Circular RNAs are a new type of non-coding RNAs that are expressed in a wide range of eukaryotes.N6-methyladenosine (m6A) is a prevalent modification in messenger RNAs and circular RNAs that plays important regulatory roles in regulating gene expression and various aspects of RNA metabolism. However, the occurrence of m6A modification in plant circular RNAs has never been reported. The widely used high-throughput method to identify RNAs with m6A modifications involves immunoprecipitation of methylated RNA using m6A-specific antibodies followed by next-generation sequencing (MeRIP-Seq, also called m6A-Seq). However, one of the limitations of MeRIP-Seq is that it does not provide the precise location of m6A in RNA with single-nucleotide resolution. Though the recent Nanopore-based direct RNA sequencing can overcome this limitation, this technology does not allow sequencing of circular RNAs as they lack poly(A) tail. To overcome this limitation, we developed a novel method to detect the precise location of m6A modification in circular RNAs of Phyllostachys edulis using Nanopore direct RNA sequencing. This study demonstrates the utility of our antibody-independent method to identify total and methylated circular RNA using Nanopore direct RNA sequencing. This method has an additional advantage of providing the quantitative profiling of m6A sites in circular RNAs at single-base resolution. Raw Nanopore DRS data has been submitted to the NCBI Gene Expression Omnibus under accession no PRJNA613867 which be used for identificaiton of circular RNA modification.
Coordinate information for circRNAs from DRS: GFF file (md5sum:d922eb6acf3978df1fd2893d86fab4b0)
Growing shoots of moso bamboo (Phyllostachys edulis) represents fast growth rate. However, expression pattern of circular RNAs remains unexplored. To better understand the potential function of circular RNAs in developing shoots, we systematically characterized circular RNAs from eight different developmental stages of rapidly growing shoots.This work has been published:Wang Y*, Gao Y*, Zhang H*, Wang H, Liu X, Xu X, Zhang Z, Kohnen M, Hu K, Wang H, Xi F, Zhao L, Lin C, Gu L#. (2019). Genome-wide profiling of circular RNAs in the rapidly growing shoots of moso bamboo (Phyllostachys edulis). Plant and Cell Physiology. DOI: 10.1093/pcp/pcz043
The customized code and data used in circular RNAs can be distributed upon request. Requests should be addressed to Lianfeng.Gu (firstname.lastname@example.org)