The M1A Landscape on Cytosolic and Mitochondrial MRNA at Single-base Resolution

Overview

Journal Nature

Specialty Science

Date 2017 Oct 27

PMID 29072297

Citations 325

Authors

Modi Safra

Aldema Sas-Chen

Ronit Nir

Roni Winkler

Aharon Nachshon

Dan Bar-Yaacov

Matthias Erlacher

Walter Rossmanith

Noam Stern-Ginossar

Schraga Schwartz

Affiliations

Soon will be listed here.

Abstract

Modifications on mRNA offer the potential of regulating mRNA fate post-transcriptionally. Recent studies suggested the widespread presence of N-methyladenosine (mA), 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 mA at single-nucleotide resolution. Within the cytosol, mA 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 mA site in the mitochondrial ND5 mRNA, catalysed by TRMT10C, with methylation levels that are highly tissue specific and tightly developmentally controlled. mA leads to translational repression, probably through a mechanism involving ribosomal scanning or translation. Our findings suggest that mA 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 mA levels was adopted as a potential means of post-transcriptional regulation.

Citing Articles

Transcriptome-wide mapping of N3-methylcytidine modification at single-base resolution.

Gao Y, Hou J, Wei S, Wu C, Yan S, Sheng J Nucleic Acids Res. 2025; 53(5).

PMID: 40071931 PMC: 11897884. DOI: 10.1093/nar/gkaf153.

In silico λ-dynamics predicts protein binding specificities to modified RNAs.

Angelo M, Zhang W, Vilseck J, Aoki S Nucleic Acids Res. 2025; 53(5).

PMID: 40066880 PMC: 11894534. DOI: 10.1093/nar/gkaf166.

Toward the use of nanopore RNA sequencing technologies in the clinic: challenges and opportunities.

Katopodi X, Begik O, Novoa E Nucleic Acids Res. 2025; 53(5).

PMID: 40057374 PMC: 11890063. DOI: 10.1093/nar/gkaf128.

De novo basecalling of RNA modifications at single molecule and nucleotide resolution.

Cruciani S, Delgado-Tejedor A, Pryszcz L, Medina R, Llovera L, Novoa E Genome Biol. 2025; 26(1):38.

PMID: 40001217 PMC: 11853310. DOI: 10.1186/s13059-025-03498-6.

The Role of mRNA Modifications in Bone Diseases.

Li Z, Meng K, Lan S, Ren Z, Lai Z, Ao X Int J Biol Sci. 2025; 21(3):1065-1080.

PMID: 39897026 PMC: 11781163. DOI: 10.7150/ijbs.104460.

References

Lovejoy A, Riordan D, Brown P . Transcriptome-wide mapping of pseudouridines: pseudouridine synthases modify specific mRNAs in S. cerevisiae. PLoS One. 2014; 9(10):e110799. PMC: 4212993. DOI: 10.1371/journal.pone.0110799. View

Schwartz S, Agarwala S, Mumbach M, Jovanovic M, Mertins P, Shishkin A . High-resolution mapping reveals a conserved, widespread, dynamic mRNA methylation program in yeast meiosis. Cell. 2013; 155(6):1409-21. PMC: 3956118. DOI: 10.1016/j.cell.2013.10.047. View

Robinson M, McCarthy D, Smyth G . edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2009; 26(1):139-40. PMC: 2796818. DOI: 10.1093/bioinformatics/btp616. View

Biggers J, Borland R . Physiological aspects of growth and development of the preimplantation mammalian embryo. Annu Rev Physiol. 1976; 38:95-119. DOI: 10.1146/annurev.ph.38.030176.000523. View

Gandin V, Sikstrom K, Alain T, Morita M, McLaughlan S, Larsson O . Polysome fractionation and analysis of mammalian translatomes on a genome-wide scale. J Vis Exp. 2014; (87). PMC: 4189431. DOI: 10.3791/51455. View

