State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China.
Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China.
Genomics Proteomics Bioinformatics. 2024 Jul 3;22(2). doi: 10.1093/gpbjnl/qzae012.
Enhancers are DNA sequences that can strengthen transcription initiation. However, the global identification of plant enhancers is complicated due to uncertainty in the distance and orientation of enhancers, especially in species with large genomes. In this study, we performed self-transcribing active regulatory region sequencing (STARR-seq) for the first time to identify enhancers across the barley genome. A total of 7323 enhancers were successfully identified, and among 45 randomly selected enhancers, over 75% were effective as validated by a dual-luciferase reporter assay system in the lower epidermis of tobacco leaves. Interestingly, up to 53.5% of the barley enhancers were repetitive sequences, especially transposable elements (TEs), thus reinforcing the vital role of repetitive enhancers in gene expression. Both the common active mark H3K4me3 and repressive mark H3K27me3 were abundant among the barley STARR-seq enhancers. In addition, the functional range of barley STARR-seq enhancers seemed much broader than that of rice or maize and extended to ±100 kb of the gene body, and this finding was consistent with the high expression levels of genes in the genome. This study specifically depicts the unique features of barley enhancers and provides available barley enhancers for further utilization.
增强子是可以增强转录起始的 DNA 序列。然而，由于增强子的距离和方向不确定，特别是在基因组较大的物种中，植物增强子的全局鉴定较为复杂。在这项研究中，我们首次进行了自我转录活性调控区测序（STARR-seq），以鉴定大麦全基因组中的增强子。成功鉴定了 7323 个增强子，在随机选择的 45 个增强子中，超过 75%的增强子在烟草叶片下表皮的双荧光素酶报告基因检测系统中被有效验证。有趣的是，高达 53.5%的大麦增强子是重复序列，尤其是转座元件（TEs），这进一步证实了重复增强子在基因表达中的重要作用。在大麦 STARR-seq 增强子中，常见的活性标记 H3K4me3 和抑制性标记 H3K27me3 都很丰富。此外，大麦 STARR-seq 增强子的功能范围似乎比水稻或玉米的更广泛，延伸到基因体的±100 kb，这一发现与基因组中基因的高表达水平一致。本研究特别描述了大麦增强子的独特特征，并为进一步利用提供了可用的大麦增强子。
