Inference and prioritization of tissue-specific regulons in Arabidopsis and Oryza

This study is led by associate professor Junxiang Gao (Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China). A regulon is a cluster of genes regulated by a transcription factor binding to specific regulatory motifs to achieve distinct biological functions. The exploration of tissue-specific regulons in plants not only unveils gene expression patterns within specific tissues but also sheds light on the functions of the associated genes, contributing to a better understanding of the fundamental principles and dynamic changes in intergenic regulation. The authors developed a novel pipeline named InferReg to infer tissue-specific regulons in Arabidopsis. Using co-expression patterns, InferReg utilizes a gene expression matrix that includes 3400 Arabidopsis transcriptomes to make initial predictions about the regulatory relationships between transcription factors (TFs) and target genes (TGs). It enhances these expected interactions by incorporating TF binding site enrichment analysis to filter out false positives that are only supported by expression data. InferReg also used a graph convolutional network trained with 133 transcription factors, supported by ChIP-seq, as positive examples to understand the regulatory relationship between TFs and TGs, thus enhancing the precision of the regulatory network. To evaluate the functionality of InferReg, the authors utilized it to discover tissue-specific regulons in 5 Arabidopsis tissues: flower, leaf, root, seed, and seedling. The authors ranked the activities of regulons for each tissue based on reliability using Borda ranking and compared with existing databases. The results demonstrated that InferReg identified known tissue-specific regulons and discovered new ones. By applying InferReg to rice expression data, the authors were able to identify rice tissue-specific regulons, showing that this approach can be applied more broadly. The authors used InferReg to successfully identify important regulons in various tissues of Arabidopsis and Oryza, which has improved our understanding of tissue-specific regulations and the roles of regulons in tissue differentiation and development.

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Inference and prioritization of tissue-specific regulons in Arabidopsis and Oryza

https://link.springer.com/article/10.1007/s42994-024-00176-2