Highly interwoven communities of a gene regulatory network unveil topologically important genes for maize seed development

• DOI: 10.1111/tpj.13750
• Publication Date: 2017-10-26T16:46:48Z
• Authors: Wenwei Xiong; Chunlei Wang; Xiangbo Zhang; Qinghua Yang; Ruixin Shao; Jinsheng Lai; Chunguang Du
• Keywords: Gene regulatory network; RNA-Seq; DECIPHER

The complex interactions between transcription factors (TFs) and their target genes in a spatially temporally specific manner are crucial to all cellular processes. Reconstruction of gene regulatory networks (GRNs) from expression profiles can help decipher TF-gene regulations variety contexts; however, the inevitable prediction errors GRNs hinder optimal data mining RNA-Seq transcriptome profiles. Here we perform an integrative study Zea mays (maize) seed development order identify key developmental process. First, reverse engineered GRN 78 maize Then, studied collective interaction patterns uncovered highly interwoven network communities as building blocks GRN. One community, composed mostly unknown interacting with opaque2, brittle endosperm1 shrunken2, contributes phenotypes. Another expressed basal endosperm transfer layer, is responsible for nutrient transport. We further integrated our inferred different compartments at various stages pathways. integration facilitated biological interpretation Our yeast one-hybrid assays verified six out eight TF-promoter bindings reconstructed This identified topologically important that may be development.