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Genome-wide analysis of the associations between polyadenylation sites and repeated sequences in Arabidopsis thaliana

In eukaryotes, polyadenylation [poly(A)] is one of the critical processes during gene expression. It plays an important role in gene expression and gene regulation. Repeated sequences are widely distributed in eukaryotic genomes, which are important parts of the genome. There are two categories of repeated sequences in genome: interspersed repeats and tandem repeats (TRs). Interspersed repeats mainly come from transposable elements (TEs). Here we focus on the study of associations between poly(A) sites and two main categories of repeated sequences - TEs and TRs. We examined the poly(A) sites associated with repeated sequences on the whole genome of Arabidopsis thaliana. The results suggest that there are some potential associations between poly(A) sites and repeated sequences. Compared to the associations of poly(A) sites with TRs, TEs have closer links with poly(A) sites, especially for subfamilies of short interspersed elements (SINEs) and long interspersed elements (LINEs). Significant bias of association of poly(A) sites with TEs on different strand was found, while there was no bias found about TRs. The distributions of the association between poly(A) sites and TEs or TRs on different chromosomes share some similarities. This study will provide general insight into the associations between poly(A) sites and repeated sequences in Arabidopsis thaliana and other plants.