conserved non-coding regulatory signatures in arabidopsis co-expressed gene modules守恒的非编码调控基因在拟南芥中的签名模块.pdf

Conserved Non-Coding Regulatory Signatures in Arabidopsis Co-Expressed Gene Modules 1 2 3 4 1,2 Jacob B. Spangler , Stephen P. Ficklin , Feng Luo , Michael Freeling , F. Alex Feltus * 1 Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America, 2 Plant and Environmental Sciences, Clemson University, Clemson, South Carolina, United States of America, 3 School of Computing, Clemson University, Clemson, South Carolina, United States of America, 4 Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America 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 GR