Integrating ATAC-seq and RNA-seq to identify differentially expressed genes with chromatin-accessible changes during photosynthetic establishment in Populus leaves

Abstract Leaves are the main photosynthetic organs to provide substance for secondary growth in woody plants. It is important to obtain an anatomical understanding and regulatory network analysis of leaf development.We first observed serial leaves of poplar anatomically using semi-thin sections, transmission electron microscopy, and scanning electron microscopy, and performed RNA-seq analysis. We found that the third leaf possesses the anatomy required for photosynthesis and the first to third leaves to represent a critical period for leaf development. Transcription factors bind to accessible promoter regions in chromatin and precisely regulate the expression of their target genes. Therefore, we selected the first and third leaves to use an assay for transposase‐accessible chromatin using sequencing (ATAC-seq) combined with RNA-seq to identify differentially expressed genes (DEGs) and their differentially accessible regions (DARs) during leaf development. We identified 390 and 345 DEGs in which DARs in promoter presented as more open (i.e. gain DARs and loss DARs) in the third and the first leaf, respectively. Meanwhile, we performed a motif enrichment analysis and found 17 and 15 upstream transcription factors (TFs) in the gain DARs and loss DARs. Furthermore, we could access the regulatory network of leaf development, which lays the molecular foundation for future understanding of leaf photosynthesis.