Chromatin and regulatory differentiation between bundle sheath and mesophyll cells in maize
Chromatin and regulatory differentiation between bundle sheath and mesophyll cells in maize
复制标题
玉米中束鞘细胞和叶肉细胞之间的染色质和调节分化。
DOI：
10.1111/tpj.15586
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发表时间：
2021-12-15
期刊：
影响因子：
7.2
通讯作者：
Li, Pinghua
中科院分区：
文献类型：
--
作者：
Dai, Xiuru;Tu, Xiaoyu;Li, Pinghua
C-4植物在维管束鞘（BS）和叶肉（M）细胞之间分配光合酶，以更好地将CO2输送到RuBisCO并减少光呼吸。为了更好地理解C-4光合作用如何在转录水平上调节，我们对从玉米叶片分离的BS和M细胞进行了RNA-seq、ATAC-seq、ChIP-seq和BS-seq。通过整合差异表达基因与染色质特征，我们发现染色质可及性与表观遗传特征，特别是H3 K27 me 3修饰和CHH甲基化协调，以调节细胞类型优先富集的基因表达。不仅染色质可及区（ACR）近端的基因（pACR），而且远端的ACR（dACR）的细胞类型优先富集表达的决定因素。我们进一步鉴定了细胞类型优先富集的基序，例如BS细胞的AAAG和M细胞的TGACC/T，并确定了它们相应的转录因子：DOF和WRKY。顺式和反式因子在C-4基因的优先表达中也存在复杂的相互作用。有趣的是，细胞类型优先富集的基因表达可以通过多个染色质特征的协调进行微调。这种协调可能是至关重要的，以确保关键C-4基因的细胞类型特异性功能。基于观察到的细胞类型优先富集的表达模式和协调的染色质特征，我们预测了一组功能未知的基因，例如Zm 00001 d 042050和Zm 00001 d 040659，是潜在的关键C-4基因。我们的研究结果为与C-4基因表达相关的结构提供了深入的见解，并可以作为进一步确定C-4物种中存在的调节机制的宝贵资源。
C-4 plants partition photosynthesis enzymes between the bundle sheath (BS) and the mesophyll (M) cells for the better delivery of CO2 to RuBisCO and to reduce photorespiration. To better understand how C-4 photosynthesis is regulated at the transcriptional level, we performed RNA-seq, ATAC-seq, ChIP-seq and Bisulfite-seq (BS-seq) on BS and M cells isolated from maize leaves. By integrating differentially expressed genes with chromatin features, we found that chromatin accessibility coordinates with epigenetic features, especially H3K27me3 modification and CHH methylation, to regulate cell type-preferentially enriched gene expression. Not only the chromatin-accessible regions (ACRs) proximal to the genes (pACRs) but also the distal ACRs (dACRs) are determinants of cell type-preferentially enriched expression. We further identified cell type-preferentially enriched motifs, e.g. AAAG for BS cells and TGACC/T for M cells, and determined their corresponding transcription factors: DOFs and WRKYs. The complex interaction between cis and trans factors in the preferential expression of C-4 genes was also observed. Interestingly, cell type-preferentially enriched gene expression can be fine-tuned by the coordination of multiple chromatin features. Such coordination may be critical in ensuring the cell type-specific function of key C-4 genes. Based on the observed cell type-preferentially enriched expression pattern and coordinated chromatin features, we predicted a set of functionally unknown genes, e.g. Zm00001d042050 and Zm00001d040659, to be potential key C-4 genes. Our findings provide deep insight into the architectures associated with C-4 gene expression and could serve as a valuable resource to further identify the regulatory mechanisms present in C-4 species.