An atlas of plant full-length RNA reveals tissue-specific and evolutionarily-conserved regulation of poly(A) tail length

Abstract

Introductory paragraphPoly(A) tail is a hallmark of eukaryotic mRNA and its length plays an essential role in regulating mRNA metabolism1-3. However, a comprehensive resource for plant poly(A) tail length has yet to be established. Here, we applied a poly(A)-enrichment-free, Nanopore-based method4,5 to profile full-length RNA with poly(A) tail information in plants. Our atlas contains over 120 million polyadenylated mRNA molecules from seven different tissues of Arabidopsis, as well as the shoot tissue of maize, soybean and rice. In most tissues, the size of plant poly(A) tails shows peaks at approximately 20 and 45 nt, presumably the sizes protected by one and two poly(A) binding proteins (PABP), respectively2,6, while the poly(A) tails in pollen exhibit a distinct pattern with strong peaks centered at 55 and 80 nt. Moreover, poly(A) tail length is regulated in a gene-specific manner -- mRNAs with short half-lives in general have long poly(A) tails, while mRNAs with long half-lives are featured with relatively short poly(A) tails that peak at ~45 nt, suggesting that protection of poly(A) tail in this size by PABP is essential for mRNA stability. Across species, poly(A) tails in the nucleus are almost twice as long as in the cytoplasm, implying a conserved rapid shortening process of poly(A) tail occurs before the mRNA is stabilized in cytoplasm. Our comprehensive dataset lays the groundwork for future functional and evolutionary studies on poly(A) tail length regulation in plants.