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Plants have evolved with complex sensory systems to recognize signals from multiple environmental conditions. A light signal is one of the most important environmental factors that regulates not only photomorphogenesis but also the developmental strategy of plants throughout their life cycle. The molecular mechanisms of the light signaling modules and the interactions between light and other environmental signals have been studied extensively. However, to enhance plant growth, particularly in crop production, we need to gain a deeper understanding of how light regulates plant development within gene regulatory networks (GRNs). Understanding GRNs is important to identify not only the novel genes and transcription factors in light signaling pathways but also the factors that connect light signaling and other environmental signals. Weighted gene co-expression network analysis (WGCNA) has been used to study GRN. We applied WGCNA to 58 RNA-seq samples of wild-type Arabidopsis grown under different light treatments and built the gene co-expression networks. We identified 14 different modules that are significantly associated with different light treatments. Among them, the honeydew1 and ivory display significant association with the dark-grown seedlings. Many hub genes identified from these modules are significantly enriched in light responses, including responses to red, far-red, blue light, light stimulus, auxin responses, and photosynthesis. Although we found many known transcription factors in these modules, we also identified several unknown genes and transcription factors that are significantly associated with the honeydew1 module and highly differentially expressed between dark and light conditions. To examine whether the hub genes in the honeydew1 module play a role in light signaling, we isolated mutants in selected hub genes and measured hypocotyl lengths under dark, red, and far-red light conditions. These assays showed that four hub genes are involved in regulating light signaling pathways. This study provides a new approach to identifying novel genes in GRNs underlying light responses in Arabidopsis.
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The Role of Core and Variable Gene Regulatory Network Modules in Tooth Development and Evolution
Synopsis Among the developmental processes that have been proposed to influence the direction of evolution, the modular organization of developmental gene regulatory networks (GRNs) has shown particular promise. In theory, GRNs have core modules comprised of essential, conserved circuits of genes, and sub-modules of downstream, secondary circuits of genes that are more susceptible to variation. While this idea has received considerable interest as of late, the field of evo-devo lacks the experimental systems needed to rigorously evaluate this hypothesis. Here, we introduce an experimental system, the vertebrate tooth, that has great potential as a model for testing this hypothesis. Tooth development and its associated GRN have been well studied and modeled in both model and non-model organisms. We propose that the existence of modules within the tooth GRN explains both the conservation of developmental mechanisms and the extraordinary diversity of teeth among vertebrates. Based on experimental data, we hypothesize that there is a conserved core module of genes that is absolutely necessary to ensure tooth or cusp initiation and development. In regard to tooth shape variation between species, we suggest that more relaxed sub-modules activated at later steps of tooth development, for example, during the morphogenesis of the tooth and its cusps, control the different axes of tooth morphological variation.
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- PAR ID:
- 10282222
- Date Published:
- Journal Name:
- Integrative and Comparative Biology
- ISSN:
- 1540-7063
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1093/icb/icaa116
