The MADS-box transcription factor PHERES1 controls imprinting in the endosperm by binding to domesticated transposons

Elife. 2019 Dec 2;8:e50541. doi: 10.7554/eLife.50541.


MADS-box transcription factors (TFs) are ubiquitous in eukaryotic organisms and play major roles during plant development. Nevertheless, their function in seed development remains largely unknown. Here, we show that the imprinted Arabidopsis thaliana MADS-box TF PHERES1 (PHE1) is a master regulator of paternally expressed imprinted genes, as well as of non-imprinted key regulators of endosperm development. PHE1 binding sites show distinct epigenetic modifications on maternal and paternal alleles, correlating with parental-specific transcriptional activity. Importantly, we show that the CArG-box-like DNA-binding motifs that are bound by PHE1 have been distributed by RC/Helitron transposable elements. Our data provide an example of the molecular domestication of these elements which, by distributing PHE1 binding sites throughout the genome, have facilitated the recruitment of crucial endosperm regulators into a single transcriptional network.

Keywords: A. thaliana; MADS-box transcription factors; PHERES1; endosperm; genetics; genomics; imprinting; plant biology; seed; transposable elements.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs
  • Arabidopsis / embryology*
  • Arabidopsis / genetics*
  • Arabidopsis Proteins / genetics
  • Arabidopsis Proteins / metabolism*
  • Base Sequence
  • Crosses, Genetic
  • DNA Transposable Elements / genetics*
  • Domestication*
  • Endosperm / genetics*
  • Epigenesis, Genetic
  • Gene Expression Regulation, Plant
  • Genes, Plant
  • Genomic Imprinting*
  • Histones / metabolism
  • Lysine / metabolism
  • MADS Domain Proteins / genetics
  • MADS Domain Proteins / metabolism*
  • Methylation
  • Polyploidy
  • Promoter Regions, Genetic / genetics
  • Protein Binding / genetics
  • Seeds / genetics


  • Arabidopsis Proteins
  • DNA Transposable Elements
  • Histones
  • MADS Domain Proteins
  • PHERES1 protein, Arabidopsis
  • Lysine

Associated data

  • GEO/GSE129744
  • GEO/GSE66585
  • GEO/GSE84122
  • GEO/GSE53642
  • GEO/GSE119915
  • GEO/GSE12404

Grant support

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.