Transcription factor binding to a DNA zip code controls interchromosomal clustering at the nuclear periphery

Dev Cell. 2012 Jun 12;22(6):1234-46. doi: 10.1016/j.devcel.2012.03.012. Epub 2012 May 10.


Active genes in yeast can be targeted to the nuclear periphery through interaction of cis-acting "DNA zip codes" with the nuclear pore complex. We find that genes with identical zip codes cluster together. This clustering was specific; pairs of genes that were targeted to the nuclear periphery by different zip codes did not cluster together. Insertion of two different zip codes (GRS I or GRS III) at an ectopic site induced clustering with endogenous genes that have that zip code. Targeting to the nuclear periphery and interaction with the nuclear pore is a prerequisite for gene clustering, but clustering can be maintained in the nucleoplasm. Finally, we find that the Put3 transcription factor recognizes the GRS I zip code to mediate both targeting to the NPC and interchromosomal clustering. These results suggest that zip-code-mediated clustering of genes at the nuclear periphery influences the three-dimensional arrangement of the yeast genome.

Publication types

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

MeSH terms

  • Chromosomes, Fungal / genetics
  • Chromosomes, Fungal / metabolism*
  • DNA / genetics*
  • Gene Expression Regulation, Fungal*
  • Glycine-tRNA Ligase / genetics
  • Glycine-tRNA Ligase / metabolism*
  • Multigene Family
  • Nuclear Pore / metabolism
  • Promoter Regions, Genetic
  • Saccharomyces cerevisiae / genetics
  • Saccharomyces cerevisiae / metabolism
  • Saccharomyces cerevisiae Proteins / genetics
  • Saccharomyces cerevisiae Proteins / metabolism*
  • Transcription Factors / metabolism*


  • PUT3 protein, S cerevisiae
  • Saccharomyces cerevisiae Proteins
  • Transcription Factors
  • DNA
  • GRS1 protein, S cerevisiae
  • Glycine-tRNA Ligase