Chromatin structure and gene expression changes associated with loss of MOP1 activity in Zea mays

Epigenetics. 2014 Jul;9(7):1047-59. doi: 10.4161/epi.29022. Epub 2014 May 1.


Though the mechanisms governing nuclear organization are not well understood, it is apparent that epigenetic modifications coordinately modulate chromatin organization as well as transcription. In maize, MEDIATOR OF PARAMUTATION1 (MOP1) is required for 24 nt siRNA-mediated epigenetic regulation and transcriptional gene silencing via a putative Pol IV- RdDM pathway. To elucidate the mechanisms of nuclear chromatin organization, we investigated the relationship between chromatin structure and transcription in response to loss of MOP1 function. We used a microarray based micrococcal nuclease sensitivity assay to identify genome-wide changes in chromatin structure in mop1-1 immature ears and observed an increase in chromatin accessibility at chromosome arms associated with loss of MOP1 function. Within the many genes misregulated in mop1 mutants, we identified one subset likely to be direct targets of epigenetic transcriptional silencing via Pol-IV RdDM. We found that target specificity for MOP1-mediated RdDM activity is governed by multiple signals that include accumulation of 24 nt siRNAs and the presence of specific classes of gene-proximal transposons, but neither of these attributes alone is sufficient to predict transcriptional misregulation in mop1-1 homozygous mutants. Our results suggest a role for MOP1 in regulation of higher-order chromatin organization where loss of MOP1 activity at a subset of loci triggers a broader cascade of transcriptional consequences and genome-wide changes in chromatin structure.

Keywords: RNA-dependent RNA polymerase2 (RDR2); RNA-directed DNA methylation (RdDM); Zea mays; chromatin; epigenetics; gene expression; mediator of paramutation1; micrococcal nuclease (MNase) sensitivity; small RNAs.

Publication types

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

MeSH terms

  • Chromatin / genetics*
  • Chromatin / metabolism
  • DNA Methylation
  • DNA Transposable Elements
  • Down-Regulation
  • Epigenesis, Genetic
  • Gene Expression Regulation, Plant
  • Gene Silencing
  • Mutation
  • Plant Proteins / genetics*
  • Plant Proteins / metabolism
  • Promoter Regions, Genetic
  • RNA, Small Interfering / metabolism
  • Seeds / genetics
  • Seeds / metabolism
  • Signal Transduction
  • Up-Regulation
  • Zea mays / genetics*
  • Zea mays / metabolism


  • Chromatin
  • DNA Transposable Elements
  • Plant Proteins
  • RNA, Small Interfering