Genome-Wide Variation in Polyadenylation Site Usage and Association Mapping in Arabidopsis MAGIC Founders

Polyadenylation, the addition of 3’ poly(A) tails to mRNAs, plays an important role in regulating eukaryotic gene expression. The use of alternative poly(A) (APA) sites can affect RNA stability or coding capacity. Studies have shown that Arabidopsis thaliana uses APA extensively to generate diversity in its transcriptome. However, little is known about how genome-wide APA site usage varies among Arabidopsis accessions or what genetic factors control this variation. To address these questions, we have investigated genome-wide variation in APA site use and performed a genetic association analysis in Arabidopsis.

We have produced deep strand-specific RNA-seq data across three tissues for the 19 sequenced founders of the Arabidopsis Multiple Advanced Generation Intercross (MAGIC) population. Our study suggests that 6% of genes with poly(A)-containing reads have poly(A) site usage which varies among the founders. The association of site usage (phenotype) with linked variants (genotype) identified cis-QTL in 10% of genes with variable site usage. Gene Ontology analysis indicates that genes with variable site usage are enriched in annotations related to response to stimulus or temperature and cellular and metabolic processes. Comparisons of the ratio of nonsynonymous to synonymous nucleotide substitutions and polymorphisms suggest that genes with polymorphic APA experience more stringent selective pressures on average.

This study provides a comprehensive view of polyadenylation variation in diverse samples and offers insights into the forces shaping variation in APA usage. A planned extension will use association mapping in the MAGIC recombinant inbred lines to identify cis and trans factors affecting poly(A) site usage.