Light and temperature regulate m(6)A-RNA modification to regulate growth in plants

N6-methyladenosine is a highly dynamic, abundant mRNA modification which is an excellent potential mechanism for fine tuning gene expression. Plants adapt to their surrounding light and temperature environment using complex gene regulatory networks. The role of m(6)A in controlling gene expression in response to variable environmental conditions has so far been unexplored. Here, we map the transcriptome-wide m(6)A landscape under various light and temperature environments. Identified m(6)A-modifications show a highly specific spatial distribution along transcripts with enrichment occurring in 5’UTR regions and around transcriptional end sites. We show that the position of m(6)A modifications on transcripts might influence cellular transcript localization and the presence of m(6)A-modifications is associated with alternative polyadenylation, a process which results in multiple RNA isoforms with varying 3’UTR lengths. RNA with m(6)A-modifications exhibit a higher preference for shorter 3’UTRs. These shorter 3’UTR regions might directly influence transcript abundance and localization by including or excluding cis-regulatory elements. We propose that environmental stimuli might change the m(6)A landscape of plants as one possible way of fine tuning gene regulation through alternative polyadenylation and transcript localization.