Integration of ATAC-seq and RNA-seq reveals the dynamics of chromatin accessibility and gene expression in zoysiagrass response to drought.

Abstract

Key message: The 'X4' accession of zoysiagrass demonstrated superior drought tolerance compared to other accessions. Integration analysis of transcriptomics and epigenomics revealed a positive correlation between ATAC-seq peak intensity and gene expression levels. Six motifs involved in regulating drought responses were identified, which are similar to the domains of the ERF and C2H2 transcription factor families. Heterologous expression of Zja11G000860 in yeast enhanced tolerance to drought stress, allowing robust growth even at high PEG6000 concentrations. Zoysiagrass is renowned for its drought tolerance and serves as an exceptional domestic turfgrass in China. However, the changes in chromatin accessibility during drought in zoysiagrass are not well understood. We conducted a preliminary evaluation of the phenotypic changes in drought tolerance for six zoysiagrass cultivars, taking into account their growth characteristics and physiological traits under drought conditions. Additionally, we utilized an integrated multi-omics strategy, encompassing RNA sequencing (RNA-seq), Assay for Transposase Accessible Chromatin using high-throughput sequencing (ATAC-seq), and reverse transcription quantitative PCR (RT-qPCR) verification experiments, to gain deeper understanding of the chromatin accessibility patterns linked to gene expression in response to drought stress in zoysiagrass. Preliminary analysis of the trends in relative water content and proline content suggested that the variety 'X4' exhibited superior drought tolerance compared to the other five accessions. The KEGG pathway enrichment analysis revealed that zoysiagrass responded to environmental stress by regulating stress response and antioxidant defense pathways. Notably, the expression levels of genes Zja03G031540 and Zja11G000860 were significantly increased in the 'X4' zoysiagrass genotype, which exhibited improved drought tolerance, compared to the 'X1' zoysiagrass genotype with reduced drought tolerance. This study suggested that 63 high-confidence genes are related to drought stress, including Zja03G031540 and Zja11G000860. Additionally, six motifs regulating drought responses were unearthed. Furthermore, the heterologous expression of Zja11G000860 in yeast enhanced tolerance to drought stress. The study discovered a positive correlation between ATAC-seq peak intensity and gene expression levels. The expression of high-confidence genes was linked to zoysiagrass resistance evaluation and phenotypic traits, implying that these genes are involved in responding to external drought stress. This study combined ATAC-seq and RNA-seq technologies for the first time to identify drought-related gene expression in zoysiagrass, elucidating the grass adaptation to environmental stress and the regulatory mechanisms underlying stress responses, and laying the groundwork for zoysiagrass improvement and breeding.