Global profiling of N⁶‐methyladenosine methylation in maize callus induction

Abstract

Callus induction is a dedifferentiation process that accompanies a cell fate transition, and epigenetic regulation plays a crucial role in the process. N 6-methyladenosine (m6A) methylation is an important mechanism in post-transcriptional epigenetic regulation and functions in cell reprogramming. However, the function of m6A methylation during callus induction is still unknown. Here, we performed transcriptome-wide m6A-seq on immature maize embryos after culturing for 2, 4, or 8 days with or without the auxin analogue 2,4-D. A total of 26,794 unique m6A peaks were detected from 17,456 maize genes; and 2,338 specific, 2,4-D-induced m6A peaks (D-specific m6A) were detected only in embryos cultured with 2,4-D. Furthermore, a positive correlation between m6A methylation and mRNA abundance was discovered in the genes with D-specific m6A deposition, especially at the beginning of callus induction. Key genes involved in callus induction, i.e. BABY BOOM and LBD transcription factors, underwent m6A methylation, increasing their transcript levels, thus improving callus induction. These results revealed the importance of m6A methylation during the early stage of callus induction and provided new insights into the molecular mechanism of callus induction at an epitranscriptomic level. Abbreviations: 2,4-D, 2,4-dichlorophenoxyacetic acid; ARF, auxin response factors; BBM, BABY BOOM; FPKM, fragments per kilobase of transcript per million reads mapped; m6A-seq, N 6-methyladenosine-sequencing; UTR, untranslated region. This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.

Transcriptome-Wide N6-Methyladenosine (m6A) Profiling of Susceptible and Resistant Wheat Varieties Reveals the Involvement of Variety-Specific m6A Modification Involved in Virus-Host Interaction Pathways

“…In the present study, more than 90% of the m 6 A peaks were found in 3 -UTRs and the stop codons of CDS (Figure 1C). We found that two high consensus motifs, UGUAY and GAACU, were significantly enriched in the m 6 A peaks identified in wheat (Figure 1D), similar to the observation in other plant species, such as rice and maize, in some previous studies (Li et al, 2014;Du et al, 2020). These results further demonstrated the conserved features of m 6 A methylation in plants.…”

Characteristics of N6-methyladenosine modification during sexual reproduction of Chlamydomonas reinhardtii

“…was significantly identified and top ranked in all of the detected stages including vegetative cells, gametes, and 1 day and 7 days zygotes. This motif is in general similar to the motifs found in rice, tomato and maize seedlings [85][86][87].…”

“…24416, 25656, 23288, 23836, 24403 and 25057 m 6 A peaks within 13255, 13367, 12969, 13313, 13564 and 13720 transcripts were identified from different stages, respectively (Figure 3A and Table S1). The distribution pattern of m 6 A modification along the transcripts were analyzed, and the results of metagene profiles revealed that m 6 A deposition was primarily enriched in 3'UTR (Figure 3B), which is interestingly consistent with the m 6 A distribution patterns in rice, potato and maize [85,86,89]. We then analyzed the distribution of m 6 A peaks within four non-overlapping regions: intergenic region, 5' UTR, coding sequence (CDS), and 3'UTR.…”

“…Consistently, m 6 A modification is also detected in plants, and the animal counterpart of writers, erasers and readers have also been identified to play critical roles [72][73][74][75][76][77][78][79][80][81][82][83]. Functional studies showed that m 6 A is also important for embryo development and sporogenesis in plants [6,75,77,[84][85][86][87]. These findings suggest that m 6 A modification may have conserved critical roles in sexual reproduction in mammals and plants [60, 69-71, 75, 77], whether and how m 6 A modification is involved in sexual reproduction and life cycle regulation of Chlamydomonas remains unknown.…”

m6A‐mediated regulation of crop development and stress responses

“…Through the combination of transcriptome‐wide m 6 A‐seq and RNA‐seq analyses, the potential relationship between m 6 A modification and mRNA abundance has been revealed in rice (Cheng et al ., 2021 ), maize (Du et al ., 2020 ; Luo et al ., 2020 ), tomato (Zhou et al ., 2019 ), strawberry (Zhou et al ., 2021 ), and pak‐choi (Liu et al ., 2020 ) under divergent physiological circumstances. In the rice root threatened with cadmium stress (Cheng et al ., 2021 ) or pak‐choi seedling treated with hot temperature (Liu et al ., 2020 ), no exact correlation between m 6 A modification and mRNA abundance was determined, although thousands of transcripts exhibited differential m 6 A enrichment or gene expression under these stress conditions.…”