Genome-Wide Identification of m6A Writers, Erasers and Readers in Poplar 84K

Abstract

N6-methyladenosine (m6A) RNA modification is a conserved mechanism to regulate gene expression that plays vital roles in the development of plants. However, the m6A RNA modification in forest trees remains limited. Here, we performed a complete analysis of m6A writers, erasers and readers in Poplar 84K, including gene location, gene structures, conserved motifs, phylogenetic relationships, promoter analysis, expression profiles and the homology modeling. We have identified 61 m6A pathway genes in Poplar84K (Populus alba x Populus glandulosa), including 14 m6A writers, 14 m6A erasers and 33 m6A readers. Phylogenetic analysis indicated that the m6A writers and erasers were clustered into four groups and m6A readers were clustered into two groups. Promoter analysis showed that m6A pathway genes were mainly responsive to low oxygen followed by ABA and ethylene. The expression of the identified m6A pathway genes showed tissue-specific expression patterns in leaves, xylem, phloem and roots. Moreover, 17 genes were significantly up-regulated and 13 genes were significantly down-regulated in poplar overexpressing the transcription factor LBD15.Homology modeling and molecular docking results suggested that PagFIP37b was most likely to be regulated by LBD15, and the qPCR showed thatPagFIP37b were up-regulated in the LBD15-oe plants. The results provide insights that aid in the future elucidation of the functions of these m6A pathway genes and the epigenetic regulation mechanism of these genes in Poplar 84K.

Genome-wide identification of the N6-methyladenosine regulatory genes reveals NtFIP37B increases drought resistance of tobacco (Nicotiana tabacum L.)

“…5 ; Table S 8 ). Similar findings were also found in other plant species such as tea [ 48 ], tomato [ 49 ], and poplar [ 67 ]. The promoter regions of m 6 A regulatory genes in tobacco encompassed a substantial proportion (46%) of light-responsive CREs.…”

“…For m 6 A writer, the genes from the same branch had similar exon–intron structures and conserved domains, except that NtMTB3 had one more exon than NtMTB4 . Interestingly, NtVIRs had a super long structure with 27 to 28 exons, which was also found in other plants such as tea [ 48 ] and poplar [ 67 ]. MT-A70 domain was found in all tobacco MT families, and NtMTB proteins also contained a MAPK-interacting and spindle-stabilizing protein-like protein domain (MISS).…”

Genome-Wide Identification and Expression Analysis of the YTH Domain-Containing RNA-Binding Protein Family in Cinnamomum camphora

“…Hence, it is deserved to further uncover the regulatory mechanism of these m 6 A readers in C. camphora. The cis-regulatory element analysis of C. camphora promoters showed that the promoter regions of the 10 CcYTH genes contain numerous cis-regulatory elements associated with stress responses (Figure 8), which is similar to the findings in various plants such as Arabidopsis, rice, poplar, and so on [23,30,[40][41][42]. The expression levels of genes related to development and stress response are generally high or significantly increased during the developmental stage or under stress treatments.…”

Identification of m6A RNA methylation genes in Oryza sativa and expression profiling in response to different developmental and environmental stimuli

“…The phylogenetic tree analysis unveiled the evolutionary patterns of m 6 A writer, eraser, and reader genes as they evolved across a spectrum of plant species, including Rhodophyta (red algae), Chlorophyte (green algae), Tracheophyte (vascular plants), and Angiosperms (comprising eudicots and monocots). In a prior study, a phylogenetic tree was created by comparing the protein sequences of N6-methyladenosine writers, erasers, and readers in Poplar 84K with their counterparts in Arabidopsis and O. sativa to explore their phylogenetic relationships [ 79 ]. In another study on m 6 A genes of Arabidopsis, it was found that methyltransferase domains from various species share close relationships, while other components of methylation are organized differently.…”