Poly(A) inclusive RNA isoform sequencing (PAIso−seq) reveals wide-spread non-adenosine residues within RNA poly(A) tails

• Published in: Nature communications Vol. 10; no. 1; pp. 5292 - 13
• Main Authors: Liu, Yusheng, Nie, Hu, Liu, Hongxiang, Lu, Falong
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 22.11.2019; Nature Publishing Group; Nature Portfolio
• Subjects: 38/39; 38/91; 631/1647/514/1949; 631/337/1645/2570; 631/61/514/1949; 64/60; Adenosine; Animals; Base composition; Cell Cycle Proteins - genetics; Cyclin B1 - genetics; Cytosine Nucleotides - analysis; Cytosine Nucleotides - chemistry; DNA (Cytosine-5-)-Methyltransferase 1 - genetics; Gametocytes; Gene sequencing; Guanine Nucleotides - analysis; Guanine Nucleotides - chemistry; Humanities and Social Sciences; Information dissemination; Isoforms; Mice; mRNA; multidisciplinary; Oocytes; Oocytes - metabolism; Poly A - analysis; Poly A - chemistry; Poly(A); Polyadenine; Polyadenylation; Protein Biosynthesis; Residues; RNA Isoforms; RNA, Messenger - analysis; RNA, Messenger - chemistry; Science; Science (multidisciplinary); Sensitivity; Sequence Analysis, RNA - methods; Single-Cell Analysis; Tissue Plasminogen Activator - genetics; Uracil Nucleotides - analysis; Uracil Nucleotides - chemistry
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-019-13228-9

Message RNA poly(A) tails are vital for their function and regulation. However, the full-length sequence of mRNA isoforms with their poly(A) tails remains undetermined. Here, we develop a method at single-cell level sensitivity that enables quantification of poly(A) tails along with the full-length cDNA while reading non-adenosine residues within poly(A) tails precisely, which we name poly(A) inclusive RNA isoform sequencing (PAIso−seq). Using this method, we can quantify isoform specific poly(A) tail length. More interestingly, we find that 17% of the mRNAs harbor non-A residues within the body of poly(A) tails in mouse GV oocytes. We show that PAIso−seq is sensitive enough to analyze single GV oocytes. These findings will not only provide an accurate and sensitive tool in studying poly(A) tails, but also open a door for the function and regulation of non-adenosine modifications within the body of poly(A) tails. The poly(A) tails on mRNA are vital for their function but it is difficult to map full-length sequences of mRNA isoforms with the entire poly(A) tails. Here the authors develop PAIso−seq which can measure isoform specific poly(A) tail length and base composition at single-cell sensitivity.