A distinct class of eukaryotic MT-A70 methyltransferases maintain symmetric DNA N6-adenine methylation at the ApT dinucleotides as an epigenetic mark associated with transcription

Nucleic Acids Res. 2019 Dec 16;47(22):11771-11789. doi: 10.1093/nar/gkz1053.


Rediscovered as a potential eukaryotic epigenetic mark, DNA N6-adenine methylation (6mA) varies across species in abundance and its relationships with transcription. Here we characterize AMT1-representing a distinct MT-A70 family methyltransferase-in the ciliate Tetrahymena thermophila. AMT1 loss-of-function leads to severe defects in growth and development. Single Molecule, Real-Time (SMRT) sequencing reveals that AMT1 is required for the bulk of 6mA and all symmetric methylation at the ApT dinucleotides. The detection of hemi-methylated ApT sites suggests a semi-conservative mechanism for maintaining symmetric methylation. AMT1 affects expression of many genes; in particular, RAB46, encoding a Rab family GTPase involved in contractile vacuole function, is likely a direct target. The distribution of 6mA resembles H3K4 methylation and H2A.Z, two conserved epigenetic marks associated with RNA polymerase II transcription. Furthermore, strong 6mA and nucleosome positioning in wild-type cells is attenuated in ΔAMT1 cells. Our results support that AMT1-catalyzed 6mA is an integral part of the transcription-associated epigenetic landscape. AMT1 homologues are generally found in protists and basal fungi featuring ApT hyper-methylation associated with transcription, which are missing in animals, plants, and true fungi. This dichotomy of 6mA functions and the underlying molecular mechanisms may have implications in eukaryotic diversification.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenine / metabolism*
  • Base Sequence
  • DNA Methylation* / genetics
  • Dinucleoside Phosphates / metabolism
  • Epigenesis, Genetic / physiology*
  • Eukaryota / genetics
  • Eukaryotic Cells
  • Genetic Markers
  • Methyltransferases / classification
  • Methyltransferases / physiology*
  • Organisms, Genetically Modified
  • Tetrahymena thermophila* / genetics
  • Tetrahymena thermophila* / metabolism
  • Transcription, Genetic*


  • Dinucleoside Phosphates
  • Genetic Markers
  • Methyltransferases
  • Adenine