DataSheet1_Genome-wide mapping of DNase I hypersensitive sites in pineapple leaves.docx

Pineapple [Ananas comosus (L.) Merr.] is the most economically important crop possessing crassulacean acid metabolism (CAM) photosynthesis which has a higher water use efficiency by control of nocturnal opening and diurnal closure of stomata. To provide novel insights into the diel regulatory landscape in pineapple leaves, we performed genome-wide mapping of DNase I hypersensitive sites (DHSs) in pineapple leaves at day (2a.m.) and night (10a.m.) using a simplified DNase-seq method. As a result, totally 33340 and 28753 DHSs were found in green-tip tissue, and 29597 and 40068 were identified in white-base tissue at 2a.m. and 10a.m., respectively. We observed that majority of the pineapple genes occupied less than two DHSs with length shorter than 1 kb, and the promotor DHSs showed a proximal trend to the transcription start site (>77% promotor DHSs within 1 kb). In addition, more intergenic DHSs were identified around transcription factors or transcription co-regulators (TFs/TCs) than other functional genes, indicating complex regulatory contexts around TFs/TCs. Through combined analysis of tissue preferential DHSs and genes, we respectively found 839 and 888 coordinately changed genes in green-tip at 2a.m. and 10a.m. (AcG2 and AcG10). Furthermore, AcG2-specific, AcG10-specific and common accessible DHSs were dissected from the total photosynthetic preferential DHSs, and the regulatory networks indicated dynamic regulations with multiple cis-regulatory elements occurred to genes preferentially expressed in photosynthetic tissues. Interestingly, binding motifs of several cycling TFs were identified in the DHSs of key CAM genes, revealing a circadian regulation to CAM coordinately diurnal expression. Our results provide a chromatin regulatory landscape in pineapple leaves during the day and night. This will provide important information to assist with deciphering the circadian regulation of CAM photosynthesis.

菠萝（Ananas comosus (L.) Merr.）作为经济效益最为显著的作物，具有石莼酸代谢（CAM）光合作用特性，通过夜间气孔的开放和白天气孔的闭合，实现了较高的水分利用效率。为了深入解析菠萝叶片昼夜节律调控的复杂图景，本研究采用简化的DNase-seq方法，对菠萝叶片在白天（凌晨2点）和夜间（上午10点）的DNase I高敏感位点（DHSs）进行了全基因组映射。结果表明，在凌晨2点和上午10点，绿色尖端组织中分别检测到33,340和28,753个DHSs，而在白色基座组织中则分别识别出29,597和40,068个DHSs。研究发现，大部分菠萝基因占据的DHSs数量少于两个，且长度短于1 kb，而启动子DHSs则呈现出靠近转录起始位点（>77%的启动子DHSs位于1 kb范围内）的趋势。此外，与其它功能基因相比，转录因子（TFs）或转录共调节因子（TCs）周围的间基因DHSs数量更多，这表明TFs/TCs周围的调控环境更为复杂。通过对组织特异性DHSs和基因的联合分析，分别在凌晨2点和上午10点的绿色尖端组织中发现了839和888个协调变化的基因（AcG2和AcG10）。进一步地，从总光合特异性DHSs中解析出了AcG2特异性、AcG10特异性和共同可及的DHSs，并通过调控网络的分析，揭示了光合组织优先表达的基因在多个顺式调控元件的作用下发生的动态调控。令人感兴趣的是，在关键CAM基因的DHSs中鉴定出了多个循环TFs的结合基序，揭示了CAM在昼夜节律调控下协调日节律表达的机制。本研究为菠萝叶片在昼夜不同时段的染色质调控景观提供了重要信息，这将有助于解码CAM光合作用的昼夜节律调控机制。