The m6A pathway protects the transcriptome integrity by restricting RNA chimera formation in plants.

Dominique Pontier,Tao Xu,Christophe Hirtz,Christel Llauro,Lisha Shen,François Roudier,Michèle Laudié,Moaine El Baidouri,Sylvie Lahmy,Aurore Attina,Claire Picart,Thierry Lagrange,Jacinthe Azevedo,Marie-Christine Carpentier

doi:10.26508/lsa.201900393

Abstract

Global, segmental, and gene duplication-related processes are driving genome size and complexity in plants. Despite their evolutionary potentials, those processes can also have adverse effects on genome regulation, thus implying the existence of specialized corrective mechanisms. Here, we report that an N6-methyladenosine (m6A)-assisted polyadenylation (m-ASP) pathway ensures transcriptome integrity in Arabidopsis thaliana Efficient m-ASP pathway activity requires the m6A methyltransferase-associated factor FIP37 and CPSF30L, an m6A reader corresponding to an YT512-B Homology Domain-containing protein (YTHDC)-type domain containing isoform of the 30-kD subunit of cleavage and polyadenylation specificity factor. Targets of the m-ASP pathway are enriched in recently rearranged gene pairs, displayed an atypical chromatin signature, and showed transcriptional readthrough and mRNA chimera formation in FIP37- and CPSF30L-deficient plants. Furthermore, we showed that the m-ASP pathway can also restrict the formation of chimeric gene/transposable-element transcript, suggesting a possible implication of this pathway in the control of transposable elements at specific locus. Taken together, our results point to selective recognition of 3'-UTR m6A as a safeguard mechanism ensuring transcriptome integrity at rearranged genomic loci in plants.

Highlights

IntroductionN6-methyl-adenosine (m6A) has recently emerged as a prevalent mRNA modification that tends to be enriched in 39-UTR within the consensus RRm6ACH motif (where R is A/G and H is A/C/U) (Dominissini et al, 2012; Meyer et al, 2012; Schwartz et al, 2013; Shen et al, 2016). mutant plants deficient in N6-adenosine (m6A) mRNA modification occurs co-transcriptionally and is driven by a conserved writer complex composed of methyltransferase-like3(METTL3/MT-A70), METTL14 (a noncatalytic METTL3-homologous protein), and Wilms tumor 1-associated protein (WTAP/FIP37) (Bokar et al, 1997; Zhong et al, 2008; Liu et al, 2014a; Shen et al, 2016; Meyer & Jaffrey, 2017)
Consistent with a role for NERD in transcription termination control at GENE1 rather than transcription control at GENE2, we did not detect any enrichment of H3K4me3, a chromatin mark associated with active promoter regions, in the corresponding intergenic regions in nerd-1 compared with WT or nerd+T plants (Fig S2D)
The first evidence that mutant plants deficient in N6-adenosine (m6A) could participate in the control of chimeric mRNA formation at specific loci in plants came from our ongoing analysis of NERD, a plant homeodomain finger- and AGO hook– containing protein that, until now, was thought to contribute to the transcriptional silencing of newly acquired genomic sequences via a non-canonical siRNA-dependent DNA methylation pathway (Garcia et al, 2012; Pontier et al, 2012)

Summary

Introduction

N6-methyl-adenosine (m6A) has recently emerged as a prevalent mRNA modification that tends to be enriched in 39-UTR within the consensus RRm6ACH motif (where R is A/G and H is A/C/U) (Dominissini et al, 2012; Meyer et al, 2012; Schwartz et al, 2013; Shen et al, 2016). m6A mRNA modification occurs co-transcriptionally and is driven by a conserved writer complex composed of methyltransferase-like3(METTL3/MT-A70), METTL14 (a noncatalytic METTL3-homologous protein), and Wilms tumor 1-associated protein (WTAP/FIP37) (Bokar et al, 1997; Zhong et al, 2008; Liu et al, 2014a; Shen et al, 2016; Meyer & Jaffrey, 2017). M6A is expected to control the fate of mRNA mostly by recruiting specific readers that belong to the YT521-B homology (YTH) domaincontaining proteins and bind m6A methyl group through a conserved hydrophobic pocket (Meyer & Jaffrey, 2017; Wu et al, 2017). Recent studies performed in animal and plant models have connected m6A-dependent recruitment of YTH-type proteins to the control of various aspects of mRNA metabolism, including stability (Wang et al, 2014; Wojtas et al, 2017), splicing (Lence et al, 2016; Xiao et al, 2016), alternative polyadenylation (APA) (Ke et al, 2015; Yue et al, 2018), nuclear export (Roundtree et al, 2017), and translation initiation (Wang et al, 2015). Whereas trans-acting effects on original genes generally entail gene silencing through natural epigenetic variation (Bender & Fink, 1995; Durand et al, 2012), cis-acting effects on a neighboring gene vary among cases, leading to epigenetic control (Zheng & Cheng, 2014; El Baidouri et al, 2018), chimeric gene formation (Thimmapuram et al, 2005; Shahmuradov et al, 2010), polyadenylation defects (Tsukamoto et al, 2010), transcriptional interference (Kashkush et al, 2003), and gene/exon transduction (Xiao et al, 2008; Zhu et al, 2016)

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