title: Conserved non-coding regulatory signatures in Arabidopsis co-expressed gene modules.
abstract: Complex traits and other polygenic processes require coordinated gene expression. Co-expression networks model mRNA co-expression: the product of gene regulatory networks. To identify regulatory mechanisms underlying coordinated gene expression in a tissue-enriched context, ten Arabidopsis thaliana co-expression networks were constructed after manually sorting 4,566 RNA profiling datasets into aerial, flower, leaf, root, rosette, seedling, seed, shoot, whole plant, and global (all samples combined) groups. Collectively, the ten networks contained 30% of the measurable genes of Arabidopsis and were circumscribed into 5,491 modules. Modules were scrutinized for cis regulatory mechanisms putatively encoded in conserved non-coding sequences (CNSs) previously identified as remnants of a whole genome duplication event. We determined the non-random association of 1,361 unique CNSs to 1,904 co-expression network gene modules. Furthermore, the CNS elements were placed in the context of known gene regulatory networks (GRNs) by connecting 250 CNS motifs with known GRN cis elements. Our results provide support for a regulatory role of some CNS elements and suggest the functional consequences of CNS activation of co-expression in specific gene sets dispersed throughout the genome.
authors.affiliation: Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America.
authors.forename: Jacob B
authors.initials: JB
authors.lastname: Spangler
authors.forename: Stephen P
authors.initials: SP
authors.lastname: Ficklin
authors.forename: Feng
authors.initials: F
authors.lastname: Luo
authors.forename: Michael
authors.initials: M
authors.lastname: Freeling
authors.forename: F Alex
authors.initials: FA
authors.lastname: Feltus
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D002874:Chromosome Mapping; D019295:Computational Biology / Q000379:methods; D017124:Conserved Sequence / Q000235:genetics*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D008954:Models, Biological; D022661:RNA, Untranslated
chemical_list: D022661:RNA, Untranslated