title: Evidence of function for conserved noncoding sequences in Arabidopsis thaliana.
abstract: • 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.
authors.affiliation: Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, USA.
authors.forename: Jacob B
authors.initials: JB
authors.lastname: Spangler
authors.affiliation: Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA.
authors.forename: Sabarinath
authors.initials: S
authors.lastname: Subramaniam
authors.affiliation: Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Freeling
authors.affiliation: Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, USA.
authors.forename: F Alex
authors.initials: FA
authors.lastname: Feltus
mesh_terms: D020121:5' Untranslated Regions / Q000235:genetics; D017360:Arabidopsis / Q000187:drug effects / Q000235:genetics* / Q000528:radiation effects; D001483:Base Sequence; D017124:Conserved Sequence / Q000235:genetics*; D021901:DNA, Intergenic / Q000235:genetics*; D018506:Gene Expression Regulation, Plant / Q000187:drug effects / Q000528:radiation effects; D020131:Genes, Duplicate / Q000235:genetics; D007438:Introns / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D010937:Plant Growth Regulators / Q000494:pharmacology; D013816:Thermodynamics; D014158:Transcription, Genetic / Q000187:drug effects / Q000528:radiation effects; D014466:Ultraviolet Rays
chemical_list: D020121:5' Untranslated Regions; D021901:DNA, Intergenic; D010937:Plant Growth Regulators