Dataset Information

Transcriptome profiling and weighted gene co-expression network analysis of early floral development in Aquilegia coerulea.

ABSTRACT: The earliest phases of floral development include a number of crucial processes that lay the foundation for the subsequent morphogenesis of floral organs and success in reproduction. Currently, key transcriptional changes during this developmental window have been characterized in the model species Arabidopsis thaliana, but little is known about how transcriptional dynamics change over the course of these developmental processes in other plant systems. Here, we have conducted the first in-depth transcriptome profiling of early floral development in Aquilegia at four finely dissected developmental stages, with eight biological replicates per stage. Using differential gene expression analysis and weighted gene co-expression network analysis, we identified both crucial genes whose expression changes mark the transitions between developmental stages and hub genes in co-expression modules. Our results support the potential functional conservation of key genes in early floral development that have been identified in other systems, but also reveal a number of previously unknown or overlooked loci that are worthy of further investigation. In addition, our results highlight not only the dynamics of transcriptional regulation during early floral development, but also the potential involvement of the complex, essential networks of small RNA and post-translational regulation to these developmental stages.

SUBMITTER: Min Y

PROVIDER: S-EPMC7665038 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

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Transcriptome profiling and weighted gene co-expression network analysis of early floral development in Aquilegia coerulea.

Min Ya Y Kramer Elena M EM

Scientific reports 20201112 1

The earliest phases of floral development include a number of crucial processes that lay the foundation for the subsequent morphogenesis of floral organs and success in reproduction. Currently, key transcriptional changes during this developmental window have been characterized in the model species Arabidopsis thaliana, but little is known about how transcriptional dynamics change over the course of these developmental processes in other plant systems. Here, we have conducted the first in-depth ...[more]

PMID: 33184405

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Project description:BACKGROUND: Epigenetic regulation is necessary for maintaining gene expression patterns in multicellular organisms. The Polycomb Group (PcG) proteins form several complexes with important and deeply conserved epigenetic functions in both the plant and animal kingdoms. One such complex, the Polycomb Repressive Complex 2 (PRC2), is critical to many developmental processes in plants including the regulation of major developmental transitions. In addition, PRC2 restricts the expression domain of various transcription factor families in Arabidopsis, including the class I KNOX genes and several of the ABCE class MADS box genes. While the functions of these transcription factors are known to be deeply conserved, whether or not their regulation by PRC2 is similarly conserved remains an open question. RESULTS: Here we use virus-induced gene silencing (VIGS) to characterize the function of the PRC2 complex in lateral organ development of Aquilegia x coerulea 'Origami', a member of the lower eudicot order Ranunculales. Leaves with PRC2 down-regulation displayed a range of phenotypes including ruffled or curled laminae, additional lobing, and an increased frequency of higher order branching. Sepals and petals were also affected, being narrowed, distorted, or, in the case of the sepals, exhibiting partial homeotic transformation. Many of the petal limbs also had a particularly intense yellow coloration due to an accumulation of carotenoid pigments. We show that the A. x coerulea floral MADS box genes AGAMOUS1 (AqAG1), APETALA3-3 (AqAP3-3) and SEPALLATA3 (AqSEP3) are up-regulated in many tissues, while expression of the class I KNOX genes and several candidate genes involved in carotenoid production or degradation are largely unaffected. CONCLUSIONS: PRC2 targeting of several floral MADS box genes may be conserved in dicots, but other known targets do not appear to be. In the case of the type I KNOX genes, this may reflect a regulatory shift associated with the evolution of compound leaves.

Project description:ObjectiveVaricose veins are a common problem worldwide and can cause significant impairments in health-related quality of life, but the etiology and pathogenesis remain not well defined. This study aims to elucidate transcriptomic regulations of varicose veins by detecting differentially expressed genes, pathways and regulator genes.MethodsWe harvested great saphenous veins (GSV) from patients who underwent coronary artery bypass grafting (CABG) and varicose veins from conventional stripping surgery. RNA-Sequencing (RNA-Seq) technique was used to obtain the complete transcriptomic data of both GSVs from CABG patients and varicose veins. Weighted Gene Co-expression network analysis (WGCNA) and further analyses were then carried out with the aim to elucidate transcriptomic regulations of varicose veins by detecting differentially expressed genes, pathways and regulator genes.ResultsFrom January 2015 to December 2016, 7 GSVs from CABG patients and 13 varicose veins were obtained. WGCNA identified 4 modules. In the brown module, gene ontology (GO) analysis showed that the biological processes were focused on response to stimulus, immune response and inflammatory response, etc. Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis showed that the biological processes were focused on cytokine-cytokine receptor interaction and TNF signaling pathway, etc. In the gray module, GO analysis showed that the biological processes were skeletal myofibril assembly related. The immunohistochemistry staining showed that the expression of ASC, Caspase-1 and NLRP3 were increased in GSVs from CABG patients compared with varicose veins. Histopathological analysis showed that in the varicose veins group, the thickness of vascular wall, tunica intima, tunica media and collagen/smooth muscle ratio were significantly increased, and that the elastic fiber/internal elastic lamina ratio was decreased.ConclusionThis study shows that there are clear differences in transcriptomic information between varicose veins and GSVs from CABG patients. Some inflammatory RNAs are down-regulated in varicose veins compared with GSVs from CABG patients. Skeletal myofibril assembly pathway may play a crucial role in the pathogenesis of varicose veins. Characterization of these RNAs may provide new targets for understanding varicose veins diagnosis, progression, and treatment.

Dataset Information

Transcriptome profiling and weighted gene co-expression network analysis of early floral development in Aquilegia coerulea.

Publications

Transcriptome profiling and weighted gene co-expression network analysis of early floral development in Aquilegia coerulea.

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