Conserved noncoding sequences highlight shared components of regulatory networks in dicotyledonous plants

Plant Cell. 2012 Oct;24(10):3949-65. doi: 10.1105/tpc.112.103010. Epub 2012 Oct 30.

Abstract

Conserved noncoding sequences (CNSs) in DNA are reliable pointers to regulatory elements controlling gene expression. Using a comparative genomics approach with four dicotyledonous plant species (Arabidopsis thaliana, papaya [Carica papaya], poplar [Populus trichocarpa], and grape [Vitis vinifera]), we detected hundreds of CNSs upstream of Arabidopsis genes. Distinct positioning, length, and enrichment for transcription factor binding sites suggest these CNSs play a functional role in transcriptional regulation. The enrichment of transcription factors within the set of genes associated with CNS is consistent with the hypothesis that together they form part of a conserved transcriptional network whose function is to regulate other transcription factors and control development. We identified a set of promoters where regulatory mechanisms are likely to be shared between the model organism Arabidopsis and other dicots, providing areas of focus for further research.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis / genetics*
  • Binding Sites
  • Carica / genetics*
  • Conserved Sequence
  • DNA, Plant / chemistry*
  • Gene Expression Regulation, Plant*
  • Gene Regulatory Networks*
  • Genomics
  • Nucleosomes / metabolism
  • Populus / genetics*
  • Sequence Analysis, DNA
  • Software
  • Vitis / genetics*

Substances

  • DNA, Plant
  • Nucleosomes