title: Upstream regulatory architecture of rice genes: summarizing the baseline towards genus-wide comparative analysis of regulatory networks and allele mining.
abstract: Dissecting the upstream regulatory architecture of rice genes and their cognate regulator proteins is at the core of network biology and its applications to comparative functional genomics. With the rapidly advancing comparative genomics resources in the genus Oryza, a reference genome annotation that defines the various cis-elements and trans-acting factors that interface each gene locus with various intrinsic and extrinsic signals for growth, development, reproduction and adaptation must be established to facilitate the understanding of phenotypic variation in the context of regulatory networks. Such information is also important to establish the foundation for mining non-coding sequence variation that defines novel alleles and epialleles across the enormous phenotypic diversity represented in rice germplasm. This review presents a synthesis of the state of knowledge and consensus trends regarding the various cis-acting and trans-acting components that define spatio-temporal regulation of rice genes based on representative examples from both foundational studies in other model and non-model plants, and more recent studies in rice. The goal is to summarize the baseline for systematic upstream sequence annotation of the rapidly advancing genome sequence resources in Oryza in preparation for genus-wide functional genomics. Perspectives on the potential applications of such information for gene discovery, network engineering and genomics-enabled rice breeding are also discussed.
authors.affiliation: School of Biology and Ecology, University of Maine, Orono, ME 04469 USA.
authors.forename: Benildo G
authors.initials: BG
authors.lastname: de Los Reyes
authors.affiliation: Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117576 Singapore.
authors.forename: Bijayalaxmi
authors.initials: B
authors.lastname: Mohanty
authors.affiliation: Department of Crop Science and Institute of Agricultural Science and Technology, Chonbuk National University, Chonju, 561-756 Korea.
authors.forename: Song Joong
authors.initials: SJ
authors.lastname: Yun
authors.affiliation: School of Biology and Ecology, University of Maine, Orono, ME 04469 USA.
authors.forename: Myoung-Ryoul
authors.initials: MR
authors.lastname: Park
authors.affiliation: Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117576 Singapore.
authors.forename: Dong-Yup
authors.initials: DY
authors.lastname: Lee
keywords: Cis-elements; Comparative genomics; Regulatory network; Spatio-temporal regulation; Trans-acting factors
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