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Suppression of the Arabidopsis cinnamoyl-CoA reductase 1-6 intronic T-DNA mutation by epigenetic modification.
Wouters, Marlies; Bastiaanse, Héloïse; Rombauts, Stephane; de Vries, Lisanne; De Pooter, Tim; Strazisar, Mojca; Neutelings, Godfrey; Vanholme, Ruben; Boerjan, Wout.
  • Wouters M; VIB Center for Plants Systems Biology, VIB, 9052 Ghent, Belgium.
  • Bastiaanse H; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.
  • Rombauts S; VIB Center for Plants Systems Biology, VIB, 9052 Ghent, Belgium.
  • de Vries L; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.
  • De Pooter T; VIB Center for Plants Systems Biology, VIB, 9052 Ghent, Belgium.
  • Strazisar M; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.
  • Neutelings G; VIB Center for Plants Systems Biology, VIB, 9052 Ghent, Belgium.
  • Vanholme R; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.
  • Boerjan W; Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, 2610 Antwerp, Belgium.
Plant Physiol ; 192(4): 3001-3016, 2023 08 03.
Article en En | MEDLINE | ID: mdl-37139862
ABSTRACT
Arabidopsis (Arabidopsis thaliana) transfer DNA (T-DNA) insertion collections are popular resources for fundamental plant research. Cinnamoyl-CoA reductase 1 (CCR1) catalyzes an essential step in the biosynthesis of the cell wall polymer lignin. Accordingly, the intronic T-DNA insertion mutant ccr1-6 has reduced lignin levels and shows a stunted growth phenotype. Here, we report restoration of the ccr1-6 mutant phenotype and CCR1 expression levels after a genetic cross with a UDP-glucosyltransferase 72e1 (ugt72e1),-e2,-e3 T-DNA mutant. We discovered that the phenotypic recovery was not dependent on the UGT72E family loss of function but due to an epigenetic phenomenon called trans T-DNA suppression. Via trans T-DNA suppression, the gene function of an intronic T-DNA mutant was restored after the introduction of an additional T-DNA sharing identical sequences, leading to heterochromatinization and splicing out of the T-DNA-containing intron. Consequently, the suppressed ccr1-6 allele was named epiccr1-6. Long-read sequencing revealed that epiccr1-6, not ccr1-6, carries dense cytosine methylation over the full length of the T-DNA. We showed that the SAIL T-DNA in the UGT72E3 locus could trigger the trans T-DNA suppression of the GABI-Kat T-DNA in the CCR1 locus. Furthermore, we scanned the literature for other potential cases of trans T-DNA suppression in Arabidopsis and found that 22% of the publications matching our query report on double or higher-order T-DNA mutants that meet the minimal requirements for trans T-DNA suppression. These combined observations indicate that intronic T-DNA mutants need to be used with caution since methylation of intronic T-DNA might derepress gene expression and can thereby confound results.
Asunto(s)

Texto completo: 1 Banco de datos: MEDLINE Asunto principal: Arabidopsis / Proteínas de Arabidopsis Idioma: En Año: 2023 Tipo del documento: Article

Texto completo: 1 Banco de datos: MEDLINE Asunto principal: Arabidopsis / Proteínas de Arabidopsis Idioma: En Año: 2023 Tipo del documento: Article