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

Leaves are the primary photosynthetic organs, providing essential substances for tree growth. It is important to obtain an anatomical understanding and regulatory network analysis of leaf development. Here, we studied leaf development in Populus Nanlin895 along a development gradient from the newly emerged leaf from the shoot apex to the sixth leaf (L1 to L6) using anatomical observations and RNA-seq analysis. It indicated that mesophyll cells possess obvious vascular, palisade, and spongy tissue with distinct intercellular spaces after L3. Additionally, vacuoles fuse while epidermal cells expand to form pavement cells. RNA-seq analysis indicated that genes highly expressed in L1 and L2 were related to cell division and differentiation, while those highly expressed in L3 were enriched in photosynthesis. Therefore, we selected L1 and L3 to integrate ATAC-seq and RNA-seq and identified 735 differentially expressed genes (DEGs) with changes in chromatin accessibility regions within their promoters, of which 87 were transcription factors (TFs), such as ABI3VP1, AP-EREBP, MYB, NAC, and GRF. Motif enrichment analysis revealed potential regulatory functions for the DEGs through upstream TFs including TCP, bZIP, HD-ZIP, Dof, BBR-BPC, and MYB. Overall, our research provides a potential molecular foundation for regulatory network exploration in leaf development during photosynthesis establishment.

Automated summary

In this study, leaf development in Populus Nanlin895 was investigated using anatomical observations and RNA-seq analysis. The results showed that mesophyll cells exhibited distinct vascular, palisade, and spongy tissue with intercellular spaces after the third leaf. RNA-seq analysis revealed that genes highly expressed in the first and second leaf were related to cell division and differentiation, while those highly expressed in the third leaf were enriched in photosynthesis. Integration of ATAC-seq and RNA-seq identified 735 differentially expressed genes (DEGs) with changes in chromatin accessibility, including 87 transcription factors (TFs). Motif enrichment analysis suggested potential regulatory functions for the DEGs through upstream TFs such as TCP, bZIP, HD-ZIP, Dof, BBR-BPC, and MYB. Overall, this research provides a potential molecular foundation for exploring the regulatory network of leaf development.