Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone modification

PLoS Biol. 2003 Dec;1(3):E67. doi: 10.1371/journal.pbio.0000067. Epub 2003 Dec 22.


Heritable, but reversible, changes in transposable element activity were first observed in maize by Barbara McClintock in the 1950s. More recently, transposon silencing has been associated with DNA methylation, histone H3 lysine-9 methylation (H3mK9), and RNA interference (RNAi). Using a genetic approach, we have investigated the role of these modifications in the epigenetic regulation and inheritance of six Arabidopsis transposons. Silencing of most of the transposons is relieved in DNA methyltransferase (met1), chromatin remodeling ATPase (ddm1), and histone modification (sil1) mutants. In contrast, only a small subset of the transposons require the H3mK9 methyltransferase KRYPTONITE, the RNAi gene ARGONAUTE1, and the CXG methyltransferase CHROMOMETHYLASE3. In crosses to wild-type plants, epigenetic inheritance of active transposons varied from mutant to mutant, indicating these genes differ in their ability to silence transposons. According to their pattern of transposon regulation, the mutants can be divided into two groups, which suggests that there are distinct, but interacting, complexes or pathways involved in transposon silencing. Furthermore, different transposons tend to be susceptible to different forms of epigenetic regulation.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Adenosine Triphosphatases / genetics
  • Arabidopsis / genetics*
  • Arabidopsis Proteins / genetics
  • Arabidopsis Proteins / metabolism
  • Argonaute Proteins
  • Chromatin / metabolism
  • Chromatin Immunoprecipitation
  • Computational Biology
  • DNA (Cytosine-5-)-Methyltransferases / genetics
  • DNA Methylation
  • DNA Primers / chemistry
  • DNA Transposable Elements*
  • DNA-Binding Proteins / metabolism
  • DNA-Cytosine Methylases
  • Gene Expression Regulation, Plant*
  • Gene Silencing
  • Genes, Plant*
  • Histone-Lysine N-Methyltransferase / genetics
  • Histones / metabolism*
  • Models, Genetic
  • Mutation
  • Open Reading Frames
  • Polymerase Chain Reaction
  • RNA Interference
  • RNA, Small Interfering / genetics*
  • Transcription Factors / metabolism
  • Transcription, Genetic


  • AGO1 protein, Arabidopsis
  • Arabidopsis Proteins
  • Argonaute Proteins
  • Chromatin
  • DDM1 protein, Arabidopsis
  • DNA Primers
  • DNA Transposable Elements
  • DNA-Binding Proteins
  • Histones
  • RNA, Small Interfering
  • Transcription Factors
  • DNA-Cytosine Methylases
  • MET1 protein, Arabidopsis
  • CMT3 protein, Arabidopsis
  • DNA (Cytosine-5-)-Methyltransferases
  • Histone-Lysine N-Methyltransferase
  • SUVH4 protein, Arabidopsis
  • Adenosine Triphosphatases