N6-Methyladenosine RNA Modification Regulates Shoot Stem Cell Fate in Arabidopsis

Abstract

N(6)-Methyladenosine (m(6)A) represents the most prevalent internal modification on mRNA and requires a multicomponent m(6)A methyltransferase complex in mammals. How their plant counterparts determine the global m(6)A modification landscape and its molecular link to plant development remain unknown. Here we show that FKBP12 INTERACTING PROTEIN 37 KD (FIP37) is a core component of the m(6)A methyltransferase complex, which underlies control of shoot stem cell fate in Arabidopsis. The mutants lacking FIP37 exhibit massive overproliferation of shoot meristems and a transcriptome-wide loss of m(6)A RNA modifications. We further demonstrate that FIP37 mediates m(6)A RNA modification on key shoot meristem genes inversely correlated with their mRNA stability, thus confining their transcript levels to prevent shoot meristem overproliferation. Our results suggest an indispensable role of FIP37 in mediating m(6)A mRNA modification, which is required for maintaining the shoot meristem as a renewable source for continuously producing all aerial organs in plants.

Identification of factors required for m6A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI

“…However, we identified a viable hypomorphic allele of FIP37 , caused by a T‐DNA insertion within its 7 th intron ( fip37‐4 , identical to that described in Shen et al . (2016); Fig. 4a).…”

“…We have circumvented this embryo lethality by establishing a collection of hypomorphic, mutants or RNAi lines for each of the proteins associated with the m 6 A writer complex in order to study the effects of reduced m 6 A in postembryonic development. In a recently published study, (Shen et al ., 2016) reported that reduced FIP37 expression resulted in increased proliferation of the shoot apical meristem. Our findings independently expand this, further revealing that impaired expression of any of the five m 6 A writer components we identify results in a range of developmental defects, including vascular formation, implying a role for m 6 A in establishing and maintaining these processes.…”

“…m 6 A appears to be involved in a broad range of biological processes including mRNA export from the nucleus (Fustin et al ., 2013), regulation of splicing (Alarcón et al ., 2015b; Haussmann et al ., 2016; Lence et al ., 2016), mRNA translatability and stability (Wang et al ., 2014a,b, 2015; Bodi et al ., 2015; Zhou et al ., 2015), alternative polyadenylation site choice (Ke et al ., 2015) and other mechanisms accompanying RNA maturation (Meyer & Jaffrey, 2014; Yue et al ., 2015). m 6 A is essential for the earliest stages of pattern formation in plants (Zhong et al ., 2008; Bodi et al ., 2012; Shen et al ., 2016) and metazoans (Meyer & Jaffrey, 2014; Geula et al ., 2015; Yue et al ., 2015; Haussmann et al ., 2016; Lence et al ., 2016), linked with diseases in humans and other mammalian species (Jia et al ., 2011; Zheng et al ., 2013) and is required for meiosis in Saccharomyces cerevisiae (Clancy et al ., 2002). Reduced levels of m 6 A also affect circadian period (Fustin et al ., 2013) and are critical for stem cell differentiation in mammals (Geula et al ., 2015).…”

“…Whilst METTL3 was part of a 200‐kDa complex, a further 875‐kDa complex component(s) was required for its in vitro activity (Bokar et al ., 1994, 1997). The identity of any of the other proteins that act together with METTL3 remained unknown until it was shown in Arabidopsis that FIP37 (FKBP12 INTERACTING PROTEIN 37) was a partner protein of MTA (the homologue of METTL3) (Zhong et al ., 2008; Shen et al ., 2016). Following this initial discovery, the homologues of FIP37, S. cerevisiae MUM2 (Muddled Meiosis 2), and mammalian WTAP (Wilms tumour 1 associated protein), were shown to interact with METTL3 (MTA) orthologues and to be required for mRNA methylation in their respective model organisms (Agarwala et al ., 2012; Ping et al ., 2014; Wang et al ., 2014b; Liu et al ., 2015).…”

Mettl3-mediated m6A regulates spermatogonial differentiation and meiosis initiation

“…Recent studies revealed m 6 A modulation of mRNA expression to be involved in obesity [19], the circadian clock [20], and the DNA damage response [21]. Additionally, it also plays important roles in a variety of biological processes including pluripotency maintenance of stem cells [22][23][24], the maternal-to-zygotic transition [25], sex determination [26,27] and plant shoot stem cell fate determination [28]. As the key 'writer' of m 6 A modification, Mettl3 has been demonstrated to modulate neuronal functions and sex determination in Drosophila and regulate early embryonic development and stem cell pluripotency in mice [22-24, 26, 27].…”