Evidence of function for conserved noncoding sequences in Arabidopsis thaliana


Author for correspondence:
F. Alex Feltus
Tel: +1 864 656 3231
Email: ffeltus@clemson.edu


  • Whole genome duplication events provide a lineage with a large reservoir of genes that can be molded by evolutionary forces into phenotypes that fit alternative environments. A well-studied whole genome duplication, the α-event, occurred in an ancestor of the model plant Arabidopsis thaliana. Retained segments of the α-event have been defined in recent years in the form of duplicate protein coding sequences (α-pairs) and associated conserved noncoding DNA sequences (CNSs). Our aim was to identify any association between CNSs and α-pair co-functionality at the gene expression level.
  • Here, we tested for correlation between CNS counts and α-pair co-expression and expression intensity across nine expression datasets: aerial tissue, flowers, leaves, roots, rosettes, seedlings, seeds, shoots and whole plants.
  • We provide evidence for a putative regulatory role of the CNSs. The association of CNSs with α-pair co-expression and expression intensity varied by gene function, subgene position and the presence of transcription factor binding motifs. A range of possible CNS regulatory mechanisms, including intron-mediated enhancement, messenger RNA fold stability and transcriptional regulation, are discussed.
  • This study provides a framework to understand how CNS motifs are involved in the maintenance of gene expression after a whole genome duplication event.