We applied single-molecule nanopore sequencing to over 120 million full-length RNAs, including the poly(A) tail, from various tissues and plant species. The resulting dataset enables the genome-wide characterization of plant poly(A) tails at the single gene level across different tissues and species.
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References
Passmore, L. A. & Coller, J. Roles of mRNA poly(A) tails in regulation of eukaryotic gene expression. Nat. Rev. Mol. Cell Biol. 23, 93–106 (2022). A review that summarizes recent advances on the roles of poly(A) tails in post-transcriptional mRNA regulation.
Jia, J. et al. Post-transcriptional splicing of nascent RNA contributes to widespread intron retention in plants. Nat. Plants 6, 780–788 (2020). This paper develops a long-read sequencing based method to simultaneously detect the splicing status and poly(A) tail length of RNA, as well as the position of RNA polymerase II on RNA, at the genome-wide level. It revealed wide-spread post-transcriptional splicing in Arabidopsis.
Long, Y. et al. FLEP-seq: simultaneous detection of RNA polymerase II position, splicing status, polyadenylation site and poly(A) tail length at genome-wide scale by single-molecule nascent RNA sequencing. Nat. Protoc. 16, 4355–4381 (2021). This paper describes a detailed protocol for cloning, sequencing, and analysing full-length nascent RNAs in plants.
Parker, M. T. et al. Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification. eLife 9, e49658 (2020). This paper describes the first characterization of poly(A) tail length in plants by nanopore direct RNA sequencing.
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This is a summary of: Jinbu J. et al. An atlas of plant full-length RNA reveals tissue-specific and monocots–dicots conserved regulation of poly(A) tail length. Nat. Plants https://doi.org/10.1038/s41477-022-01224-9 (2022).
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An atlas of plant poly(A) tail length reveals phased peaks and tissue-specific patterns. Nat. Plants 8, 994–995 (2022). https://doi.org/10.1038/s41477-022-01225-8
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DOI: https://doi.org/10.1038/s41477-022-01225-8
