Heterochromatin dynamics during developmental transitions in Arabidopsis - a focus on ribosomal DNA loci

Gene. 2013 Aug 15;526(1):39-45. doi: 10.1016/j.gene.2013.01.060. Epub 2013 Feb 12.


The Arabidopsis chromosomes contain conspicuous heterochromatin domains comprising the repetitive 45S and 5S ribosomal DNA loci as well as centromeric and pericentromeric repeats that organize into chromocenters during interphase. During developmental phase transitions such as seed maturation, germination, seedling growth and flowering that require large-scale reprogramming of gene expression patterns, the organization of repetitive sequences into chromocenters dynamically changes. Here we illustrate recent studies that shed light on the heterochromatin dynamics in cotyledons, the first aerial tissues preformed in the embryo, and in true leaves. We will summarize available data for the 5S rDNA repeat loci, in particular their chromatin organization and expression dynamics during the first days of post-germination development, and discuss how the plant accommodates 5S rRNA transcription during large-scale chromatin reorganization events.

Keywords: 4′,6′-diamidino-2-phenylindole; 5 methylcytosine; 5mC; Arabidopsis thaliana; Cotyledon; DAPI; Development; FISH; Heterochromatin; Phase transition; RHF; RNA-directed DNA methylation; ROS; RdDM; Ribosomal DNA; TFIIIA; fluorescence in situ hybridization; rDNA/rRNA; relative heterochromatin fraction; repressor of silencing 1; ribosomal DNA/RNA; si-RNA; small interfering RNA; transcription factor IIIA.

Publication types

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

MeSH terms

  • Arabidopsis / genetics*
  • Arabidopsis / growth & development
  • Arabidopsis / metabolism*
  • Cotyledon / embryology
  • Cotyledon / metabolism
  • DNA, Plant / genetics*
  • DNA, Plant / metabolism*
  • DNA, Ribosomal / genetics*
  • DNA, Ribosomal / metabolism*
  • Gene Expression Regulation, Developmental
  • Gene Expression Regulation, Plant
  • Germination
  • Heterochromatin / genetics
  • Heterochromatin / metabolism
  • RNA, Plant / genetics
  • RNA, Plant / metabolism
  • RNA, Ribosomal, 5S / genetics
  • RNA, Ribosomal, 5S / metabolism
  • Seedlings / growth & development
  • Seedlings / metabolism


  • DNA, Plant
  • DNA, Ribosomal
  • Heterochromatin
  • RNA, Plant
  • RNA, Ribosomal, 5S