Enter exitrons

doi:10.1186/s13059-015-0704-3

Comment

. 2015 Jul 7;16(1):136.

doi: 10.1186/s13059-015-0704-3.

Enter exitrons

Dorothee Staiger¹, Gordon G Simpson^{2

3}

Affiliations

¹ Molecular Cell Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany. dorothee.staiger@uni-bielefeld.de.
² Division of Plant Sciences, Life Sciences, University of Dundee at The James Hutton Institute, Invergowrie, DD2 5DA, UK. g.g.simpson@dundee.ac.uk.
³ Cell & Molecular Sciences, The James Hutton Institute, Invergowrie, DD2 5DA, UK. g.g.simpson@dundee.ac.uk.

PMID: 26149172
PMCID: PMC4494720
DOI: 10.1186/s13059-015-0704-3

Comment

Enter exitrons

Dorothee Staiger et al. Genome Biol. 2015.

. 2015 Jul 7;16(1):136.

doi: 10.1186/s13059-015-0704-3.

Authors

Dorothee Staiger¹, Gordon G Simpson^{2

3}

Affiliations

¹ Molecular Cell Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany. dorothee.staiger@uni-bielefeld.de.
² Division of Plant Sciences, Life Sciences, University of Dundee at The James Hutton Institute, Invergowrie, DD2 5DA, UK. g.g.simpson@dundee.ac.uk.
³ Cell & Molecular Sciences, The James Hutton Institute, Invergowrie, DD2 5DA, UK. g.g.simpson@dundee.ac.uk.

PMID: 26149172
PMCID: PMC4494720
DOI: 10.1186/s13059-015-0704-3

Abstract

Exitrons are exon-like introns located within protein-coding exons. Removal or retention of exitrons through alternative splicing increases proteome complexity and thus adds to phenotypic diversity.

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Comment on

Unmasking alternative splicing inside protein-coding exons defines exitrons and their role in proteome plasticity.
Marquez Y, Höpfler M, Ayatollahi Z, Barta A, Kalyna M. Marquez Y, et al. Genome Res. 2015 Jul;25(7):995-1007. doi: 10.1101/gr.186585.114. Epub 2015 May 1. Genome Res. 2015. PMID: 25934563 Free PMC article.

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The Evolutionary Basis of Translational Accuracy in Plants.
Camiolo S, Sablok G, Porceddu A. Camiolo S, et al. G3 (Bethesda). 2017 Jul 5;7(7):2363-2373. doi: 10.1534/g3.117.040626. G3 (Bethesda). 2017. PMID: 28533334 Free PMC article.
At-RS31 orchestrates hierarchical cross-regulation of splicing factors and integrates alternative splicing with TOR-ABA pathways.
Köster T, Venhuizen P, Lewinski M, Petrillo E, Marquez Y, Fuchs A, Ray D, Nimeth BA, Riegler S, Franzmeier S, Zheng H, Hughes T, Morris Q, Barta A, Staiger D, Kalyna M. Köster T, et al. bioRxiv [Preprint]. 2024 Dec 7:2024.12.04.626797. doi: 10.1101/2024.12.04.626797. bioRxiv. 2024. Update in: New Phytol. 2025 Jul;247(2):738-759. doi: 10.1111/nph.70221. PMID: 39677721 Free PMC article. Updated. Preprint.
Does co-transcriptional regulation of alternative splicing mediate plant stress responses?
Jabre I, Reddy ASN, Kalyna M, Chaudhary S, Khokhar W, Byrne LJ, Wilson CM, Syed NH. Jabre I, et al. Nucleic Acids Res. 2019 Apr 8;47(6):2716-2726. doi: 10.1093/nar/gkz121. Nucleic Acids Res. 2019. PMID: 30793202 Free PMC article. Review.
Alternative splicing of helicase-like transcription factor (Hltf): Intron retention-dependent activation of immune tolerance at the feto-maternal interface.
Kaur G, Helmer RA, Smith LA, Martinez-Zaguilan R, Dufour JM, Chilton BS. Kaur G, et al. PLoS One. 2018 Jul 5;13(7):e0200211. doi: 10.1371/journal.pone.0200211. eCollection 2018. PLoS One. 2018. PMID: 29975766 Free PMC article.
The integral spliceosomal component CWC15 is required for development in Arabidopsis.
Slane D, Lee CH, Kolb M, Dent C, Miao Y, Franz-Wachtel M, Lau S, Maček B, Balasubramanian S, Bayer M, Jürgens G. Slane D, et al. Sci Rep. 2020 Aug 7;10(1):13336. doi: 10.1038/s41598-020-70324-3. Sci Rep. 2020. PMID: 32770129 Free PMC article.

