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Genome-Wide Analysis of PAPS1-Dependent Polyadenylation Identifies Novel Roles for Functionally Specialized Poly(A) Polymerases in Arabidopsis thaliana

2015-08-25Journal article Open access
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dc.contributor.authorKappel, Christian
dc.contributor.authorTrost, Gerda
dc.contributor.authorCzesnick, Hjördis
dc.contributor.authorRamming, Anna
dc.contributor.authorKolbe, Benjamin
dc.contributor.authorVi, Son Lang
dc.contributor.authorBispo, Cláudia
dc.contributor.authorBecker, Jörg D.
dc.contributor.authorde Moor, Cornelia
dc.contributor.authorLenhard, Michael
dc.date.accessioned2015-10-14T12:12:21Z
dc.date.available2015-10-14T12:12:21Z
dc.date.issued2015-08-25
dc.description.abstractThe poly(A) tail at 3' ends of eukaryotic mRNAs promotes their nuclear export, stability and translational efficiency, and changes in its length can strongly impact gene expression. The Arabidopsis thaliana genome encodes three canonical nuclear poly(A) polymerases, PAPS1, PAPS2 and PAPS4. As shown by their different mutant phenotypes, these three isoforms are functionally specialized, with PAPS1 modifying organ growth and suppressing a constitutive immune response. However, the molecular basis of this specialization is largely unknown. Here, we have estimated poly(A)-tail lengths on a transcriptome-wide scale in wild-type and paps1 mutants. This identified categories of genes as particularly strongly affected in paps1 mutants, including genes encoding ribosomal proteins, cell-division factors and major carbohydrate-metabolic proteins. We experimentally verified two novel functions of PAPS1 in ribosome biogenesis and redox homoeostasis that were predicted based on the analysis of poly(A)-tail length changes in paps1 mutants. When overlaying the PAPS1-dependent effects observed here with coexpression analysis based on independent microarray data, the two clusters of transcripts that are most closely coexpressed with PAPS1 show the strongest change in poly(A)-tail length and transcript abundance in paps1 mutants in our analysis. This suggests that their coexpression reflects at least partly the preferential polyadenylation of these transcripts by PAPS1 versus the other two poly(A)-polymerase isoforms. Thus, transcriptome-wide analysis of poly(A)-tail lengths identifies novel biological functions and likely target transcripts for polyadenylation by PAPS1. Data integration with large-scale co-expression data suggests that changes in the relative activities of the isoforms are used as an endogenous mechanism to co-ordinately modulate plant gene expression.pt_PT
dc.identifier10.1371/journal.pgen.1005474
dc.identifier.citationKappel C, Trost G, Czesnick H, Ramming A, Kolbe B, Vi SL, et al. (2015) Genome-Wide Analysis of PAPS1-Dependent Polyadenylation Identifies Novel Roles for Functionally Specialized Poly(A) Polymerases in Arabidopsis thaliana. PLoS Genet 11(8): e1005474. doi:10.1371/journal. pgen.1005474pt_PT
dc.identifier.doi10.1371/journal.pgen.1005474
dc.identifier.urihttp://hdl.handle.net/10400.7/399
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherPLOSpt_PT
dc.relation.publisherversionhttp://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005474pt_PT
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/pt_PT
dc.subjectGenome-Widept_PT
dc.subjectArabidopsispt_PT
dc.titleGenome-Wide Analysis of PAPS1-Dependent Polyadenylation Identifies Novel Roles for Functionally Specialized Poly(A) Polymerases in Arabidopsis thalianapt_PT
dc.typejournal article
dspace.entity.typePublication
oaire.citation.endPage30pt_PT
oaire.citation.issue8pt_PT
oaire.citation.startPage1pt_PT
oaire.citation.titlePLOS Geneticspt_PT
oaire.citation.volume11pt_PT
rcaap.rightsopenAccesspt_PT
rcaap.typearticlept_PT

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