16712733.
  18. ^ . Genome.gov. Archived from the original on 2023-03-16. Retrieved 2023-03-23.
  19. ^ . www.nature.com. Scitable. Archived from the original on 2023-03-23. Retrieved 2023-03-23.

Bibliography edit

  • Zhang MQ (May 1998). "Statistical features of human exons and their flanking regions". Human Molecular Genetics. 7 (5): 919–32. doi:10.1093/hmg/7.5.919. PMID 9536098.
  • Thanaraj TA, Robinson AJ (November 2000). "Prediction of exact boundaries of exons". Brief. Bioinform. 1 (4): 343–56. doi:10.1093/bib/1.4.343. PMID 11465052.

External links edit

 
Look up exon in Wiktionary, the free dictionary.
  • Exon-intron graphic maker

February 15, 2024
exon, other, uses, disambiguation, confused, with, axon, exxon, hexon, nexon, exon, part, gene, that, will, form, part, final, mature, produced, that, gene, after, introns, have, been, removed, splicing, term, exon, refers, both, sequence, within, gene, corres. For other uses see Exon disambiguation Not to be confused with Axon Exxon Hexon or Nexon An exon is any part of a gene that will form 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 RNA Just as the entire set of genes for a species constitutes the genome the entire set of exons constitutes the exome Introns are removed and exons joined in the process of RNA splicing RNAs could be mRNA or non coding RNA Contents 1 History 2 Contribution to genomes and size distribution 3 Structure and function 4 Experimental approaches using exons 5 Common misuse of the term 6 See also 7 References 7 1 Bibliography 8 External linksHistory editThe 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 other ncRNA 4 and it also was used later for RNA molecules originating from different parts of the genome that are then ligated by trans splicing 5 Contribution to genomes and size distribution editAlthough 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 6 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 protein coding gene The average exon encoded 30 36 amino acids 7 While the longest exon in the human genome is 11555 bp long several exons have been found to be only 2 bp long 8 A single nucleotide exon has been reported from the Arabidopsis genome 9 In humans like protein coding mRNA most non coding RNA also contain multiple exons 10 Structure and function edit nbsp 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 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 11 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 12 Experimental approaches using exons editExon trapping or gene trapping is a molecular biology technique that exploits the existence of the intron exon splicing to find new genes 13 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 14 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 Common misuse of the term editCommon incorrect uses of the term exon are that exons code for protein or exons code for amino acids or exons are translated However these sorts of definitions only cover protein coding genes and omit those exons that become part of a non coding RNA 15 or the untranslated region of an mRNA 16 17 Such incorrect definitions still occur in overall reputable secondary sources 18 19 See also editDBASS3 5 Exitron Exon intron database Exon shuffling Interrupted gene Outron Twintron Untranslated region UTR References edit Gilbert W February 1978 Why genes in pieces Nature 271 5645 501 Bibcode 1978Natur 271 501G doi 10 1038 271501a0 PMID 622185 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 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 Bibcode 1978PNAS 75 190V doi 10 1073 pnas 75 1 190 PMC 411211 PMID 343104 Khan MR Wellinger RJ Laurent B August 2021 Exploring the Alternative Splicing of Long Noncoding RNAs Trends in Genetics 37 8 695 698 doi 10 1016 j tig 2021 03 010 PMID 33892960 S2CID 233382870 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 Venter J C et al 2000 The Sequence of the Human Genome Science 291 5507 1304 51 Bibcode 2001Sci 291 1304V doi 10 1126 science 1058040 PMID 11181995 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 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 Guo Lei Liu Chun Ming 2015 A single nucleotide exon found inArabidopsis Scientific Reports 5 18087 Bibcode 2015NatSR 518087G doi 10 1038 srep18087 PMC 4674806 PMID 26657562 Derrien T Johnson R Bussotti G Tanzer A Djebali S Tilgner H Guernec G Martin D Merkel A Knowles DG Lagarde J Veeravalli L Ruan X Ruan Y Lassmann T Carninci P Brown JB Lipovich L Gonzalez JM Thomas M Davis CA Shiekhattar R Gingeras TR Hubbard TJ Notredame C Harrow J Guigo R September 2012 The GENCODE v7 catalog of human long noncoding RNAs analysis of their gene structure evolution and expression Genome Research 22 9 1775 89 doi 10 1101 gr 132159 111 PMC 3431493 PMID 22955988 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 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 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 Bibcode 1990PNAS 87 8995D doi 10 1073 pnas 87 22 8995 PMC 55087 PMID 2247475 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 Khan MR Wellinger RJ Laurent B August 2021 Exploring the Alternative Splicing of Long Noncoding RNAs Trends in Genetics 37 8 695 698 doi 10 1016 j tig 2021 03 010 PMID 33892960 S2CID 233382870 Lu J Williams JA Luke J Zhang F Chu K Kay MA January 2017 A 5 Noncoding Exon Containing Engineered Intron Enhances Transgene Expression from Recombinant AAV Vectors in vivo Human Gene Therapy 28 1 125 134 doi 10 1089 hum 2016 140 PMC 5278795 PMID 27903072 Chung BY Simons C Firth AE Brown CM Hellens RP 19 May 2006 Effect of 5 UTR introns on gene expression in Arabidopsis thaliana BMC Genomics 7 120 doi 10 1186 1471 2164 7 120 PMC 1482700 PMID 16712733 Exon Genome gov Archived from the original on 2023 03 16 Retrieved 2023 03 23 Exon www nature com Scitable Archived from the original on 2023 03 23 Retrieved 2023 03 23 Bibliography edit Zhang MQ May 1998 Statistical features of human exons and their flanking regions Human Molecular Genetics 7 5 919 32 doi 10 1093 hmg 7 5 919 PMID 9536098 Thanaraj TA Robinson AJ November 2000 Prediction of exact boundaries of exons Brief Bioinform 1 4 343 56 doi 10 1093 bib 1 4 343 PMID 11465052 External links edit nbsp Look up exon in Wiktionary the free dictionary Exon intron graphic maker Retrieved from https en wikipedia org w index php title Exon amp oldid 1193000910, wikipedia, wiki, book, books, library,

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