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References

1. Braunschweig U, Gueroussov S, Plocik AM, Graveley BR, Blencowe BJ. Dynamic integration of splicing within gene regulatory pathways. Cell. 2013;152:1252–1869. doi: 10.1016/j.cell.2013.02.034. - DOI - PMC - PubMed
1. Staiger D, Brown JWS. Alternative splicing at the intersection of biological timing, development, and stress responses. Plant Cell. 2013;25:3640–3656. doi: 10.1105/tpc.113.113803. - DOI - PMC - PubMed
1. Marquez Y, Höpfler M, Ayatollahi Z, Barta A, Kalyna M. Unmasking alternative splicing inside protein-coding exons defines exitrons and their role in proteome plasticity. Genome Res. 2015 - PMC - PubMed
1. Ner-Gaon H, Halachmi R, Savaldi-Goldstein S, Rubin E, Ophir R, Fluhr R. Intron retention is a major phenomenon in alternative splicing in Arabidopsis. Plant J. 2004;39:877–885. doi: 10.1111/j.1365-313X.2004.02172.x. - DOI - PubMed
1. Braunschweig U, Barbosa-Morais NL, Pan Q, Nachman EN, Alipanahi B, Gonatopoulos-Pournatzis T, et al. Widespread intron retention in mammals functionally tunes transcriptomes. Genome Res. 2014;24:1774–1786. doi: 10.1101/gr.177790.114. - DOI - PMC - PubMed

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[1] Braunschweig U, Gueroussov S, Plocik AM, Graveley BR, Blencowe BJ. Dynamic integration of splicing within gene regulatory pathways. Cell. 2013;152:1252–1869. doi: 10.1016/j.cell.2013.02.034. - DOI - PMC - PubMed

[2] Braunschweig U, Gueroussov S, Plocik AM, Graveley BR, Blencowe BJ. Dynamic integration of splicing within gene regulatory pathways. Cell. 2013;152:1252–1869. doi: 10.1016/j.cell.2013.02.034. - DOI - PMC - PubMed

[3] Staiger D, Brown JWS. Alternative splicing at the intersection of biological timing, development, and stress responses. Plant Cell. 2013;25:3640–3656. doi: 10.1105/tpc.113.113803. - DOI - PMC - PubMed

[4] Staiger D, Brown JWS. Alternative splicing at the intersection of biological timing, development, and stress responses. Plant Cell. 2013;25:3640–3656. doi: 10.1105/tpc.113.113803. - DOI - PMC - PubMed

[5] Marquez Y, Höpfler M, Ayatollahi Z, Barta A, Kalyna M. Unmasking alternative splicing inside protein-coding exons defines exitrons and their role in proteome plasticity. Genome Res. 2015 - PMC - PubMed

[6] Marquez Y, Höpfler M, Ayatollahi Z, Barta A, Kalyna M. Unmasking alternative splicing inside protein-coding exons defines exitrons and their role in proteome plasticity. Genome Res. 2015 - PMC - PubMed

[7] Ner-Gaon H, Halachmi R, Savaldi-Goldstein S, Rubin E, Ophir R, Fluhr R. Intron retention is a major phenomenon in alternative splicing in Arabidopsis. Plant J. 2004;39:877–885. doi: 10.1111/j.1365-313X.2004.02172.x. - DOI - PubMed

[8] Ner-Gaon H, Halachmi R, Savaldi-Goldstein S, Rubin E, Ophir R, Fluhr R. Intron retention is a major phenomenon in alternative splicing in Arabidopsis. Plant J. 2004;39:877–885. doi: 10.1111/j.1365-313X.2004.02172.x. - DOI - PubMed

[9] Braunschweig U, Barbosa-Morais NL, Pan Q, Nachman EN, Alipanahi B, Gonatopoulos-Pournatzis T, et al. Widespread intron retention in mammals functionally tunes transcriptomes. Genome Res. 2014;24:1774–1786. doi: 10.1101/gr.177790.114. - DOI - PMC - PubMed

[10] Braunschweig U, Barbosa-Morais NL, Pan Q, Nachman EN, Alipanahi B, Gonatopoulos-Pournatzis T, et al. Widespread intron retention in mammals functionally tunes transcriptomes. Genome Res. 2014;24:1774–1786. doi: 10.1101/gr.177790.114. - DOI - PMC - PubMed

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Enter exitrons

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