MTA influences RNA Polymerase II transcription dynamics and regulates the cold response in Arabidopsis

ABSTRACT RNA methylation at the N6 position of adenosine residues (m 6 A) has been demonstrated to be a vital epigenetic mark in eukaryotes. In plants, it is involved in a myriad of developmental and stress responsive pathways, such as cold stress. However, the role of MTA (m 6 A writer) itself in such processes remains obscured. Here, we show that the cold induced changes in abundance of differentially methylated transcripts are at-least partly due to the differences in the rates of transcription of such transcripts. RNAPII stalling was observed only on RNA methylation motifs that were decorated with m 6 A, and those that had a specific nucleotide composition. We note that the downregulation of genes in a mta mutant is a result of lower transcription of these genes. Moreover, 5’ ends of transcripts from a subset of genes are disproportionately more accumulated in mta as compared to wild type under cold stress. In the mta mutant, genes corresponding to these transcripts had significantly reduced RNAPII occupancy on their 3’ ends but not on 5’ ends indicating that mta serves as an important factor for RNAPII elongation in a subset of genes. Taken together, our data suggest a novel direct role for MTA as a gene specific influencer of RNAPII elongation dynamics and thus introduces a new path by which the m 6 A methylation machinery may affect differential gene expression during stress in plants.