BORDER proteins protect expression of neighboring genes by promoting 3' Pol II pausing in plants

Nat Commun. 2019 Sep 25;10(1):4359. doi: 10.1038/s41467-019-12328-w.


Ensuring that one gene's transcription does not inappropriately affect the expression of its neighbors is a fundamental challenge to gene regulation in a genomic context. In plants, which lack homologs of animal insulator proteins, the mechanisms that prevent transcriptional interference are not well understood. Here we show that BORDER proteins are enriched in intergenic regions and prevent interference between closely spaced genes on the same strand by promoting the 3' pausing of RNA polymerase II at the upstream gene. In the absence of BORDER proteins, 3' pausing associated with the upstream gene is reduced and shifts into the promoter region of the downstream gene. This is consistent with a model in which BORDER proteins inhibit transcriptional interference by preventing RNA polymerase from intruding into the promoters of downstream genes.

Publication types

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

MeSH terms

  • Arabidopsis / genetics*
  • Arabidopsis / growth & development
  • Arabidopsis / metabolism
  • Arabidopsis Proteins / genetics*
  • Arabidopsis Proteins / metabolism
  • Gene Expression Profiling / methods
  • Gene Expression Regulation, Developmental*
  • Gene Expression Regulation, Plant*
  • Mutation
  • Plant Roots / genetics*
  • Plant Roots / growth & development
  • Plant Roots / metabolism
  • Protein Isoforms / genetics
  • Protein Isoforms / metabolism
  • RNA Polymerase II / genetics*
  • RNA Polymerase II / metabolism
  • Seedlings / genetics
  • Seedlings / growth & development
  • Seedlings / metabolism
  • Transcriptional Elongation Factors / genetics*
  • Transcriptional Elongation Factors / metabolism


  • Arabidopsis Proteins
  • At2g25640 protein, Arabidopsis
  • At5g11430 protein, Arabidopsis
  • At5g25520 protein, Arabidopsis
  • Protein Isoforms
  • Transcriptional Elongation Factors
  • RNA Polymerase II