Transposon clusters as substrates for aberrant splice-site activation
Transposon clusters as substrates for aberrant splice-site activation
Transposed elements (TEs) have dramatically shaped evolution of the exon-intron structure and significantly contributed to morbidity, but how recent TE invasions into older TEs cooperate in generating new coding sequences is poorly understood. Employing an updated repository of new exon-intron boundaries induced by pathogenic mutations, termed DBASS, here we identify novel TE clusters that facilitated exon selection. To explore the extent to which such TE exons maintain RNA secondary structure of their progenitors, we carried out structural studies with a composite exon that was derived from a long terminal repeat (LTR78) and AluJ and was activated by a C > T mutation optimizing the 5ʹ splice site. Using a combination of SHAPE, DMS and enzymatic probing, we show that the disease-causing mutation disrupted a conserved AluJ stem that evolved from helix 3.3 (or 5b) of 7SL RNA, liberating a primordial GC 5ʹ splice site from the paired conformation for interactions with the spliceosome. The mutation also reduced flexibility of conserved residues in adjacent exon-derived loops of the central Alu hairpin, revealing a cross-talk between traditional and auxilliary splicing motifs that evolved from opposite termini of 7SL RNA and were approximated by Watson-Crick base-pairing already in organisms without spliceosomal introns. We also identify existing Alu exons activated by the same RNA rearrangement. Collectively, these results provide valuable TE exon models for studying formation and kinetics of pre-mRNA building blocks required for splice-site selection and will be useful for fine-tuning auxilliary splicing motifs and exon and intron size constraints that govern aberrant splice-site activation.
DBASS3, DBASS5, RNA processing, RNA secondary structure, Transposed element, genetic disease, lariat branch point, mutation, splice site
354-367
Alvarez, Maria Elena Vilar
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Chivers, Martin
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Borovska, Ivana
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Monger, Steven
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Giannoulatou, Eleni
58e18e42-a756-406f-9d70-33a6b53a3835
Kralovicova, Jana
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Vorechovsky, Igor
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Alvarez, Maria Elena Vilar
eeadb5fa-f523-40be-85fa-825612691f98
Chivers, Martin
639fadfe-5293-45eb-8c38-22cbbf3f4b68
Borovska, Ivana
d2d23654-81da-45a7-8a93-3fc55826e4bc
Monger, Steven
1b801d95-9bce-47c7-b448-e71ed8835fe9
Giannoulatou, Eleni
58e18e42-a756-406f-9d70-33a6b53a3835
Kralovicova, Jana
b3e0c1e7-05ed-445d-b3d9-ace11e3b4878
Vorechovsky, Igor
7245de2f-8c9b-4034-8935-9a451d9b682e
Alvarez, Maria Elena Vilar, Chivers, Martin, Borovska, Ivana, Monger, Steven, Giannoulatou, Eleni, Kralovicova, Jana and Vorechovsky, Igor
(2020)
Transposon clusters as substrates for aberrant splice-site activation.
RNA Biology, 18 (3), .
(doi:10.1080/15476286.2020.1805909).
Abstract
Transposed elements (TEs) have dramatically shaped evolution of the exon-intron structure and significantly contributed to morbidity, but how recent TE invasions into older TEs cooperate in generating new coding sequences is poorly understood. Employing an updated repository of new exon-intron boundaries induced by pathogenic mutations, termed DBASS, here we identify novel TE clusters that facilitated exon selection. To explore the extent to which such TE exons maintain RNA secondary structure of their progenitors, we carried out structural studies with a composite exon that was derived from a long terminal repeat (LTR78) and AluJ and was activated by a C > T mutation optimizing the 5ʹ splice site. Using a combination of SHAPE, DMS and enzymatic probing, we show that the disease-causing mutation disrupted a conserved AluJ stem that evolved from helix 3.3 (or 5b) of 7SL RNA, liberating a primordial GC 5ʹ splice site from the paired conformation for interactions with the spliceosome. The mutation also reduced flexibility of conserved residues in adjacent exon-derived loops of the central Alu hairpin, revealing a cross-talk between traditional and auxilliary splicing motifs that evolved from opposite termini of 7SL RNA and were approximated by Watson-Crick base-pairing already in organisms without spliceosomal introns. We also identify existing Alu exons activated by the same RNA rearrangement. Collectively, these results provide valuable TE exon models for studying formation and kinetics of pre-mRNA building blocks required for splice-site selection and will be useful for fine-tuning auxilliary splicing motifs and exon and intron size constraints that govern aberrant splice-site activation.
Text
2020 RNA Biol by Alvarez et al
- Accepted Manuscript
Text
2020 RNA Biol - Transposon clusters as substrates for aberrant splice site activation
- Version of Record
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Accepted/In Press date: 1 August 2020
e-pub ahead of print date: 23 September 2020
Keywords:
DBASS3, DBASS5, RNA processing, RNA secondary structure, Transposed element, genetic disease, lariat branch point, mutation, splice site
Identifiers
Local EPrints ID: 444241
URI: http://eprints.soton.ac.uk/id/eprint/444241
ISSN: 1547-6286
PURE UUID: ad3f1ea3-4d3f-4479-bbaa-2c975e7f9d92
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Date deposited: 02 Oct 2020 16:31
Last modified: 17 Mar 2024 05:48
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Contributors
Author:
Maria Elena Vilar Alvarez
Author:
Martin Chivers
Author:
Ivana Borovska
Author:
Steven Monger
Author:
Eleni Giannoulatou
Author:
Jana Kralovicova
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