Genome-wide prediction of Polycomb/Trithorax response elements in Drosophila melanogaster

Dev Cell. 2003 Nov;5(5):759-71. doi: 10.1016/s1534-5807(03)00337-x.


Polycomb/Trithorax response elements (PRE/TREs) maintain transcriptional decisions to ensure correct cell identity during development and differentiation. There are thought to be over 100 PRE/TREs in the Drosophila genome, but only very few have been identified due to the lack of a defining consensus sequence. Here we report the definition of sequence criteria that distinguish PRE/TREs from non-PRE/TREs. Using this approach for genome-wide PRE/TRE prediction, we identify 167 candidate PRE/TREs, which map to genes involved in development and cell proliferation. We show that candidate PRE/TREs are bound and regulated by Polycomb proteins in vivo, thus demonstrating the validity of PRE/TRE prediction. Using the larger data set thus generated, we identify three sequence motifs that are conserved in PRE/TRE sequences.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Base Sequence
  • Cell Division / physiology
  • Cell Line
  • Cluster Analysis
  • DNA-Binding Proteins / genetics*
  • DNA-Binding Proteins / metabolism
  • Drosophila Proteins / genetics*
  • Drosophila Proteins / metabolism
  • Drosophila melanogaster / anatomy & histology
  • Drosophila melanogaster / genetics*
  • Drosophila melanogaster / physiology
  • Female
  • Gene Expression Regulation
  • Genome*
  • Male
  • Molecular Sequence Data
  • Polycomb Repressive Complex 1
  • Response Elements / genetics*
  • Sequence Analysis, DNA
  • Transcription Factors*
  • Transgenes


  • DNA-Binding Proteins
  • Drosophila Proteins
  • Pc protein, Drosophila
  • Transcription Factors
  • Trl protein, Drosophila
  • Polycomb Repressive Complex 1