Long-range control of gene expression via RNA-directed DNA methylation

M. Jordan Rowley, M. Hafiz Rothi, Gudrun Böhmdorfer, Jan Kuciński, Andrzej T. Wierzbicki

Research output: Contribution to journalArticle

12 Scopus citations

Abstract

RNA-mediated transcriptional silencing, in plants known as RNA-directed DNA methylation (RdDM), is a conserved process where small interfering RNA (siRNA) and long non-coding RNA (lncRNA) help establish repressive chromatin modifications. This process represses transposons and affects the expression of protein-coding genes. We found that in Arabidopsis thaliana AGO4 binding sites are often located distant from genes differentially expressed in ago4. Using Hi-C to compare interactions between genotypes, we show that RdDM-targeted loci have the potential to engage in chromosomal interactions, but these interactions are inhibited in wild-type conditions. In mutants defective in RdDM, the frequency of chromosomal interactions at RdDM targets is increased. This includes increased frequency of interactions between Pol V methylated sites and distal genes that are repressed by RdDM. We propose a model, where RdDM prevents the formation of chromosomal interactions between genes and their distant regulatory elements.

Original languageEnglish (US)
Article numbere1006749
JournalPLoS genetics
Volume13
Issue number5
DOIs
StatePublished - May 2017

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ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics
  • Genetics(clinical)
  • Cancer Research

Cite this

Rowley, M. J., Rothi, M. H., Böhmdorfer, G., Kuciński, J., & Wierzbicki, A. T. (2017). Long-range control of gene expression via RNA-directed DNA methylation. PLoS genetics, 13(5), [e1006749]. https://doi.org/10.1371/journal.pgen.1006749