Production of aberrant promoter transcripts contributes to methylation and silencing of unlinked homologous promoters in trans

EMBO J. 1999 Jan 4;18(1):241-8. doi: 10.1093/emboj/18.1.241.


Previous work has suggested that de novo methylation of plant nuclear genes can be triggered by an RNA-DNA interaction. To test whether transcription of a promoter would induce de novo methylation and silencing of unlinked genes driven by the same promoter, a chimeric 'gene' consisting of a nopaline synthase promoter (NOSpro) positioned downstream of the cauliflower mosaic virus 35S promoter (35Spro) and flanked at the 3' end by a NOS terminator (NOSter) was constructed and introduced into the genome of a plant that normally expresses an unmethylated NOSpro-neomycinphosphotransferase (nptII) gene. Transformants were tested for kanamycin resistance and NOSpro RNA synthesis. Most produced a full-length polyadenylated NOSpro RNA, which did not induce silencing or methylation at the NOSpro-nptII target gene. One, however, contained truncated non-polyadenylated NOSpro RNA; in this plant, the NOSpro-nptII gene became silenced and methylated in the NOSpro region. Molecular analysis of the NOSpro silencing locus revealed two incomplete copies of the 35Spro-NOSpro gene arranged as an inverted repeat with NOSpro sequences at the center. Reducing NOSpro transcription by crossing a 35Spro-silencing locus partially reactivated nptII gene expression and decreased NOSpro methylation at the target locus, thus implicating aberrant NOSpro RNA in this trans-silencing phenomenon.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Oxidoreductases / genetics
  • Chimera / genetics
  • DNA Methylation*
  • DNA, Plant / genetics*
  • DNA, Plant / metabolism*
  • Gene Expression Regulation, Enzymologic
  • Gene Expression Regulation, Plant
  • Genes, Plant*
  • Kanamycin Resistance / genetics
  • Plants, Genetically Modified
  • Promoter Regions, Genetic*
  • RNA, Plant / genetics
  • RNA, Plant / metabolism
  • Transcription, Genetic


  • DNA, Plant
  • RNA, Plant
  • Amino Acid Oxidoreductases
  • nopaline synthase

Associated data

  • GENBANK/AJ007903