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Published on: October 4, 2018
The m1A landscape on cytosolic and mitochondrial mRNA at single-base resolution
Modi Safra1, Aldema Sas-Chen1, Ronit Nir1
1Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
Abstract:
Modifications on mRNA offer the potential of regulating mRNA fate post-transcriptionally. Recent studies suggested the widespread presence of N1-methyladenosine (m1A), which disrupts Watson-Crick base pairing, at internal sites of mRNAs. These studies lacked the resolution of identifying individual modified bases, and did not identify specific sequence motifs undergoing the modification or an enzymatic machinery catalysing them, rendering it challenging to validate and functionally characterize putative sites. Here we develop an approach that allows the transcriptome-wide mapping of m1A at single-nucleotide resolution. Within the cytosol, m1A is present in a low number of mRNAs, typically at low stoichiometries, and almost invariably in tRNA T-loop-like structures, where it is introduced by the TRMT6/TRMT61A complex. We identify a single m1A site in the mitochondrial ND5 mRNA, catalysed by TRMT10C, with methylation levels that are highly tissue specific and tightly developmentally controlled. m1A leads to translational repression, probably through a mechanism involving ribosomal scanning or translation. Our findings suggest that m1A on mRNA, probably because of its disruptive impact on base pairing, leads to translational repression, and is generally avoided by cells, while revealing one case in mitochondria where tight spatiotemporal control over m1A levels was adopted as a potential means of post-transcriptional regulation.
Insights
N1-methyladenosine (m1A) modifications on mRNA can regulate gene expression. This study maps m1A sites, revealing its role in translational repression, particularly in mitochondria.
Area of Science:
- Molecular Biology
- RNA Biology
- Epigenetics
Background:
- mRNA modifications regulate gene expression post-transcriptionally.
- N1-methyladenosine (m1A) is a widespread mRNA modification, but its precise locations and functions are poorly understood.
- Previous studies lacked single-nucleotide resolution for m1A mapping and identification of modifying enzymes.
Purpose of the Study:
- To develop a method for transcriptome-wide mapping of m1A at single-nucleotide resolution.
- To identify the enzymes responsible for m1A formation in mRNA.
- To investigate the functional consequences of m1A on mRNA translation.
Main Methods:
- Development of a novel approach for single-nucleotide resolution m1A mapping.
- Transcriptome-wide analysis of m1A distribution in cytosolic and mitochondrial mRNA.
- Identification of m1A-modifying enzymes using biochemical and genetic approaches.
Main Results:
- m1A is found at low levels in specific cytosolic mRNAs and tRNA T-loops, catalyzed by the TRMT6/TRMT61A complex.
- A unique m1A site was identified in mitochondrial ND5 mRNA, regulated by TRMT10C in a tissue-specific and developmentally controlled manner.
- m1A modification leads to translational repression, likely via interference with ribosomal scanning.
Conclusions:
- m1A on mRNA generally disrupts base pairing, leading to translational repression and is typically avoided by cells.
- The study reveals a specific instance of m1A-mediated post-transcriptional regulation in mitochondria, with tight spatiotemporal control.
- This work provides a foundation for understanding the roles of m1A in gene regulation.
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