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

文献类型： 外文期刊

作者： Zhang, Sheng-Ying 1 ; Zhao, Biligen-Gaowa 1 ; Shen, Zhuo 3 ; Mei, Ying-Chang 1 ; Li, Guo 1 ; Dong, Feng-Qin 2 ; Zhang, Jiao 1 ; Chao, Qing 1 ; Wang, Bai-Chen 1 ;

作者机构： 1.Chinese Acad Sci, Inst Bot, Photosynth Res Ctr, Key Lab Photobiol, Beijing 100093, Peoples R China

2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China

3.Guangdong Acad Agr Sci, Vegetable Res Inst, Guangdong Key Lab New Technol Res Vegetables, Guangzhou 510640, Peoples R China

4.Northeast Forestry Univ, State Key Lab Tree Genet & Breeding, Harbin 150040, Peoples R China

5.Chinese Acad Sci, Inst Bot, Key Lab Plant Mol Physiol, Beijing, Peoples R China

关键词： Leaf anatomy; RNA-seq; ATAC-seq; Different expression genes; Different accessible regions; Transcription factors

期刊名称：PLANT MOLECULAR BIOLOGY （ 影响因子：5.1； 五年影响因子：5.3 ）

ISSN： 0167-4412

年卷期： 2023 年 113 卷 1-3 期

页码：

收录情况： SCI

摘要： 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.

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