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

Poly(A) tail is a hallmark of eukaryotic messenger RNA and its length plays an essential role in regulating mRNA metabolism. 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 method to profile full-le...

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Veröffentlicht in:Nature plants 2022-09, Vol.8 (9), p.1118-1126
Hauptverfasser: Jia, Jinbu, Lu, Wenqin, Liu, Bo, Fang, Huihui, Yu, Yiming, Mo, Weipeng, Zhang, Hong, Jin, Xianhao, Shu, Yi, Long, Yanping, Pei, Yanxi, Zhai, Jixian
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container_issue 9
container_start_page 1118
container_title Nature plants
container_volume 8
creator Jia, Jinbu
Lu, Wenqin
Liu, Bo
Fang, Huihui
Yu, Yiming
Mo, Weipeng
Zhang, Hong
Jin, Xianhao
Shu, Yi
Long, Yanping
Pei, Yanxi
Zhai, Jixian
description Poly(A) tail is a hallmark of eukaryotic messenger RNA and its length plays an essential role in regulating mRNA metabolism. 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 method 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 nucleotides, while the poly(A) tails in pollen exhibit a distinct pattern with strong peaks centred at 55 and 80 nucleotides. 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 nucleotides. Across species, poly(A) tails in the nucleus are almost twice as long as in the cytoplasm. Our comprehensive dataset lays the groundwork for future functional and evolutionary studies on poly(A) tail length regulation in plants. This study established a comprehensive poly(A) tail atlas comprising over 120 million full-length RNA reads from various tissues and plant species and found that plant poly(A) tails peaked at 20 and 45 nucleotides, except in pollen and seed where they peaked at longer sizes.
doi_str_mv 10.1038/s41477-022-01224-9
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subjects 38/91
631/1647/48
631/1647/514/1949
631/208/212/2019
631/208/514/1949
Biomedical and Life Sciences
Cytoplasm
Genes
Half-life
Laboratories
Life Sciences
mRNA
Nucleotides
Plant Sciences
Plant species
Plants (botany)
Pollen
Polyadenine
Polyadenylation
Resource
Ribonucleic acid
RNA
Science
Small mammals
Soybeans
Tissues
title An atlas of plant full-length RNA reveals tissue-specific and monocots–dicots conserved regulation of poly(A) tail length
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