The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel.
School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, United States.
Bioinformatics. 2024 Mar 4;40(3). doi: 10.1093/bioinformatics/btae110.
Prediction and identification of core promoter elements and transcription factor binding sites is essential for understanding the mechanism of transcription initiation and deciphering the biological activity of a specific locus. Thus, there is a need for an up-to-date tool to detect and curate core promoter elements/motifs in any provided nucleotide sequences.
Here, we introduce ElemeNT 2023-a new and enhanced version of the Elements Navigation Tool, which provides novel capabilities for assessing evolutionary conservation and for readily evaluating the quality of high-throughput transcription start site (TSS) datasets, leveraging preferential motif positioning. ElemeNT 2023 is accessible both as a fast web-based tool and via command line (no coding skills are required to run the tool). While this tool is focused on core promoter elements, it can also be used for searching any user-defined motif, including sequence-specific DNA binding sites. Furthermore, ElemeNT's CORE database, which contains predicted core promoter elements around annotated TSSs, is now expanded to cover 10 species, ranging from worms to human. In this applications note, we describe the new workflow and demonstrate a case study using ElemeNT 2023 for core promoter composition analysis of diverse species, revealing motif prevalence and highlighting evolutionary insights. We discuss how this tool facilitates the exploration of uncharted transcriptomic data, appraises TSS quality, and aids in designing synthetic promoters for gene expression optimization. Taken together, ElemeNT 2023 empowers researchers with comprehensive tools for meticulous analysis of sequence elements and gene expression strategies.
ElemeNT 2023 is freely available at https://www.juven-gershonlab.org/resources/element-v2023/. The source code and command line version of ElemeNT 2023 are available at https://github.com/OritAdato/ElemeNT. No coding skills are required to run the tool.
预测和识别核心启动子元件和转录因子结合位点对于理解转录起始机制和破译特定基因座的生物学活性至关重要。因此，需要有一个最新的工具来检测和整理任何提供的核苷酸序列中的核心启动子元件/基序。
在这里，我们引入了 ElemeNT 2023——Elements Navigation Tool 的新版本和增强版，它提供了评估进化保守性和轻松评估高通量转录起始位点 (TSS) 数据集质量的新功能，利用了优先基序定位。ElemeNT 2023 既可以作为快速的基于网络的工具使用，也可以通过命令行使用（运行工具不需要编码技能）。虽然这个工具专注于核心启动子元件，但它也可以用于搜索任何用户定义的基序，包括序列特异性 DNA 结合位点。此外，ElemeNT 的 CORE 数据库，其中包含注释 TSS 周围预测的核心启动子元件，现在扩展到涵盖 10 个物种，从蠕虫到人类。在本应用说明中，我们描述了新的工作流程，并展示了使用 ElemeNT 2023 对不同物种的核心启动子组成进行分析的案例研究，揭示了基序的普遍性，并强调了进化见解。我们讨论了该工具如何促进对未知转录组数据的探索，评估 TSS 质量，并有助于设计用于基因表达优化的合成启动子。总之，ElemeNT 2023 为研究人员提供了全面的工具，用于对序列元件和基因表达策略进行细致分析。
ElemeNT 2023 可在 https://www.juven-gershonlab.org/resources/element-v2023/ 免费获得。ElemeNT 2023 的源代码和命令行版本可在 https://github.com/OritAdato/ElemeNT 获得。运行该工具不需要编码技能。
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