Profiling of circular RNA N6-methyladenosine in moso bamboo (Phyllostachys edulis) using nanopore-based direct RNA sequencing

• 作者: Anireddy S.N.Reddy Feihu Xi Hangxiao Zhang Huihui Wang Huiyuan Wang Lianfeng Gu Markus V.Kohnen Qiang Zhu Qianyue Zhang Wentao Wei Ximei Han Yongsheng Wang Yushan Zheng
• 来源期刊: 植物学报（英文版）
• 年，卷（期）: 2020,（12）
• 所属期刊栏目: New Technology
• 页码范围: 1823-1838
• 页数: 16页
• 语种: 英文
• DOI: 10.1111/jipb.13002

摘要

N6-methyladenosine (m6A) is a prevalent modification in messenger RNAs and circular RNAs that play important roles in regulating various aspects of RNA metabolism. However, the occurrence of the m6A modification in plant circular RNAs has not been re-ported. A widely used method to identify m6A mod-ifications relies on m6A-specific antibodies followed by next-generation sequencing of precipitated RNAs (MeRIP-Seq). However, one limitation of MeRIP-Seq is that it does not provide the precise location of m6A at single-nucleotide resolution. Although more recent se-quencing techniques such as Nanopore-based direct RNA sequencing (DRS) can overcome such limitations, the technology does not allow sequencing of circular RNAs, as these molecules lack a poly(A) tail. Here, we developed a novel method to detect the precise location of m6A modifications in circular RNAs using Nanopore DRS. We first enriched our samples for circular RNAs, which we then fragmented and sequenced on the Nanopore platform with a customized protocol. Using this method, we identified 470 unique circular RNAs from DRS reads based on the back-spliced junction re-gion. Among exonic circular RNAs, about 10％contained m6A sites, which mainly occurred around acceptor and donor splice sites. This study demonstrates the utility of our antibody-independent method in identifying total and methylated circular RNAs using Nanopore DRS. This method has the additional advantage of providing the exact location of m6A sites at single-base resolution in circular RNAs or linear transcripts from non-coding RNA without poly(A) tails.

作者信息

序号	姓名	单位	发文数	被引次数	H指数	G指数
1	Yongsheng Wang		1	0	0.0	0.0
2	Huihui Wang		1	0	0.0	0.0
3	Feihu Xi		1	0	0.0	0.0
4	Huiyuan Wang		1	0	0.0	0.0
5	Ximei Han		1	0	0.0	0.0
6	Wentao Wei		1	0	0.0	0.0
7	Hangxiao Zhang		1	0	0.0	0.0
8	Qianyue Zhang		1	0	0.0	0.0
9	Yushan Zheng		1	0	0.0	0.0
10	Qiang Zhu		1	0	0.0	0.0
11	Markus V.Kohnen		1	0	0.0	0.0
12	Anireddy S.N.Reddy		1	0	0.0	0.0
13	Lianfeng Gu		1	0	0.0	0.0