Kai Ouyang, Qifu Liang, Li Miao, Zhiliang Zhang, Zhanjie Li

Front Genet.; 2023 Jul 4; 14:1086554. doi: 10.3389/fgene.2023.1086554.

Abstract

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.

See https://pubmed.ncbi.nlm.nih.gov/37470036/

Figure 2:  Genome-wide distribution of DHSs and annotation based on location. (A). Pineapple leaf sections were collected for analysis. Photosynthetic (green tip) and non-photosynthetic (white base) areas are indicated. (B). The genome-wide distribution of DHSs across 25 pineapple chromosomes. From outside to inside, the circles represented the chromosome, gene density and DHS abundance in four pineapple leaf tissues (orange for AcW10, blue for AcW2, green for AcG10, and purple for AcG2). (C). The distribution of DHSs relative to different gene regions in each sample. (D). The distribution of genes with different number of DHSs in the four pineapple tissues. (E). The distribution of genes with different length of DHSs in the four pineapple tissues.