Identification of highly repetitive barley enhancers with long-range regulation potential via STARR-seq

IF 11.5 2区生物学 Q1 GENETICS & HEREDITY Genomics, Proteomics & Bioinformatics Pub Date : 2024-02-21 DOI:10.1093/gpbjnl/qzae012

Wanlin Zhou, Haoran Shi, Zhiqiang Wang, Yuxin Huang, Lin Ni, Xudong Chen, Yan Liu, Haojie Li, Caixia Li, Yaxi Liu

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Abstract 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 transcription mark H3K4me3 and repressive histone 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 work specifically depicts the unique features of barley enhancers and provides available barley enhancers for further utilization.

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通过 STARR-seq 鉴定具有长程调控潜力的高度重复大麦增强子

摘要增强子是能够加强转录启动的 DNA 序列。然而，由于增强子的距离和方向不确定，植物增强子的全球鉴定非常复杂，尤其是在基因组较大的物种中。在这项研究中，我们首次进行了自转录活性调控区测序（STARR-seq），以鉴定大麦基因组中的增强子。共成功鉴定出7323个增强子，在随机选择的45个增强子中，超过75%的增强子通过烟草叶片下表皮的双荧光素酶报告检测系统验证是有效的。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（TE），从而加强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，常见的活性转录标记 H3K4me3 和抑制性组蛋白标记 H3K27me3 都很丰富。此外，与水稻和玉米相比，大麦 STARR-seq 增强子的功能范围似乎更广，可延伸至基因体的±100 kb，这一发现与基因组中基因的高表达水平相一致。这项工作具体描述了大麦增强子的独特特征，并提供了可供进一步利用的大麦增强子。

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来源期刊

Genomics, Proteomics & Bioinformatics Biochemistry, Genetics and Molecular Biology-Biochemistry

CiteScore

14.30

自引率

4.20%

发文量

844

审稿时长

61 days

期刊介绍： Genomics, Proteomics and Bioinformatics (GPB) is the official journal of the Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation and Genetics Society of China. It aims to disseminate new developments in the field of omics and bioinformatics, publish high-quality discoveries quickly, and promote open access and online publication. GPB welcomes submissions in all areas of life science, biology, and biomedicine, with a focus on large data acquisition, analysis, and curation. Manuscripts covering omics and related bioinformatics topics are particularly encouraged. GPB is indexed/abstracted by PubMed/MEDLINE, PubMed Central, Scopus, BIOSIS Previews, Chemical Abstracts, CSCD, among others.