Dataset Information

Expression and Functional Analyses of the WIP Gene Family in Arabidopsis.

ABSTRACT: The WIP family of transcription factors comprises the A1d subgroup of C2H2 zinc finger proteins. This family has six members in Arabidopsis thaliana and most of the known functions have been described by analyzing single knockout mutants. However, it has been shown that WIP2 and its closest paralogs WIP4 and WIP5 have a redundant and essential function in root meristems. It is likely that these and other WIP genes perform more, still unknown, functions. To obtain hints about these other functions, the expression of the six WIP genes was explored. Moreover, phenotypic ana-lyses of overexpressors and wip mutants revealed functions in modulating organ and cell size, stomatal density, and vasculature development.

SUBMITTER: Diaz-Ramirez D

PROVIDER: S-EPMC9425439 | biostudies-literature | 2022 Aug

REPOSITORIES: biostudies-literature

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Expression and Functional Analyses of the WIP Gene Family in Arabidopsis.

Diaz-Ramirez David D Diaz-Garcia Ury Sarai US Magdaleno-Garcia Guadalupe G Huep Gunnar G Appelhagen Ingo I Sagasser Martin M Marsch-Martinez Nayelli N

Plants (Basel, Switzerland) 20220801 15

The WIP family of transcription factors comprises the A1d subgroup of C2H2 zinc finger proteins. This family has six members in Arabidopsis thaliana and most of the known functions have been described by analyzing single knockout mutants. However, it has been shown that WIP2 and its closest paralogs WIP4 and WIP5 have a redundant and essential function in root meristems. It is likely that these and other WIP genes perform more, still unknown, functions. To obta ...[more]

PMID: 35956487

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Project description:BACKGROUND: Biological networks characterize the interactions of biomolecules at a systems-level. One important property of biological networks is the modular structure, in which nodes are densely connected with each other, but between which there are only sparse connections. In this report, we attempted to find the relationship between the network topology and formation of modular structure by comparing gene co-expression networks with random networks. The organization of gene functional modules was also investigated. RESULTS: We constructed a genome-wide Arabidopsis gene co-expression network (AGCN) by using 1094 microarrays. We then analyzed the topological properties of AGCN and partitioned the network into modules by using an efficient graph clustering algorithm. In the AGCN, 382 hub genes formed a clique, and they were densely connected only to a small subset of the network. At the module level, the network clustering results provide a systems-level understanding of the gene modules that coordinate multiple biological processes to carry out specific biological functions. For instance, the photosynthesis module in AGCN involves a very large number (> 1000) of genes which participate in various biological processes including photosynthesis, electron transport, pigment metabolism, chloroplast organization and biogenesis, cofactor metabolism, protein biosynthesis, and vitamin metabolism. The cell cycle module orchestrated the coordinated expression of hundreds of genes involved in cell cycle, DNA metabolism, and cytoskeleton organization and biogenesis. We also compared the AGCN constructed in this study with a graphical Gaussian model (GGM) based Arabidopsis gene network. The photosynthesis, protein biosynthesis, and cell cycle modules identified from the GGM network had much smaller module sizes compared with the modules found in the AGCN, respectively. CONCLUSION: This study reveals new insight into the topological properties of biological networks. The preferential hub-hub connections might be necessary for the formation of modular structure in gene co-expression networks. The study also reveals new insight into the organization of gene functional modules.

Dataset Information

Expression and Functional Analyses of the WIP Gene Family in Arabidopsis.

Publications

Expression and Functional Analyses of the <i>WIP</i> Gene Family in Arabidopsis.

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