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Genome-wide analysis of PAPS1-dependent polyadenylation identifies novel roles for functionally specialized poly(A) polymerases in Arabidopsis thaliana

Kappel, Christian; Trost, Gerda; Cseznick, Hjordis; Ramming, Anna; Kolbe, Benjamin; Vi, Son Lang; Becker, Jörg D.; de Moor, Cornelia H.; Lenhard, Michael


Christian Kappel

Gerda Trost

Hjordis Cseznick

Anna Ramming

Benjamin Kolbe

Son Lang Vi

Jörg D. Becker

Cornelia H. de Moor

Michael Lenhard


The 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.


Kappel, C., Trost, G., Cseznick, H., Ramming, A., Kolbe, B., Vi, S. L., …Lenhard, M. (2015). Genome-wide analysis of PAPS1-dependent polyadenylation identifies novel roles for functionally specialized poly(A) polymerases in Arabidopsis thaliana. PLoS Genetics, 11(8), doi:10.1371/journal.pgen.1005474

Journal Article Type Article
Acceptance Date Jul 28, 2015
Publication Date Aug 25, 2015
Deposit Date Oct 13, 2016
Publicly Available Date Oct 13, 2016
Journal PLoS Genetics
Print ISSN 1553-7390
Electronic ISSN 1553-7404
Publisher Public Library of Science
Peer Reviewed Peer Reviewed
Volume 11
Issue 8
Article Number e1005474
Public URL
Publisher URL
Copyright Statement Copyright information regarding this work can be found at the following address:


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