Li B, Dewey C . RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 2011; 12:323. PMC: 3163565. DOI: 10.1186/1471-2105-12-323. View

PIKO L, Taylor K . Amounts of mitochondrial DNA and abundance of some mitochondrial gene transcripts in early mouse embryos. Dev Biol. 1987; 123(2):364-74. DOI: 10.1016/0012-1606(87)90395-2. View

Li X, Xiong X, Wang K, Wang L, Shu X, Ma S . Transcriptome-wide mapping reveals reversible and dynamic N(1)-methyladenosine methylome. Nat Chem Biol. 2016; 12(5):311-6. DOI: 10.1038/nchembio.2040. View

Brown M, Sun F, Wallace D . Clustering of Caucasian Leber hereditary optic neuropathy patients containing the 11778 or 14484 mutations on an mtDNA lineage. Am J Hum Genet. 1997; 60(2):381-7. PMC: 1712415. View

10.

Schwartz S, Bernstein D, Mumbach M, Jovanovic M, Herbst R, Leon-Ricardo B . Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA. Cell. 2014; 159(1):148-162. PMC: 4180118. DOI: 10.1016/j.cell.2014.08.028. View

11.

Juhling F, Morl M, Hartmann R, Sprinzl M, Stadler P, Putz J . tRNAdb 2009: compilation of tRNA sequences and tRNA genes. Nucleic Acids Res. 2008; 37(Database issue):D159-62. PMC: 2686557. DOI: 10.1093/nar/gkn772. View

12.

Bar-Yaacov D, Frumkin I, Yashiro Y, Chujo T, Ishigami Y, Chemla Y . Mitochondrial 16S rRNA Is Methylated by tRNA Methyltransferase TRMT61B in All Vertebrates. PLoS Biol. 2016; 14(9):e1002557. PMC: 5025228. DOI: 10.1371/journal.pbio.1002557. View

13.

Dobin A, Davis C, Schlesinger F, Drenkow J, Zaleski C, Jha S . STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2012; 29(1):15-21. PMC: 3530905. DOI: 10.1093/bioinformatics/bts635. View

14.

Torroni A, Petrozzi M, DUrbano L, Sellitto D, Zeviani M, Carrara F . Haplotype and phylogenetic analyses suggest that one European-specific mtDNA background plays a role in the expression of Leber hereditary optic neuropathy by increasing the penetrance of the primary mutations 11778 and 14484. Am J Hum Genet. 1997; 60(5):1107-21. PMC: 1712418. View

15.

Ginsberg L, Hillman N . ATP metabolism in cleavage-staged mouse embryos. J Embryol Exp Morphol. 1973; 30(1):267-82. View

16.

Engreitz J, Pandya-Jones A, McDonel P, Shishkin A, Sirokman K, Surka C . The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome. Science. 2013; 341(6147):1237973. PMC: 3778663. DOI: 10.1126/science.1237973. View

17.

Mohr S, Ghanem E, Smith W, Sheeter D, Qin Y, King O . Thermostable group II intron reverse transcriptase fusion proteins and their use in cDNA synthesis and next-generation RNA sequencing. RNA. 2013; 19(7):958-70. PMC: 3683930. DOI: 10.1261/rna.039743.113. View

18.

Yan L, Yang M, Guo H, Yang L, Wu J, Li R . Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells. Nat Struct Mol Biol. 2013; 20(9):1131-9. DOI: 10.1038/nsmb.2660. View

19.

Wassarman P, Josefowicz W . Oocyte development in the mouse: an ultrastructural comparison of oocytes isolated at various stages of growth and meiotic competence. J Morphol. 1978; 156(2):209-35. DOI: 10.1002/jmor.1051560206. View

20.

Machnicka M, Milanowska K, Oglou O, Purta E, Kurkowska M, Olchowik A . MODOMICS: a database of RNA modification pathways--2013 update. Nucleic Acids Res. 2012; 41(Database issue):D262-7. PMC: 3531130. DOI: 10.1093/nar/gks1007. View