The poly(A) polymerase PAPS1 interacts with the RNA‐directed DNA‐methylation pathway in sporophyte and pollen development

• Published in: The Plant journal : for cell and molecular biology Vol. 99; no. 4; pp. 655 - 672
• Main Authors: Zhang, Yunming, Ramming, Anna, Heinke, Lisa, Altschmied, Lothar, Slotkin, R. Keith, Becker, Jörg D., Kappel, Christian, Lenhard, Michael
• Format: Journal Article
• Language: English
• Published: England Blackwell Publishing Ltd 01.08.2019
• Subjects: Arabidopsis thaliana; Deoxyribonucleic acid; Depletion; Disruption; DNA; DNA methylation; DNA-directed RNA polymerase; Fluorescence; Gene expression; Gene sequencing; gynoecium development; Labeling; miRNA; mRNA processing; Mutation; Nucleotides; Phenotypes; Pollen; pollen development; poly(A) polymerase; Polyadenine; Polyadenylation; Polynucleotide adenylyltransferase; Ribonucleic acid; RNA; RNA polymerase; RNA-mediated interference; RNA‐directed DNA methylation; siRNA; siRNAs; transposable elements; Transposons; Yeast; Yeasts; Arabidopsis thaliana; pollen development; poly(A) polymerase; gynoecium development; RNA-directed DNA methylation; transposable elements; siRNAs
• DOI: 10.1111/tpj.14348
• ISSN: 0960-7412

Summary RNA‐based processes play key roles in the regulation of eukaryotic gene expression. This includes both the processing of pre‐mRNAs into mature mRNAs ready for translation and RNA‐based silencing processes, such as RNA‐directed DNA methylation (RdDM). Polyadenylation of pre‐mRNAs is one important step in their processing and is carried out by three functionally specialized canonical nuclear poly(A) polymerases in Arabidopsis thaliana. Null mutations in one of these, termed PAPS1, result in a male gametophytic defect. Using a fluorescence‐labelling strategy, we have characterized this defect in more detail using RNA and small‐RNA sequencing. In addition to global defects in the expression of pollen‐differentiation genes, paps1 null‐mutant pollen shows a strong overaccumulation of transposable element (TE) transcripts, yet a depletion of 21‐ and particularly 24‐nucleotide‐long short interfering RNAs (siRNAs) and microRNAs (miRNAs) targeting the corresponding TEs. Double‐mutant analyses support a specific functional interaction between PAPS1 and components of the RdDM pathway, as evident from strong synergistic phenotypes in mutant combinations involving paps1, but not paps2 paps4, mutations. In particular, the double‐mutant of paps1 and rna‐dependent rna polymerase 6 (rdr6) shows a synergistic developmental phenotype disrupting the formation of the transmitting tract in the female gynoecium. Thus, our findings in A. thaliana uncover a potentially general link between canonical poly(A) polymerases as components of mRNA processing and RdDM, reflecting an analogous interaction in fission yeast. Significance Statement This work identifies a functional connection between mRNA processing and RNA‐directed DNA methylation, involving a specific poly(A) polymerase in A. thaliana.