Abstract
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.
Highlights
The poly(A) tail is an essential modification found at the 3’ ends of virtually all eukaryotic mRNAs [1,2,3]
The poly(A) tail of eukaryotic mRNAs promotes export from the nucleus, translation in the cytoplasm and stability of the mRNA, and changes in poly(A)-tail length can strongly impact on gene expression
By overlaying our results with information about genome-wide coexpression, we demonstrate that genes co-expressed with PAPS1 are the most strongly affected in terms of poly(A)-tail length and total-abundance changes in the paps1 mutants
Summary
The poly(A) tail is an essential modification found at the 3’ ends of virtually all eukaryotic mRNAs [1,2,3]. The poly(A) tail stimulates translation of the mRNA by promoting a close contact between the 3’ and 5’ ends of the mRNA and promotes efficient translational initiation [7,8] This is mediated by interactions between the cytoplasmic poly(A)-binding protein PABPC bound to the poly(A) tail and translation initiation factors, in particular eIF4G, bound to the 5’ cap. Most mRNAs in yeast and mammals are believed to start out with a rather uniform length of the poly(A) tail of around 70–80 and 250 As, respectively, and deadenylation occurs with transcript-specific rates [12,15]. This rate of deadenylation is a major determinant of transcript half-life. Large-scale studies of poly(A)-tail length in mammalian cells have identified a number of very stable transcripts with only very short poly(A) tails [16,17], likely reflecting a high stability of the oligoadenylated state
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
