The prevalence, evolution and chromatin signatures of plant regulatory elements

Nat Plants. 2019 Dec;5(12):1250-1259. doi: 10.1038/s41477-019-0548-z. Epub 2019 Nov 18.


Chromatin accessibility and modification is a hallmark of regulatory DNA, the study of which led to the discovery of cis-regulatory elements (CREs). Here, we characterize chromatin accessibility, histone modifications and sequence conservation in 13 plant species. We identified thousands of putative CREs and revealed that distal CREs are prevalent in plants, especially in species with large and complex genomes. The majority of distal CREs have been moved away from their target genes by transposable-element (TE) proliferation, but a substantial number of distal CREs also seem to be created by TEs. Finally, plant distal CREs are associated with three major types of chromatin signatures that are distinct from metazoans. Taken together, these results suggest that CREs are prevalent in plants, highly dynamic during evolution and function through distinct chromatin pathways to regulate gene expression.

Publication types

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

MeSH terms

  • Chromatin / genetics*
  • Chromatin / metabolism
  • DNA Transposable Elements
  • Gene Expression Regulation, Plant
  • Genome, Plant*
  • Phylogeny
  • Plant Proteins / genetics*
  • Plant Proteins / metabolism
  • Plants / classification
  • Plants / genetics*
  • Plants / metabolism
  • Regulatory Sequences, Nucleic Acid*


  • Chromatin
  • DNA Transposable Elements
  • Plant Proteins