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<p>Identification of transcription start sites (TSSs) of genes is critical for understanding promoter architecture and transcription initiation. A well-characterized and widely used method to determine TSSs is Cap Analysis of Gene Expression (CAGE). CAGE has been commonly used in animal studies, whereas the precise identifications of TSS and core promoter landscapes remains insufficient in plant species. Soybean is an economically valuable species. In this study, we present the results of nanoCAGE sequencing to reveal the genome-wide TSS in shoot and root tissues of the soybean cultivar Williams 82. Our analysis identified 711,689 TSSs that aggregated into 27,321 CAGE TSS clusters (TCs), corresponding to 16,100 genes. We observed a predominant prevalence of “sharp” over “broad” promoter shapes among soybean TCs. Furthermore, we also found enriched TA motifs in the promoter, indicative of the TATA-box elements. Overall, the release of these experimentally determined TSSs provides a critical resource for improving soybean genome annotation, better understanding the regulation of transcription and supporting future soybean molecular breeding.</p>

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Genome level identification of transcription start sites by nanoCAGE sequence in soybean

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年10月30日

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  • Weiwei Fang,
  • Haiying Yang,
  • Huawei Feng,
  • Baoxing Song,
  • Qing Sang

摘要

Identification of transcription start sites (TSSs) of genes is critical for understanding promoter architecture and transcription initiation. A well-characterized and widely used method to determine TSSs is Cap Analysis of Gene Expression (CAGE). CAGE has been commonly used in animal studies, whereas the precise identifications of TSS and core promoter landscapes remains insufficient in plant species. Soybean is an economically valuable species. In this study, we present the results of nanoCAGE sequencing to reveal the genome-wide TSS in shoot and root tissues of the soybean cultivar Williams 82. Our analysis identified 711,689 TSSs that aggregated into 27,321 CAGE TSS clusters (TCs), corresponding to 16,100 genes. We observed a predominant prevalence of “sharp” over “broad” promoter shapes among soybean TCs. Furthermore, we also found enriched TA motifs in the promoter, indicative of the TATA-box elements. Overall, the release of these experimentally determined TSSs provides a critical resource for improving soybean genome annotation, better understanding the regulation of transcription and supporting future soybean molecular breeding.