spotter: a single-nucleotide resolution stochastic simulation model of supercoiling-mediated transcription and translation in prokaryotes.
spotter: a single-nucleotide resolution stochastic simulation model of supercoiling-mediated transcription and translation in prokaryotes.
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发现者：超螺旋介导的转录和原核生物中的单核苷酸随机模拟模型。
DOI：
10.1093/nar/gkad682
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发表时间：
2023-09-22
影响因子：
14.9
通讯作者：
Elcock, Adrian H.
中科院分区：
文献类型：
--
作者：
Hacker, William C.;Elcock, Adrian H.
随机模拟模型在理解原核生物转录和翻译的机制基础方面发挥了重要作用。尽管这些过程在细菌细胞中的基本联系，然而，大多数模拟模型已被限制在转录或翻译的代表。此外，可用的模拟模型通常试图概括来自单分子实验的数据而不考虑细胞规模的高通量测序数据，或者相反地，试图再现细胞规模的数据而不密切关注许多机制细节。为了解决这些局限性，我们在这里提出了spotter（Proximal Operon Transcription & Translation Elongation Reactions的模拟），这是一个灵活的，用户友好的模拟模型，提供了原核生物转录，翻译和DNA超螺旋的高度详细的组合表示。在整合新生转录本和核糖体分析测序数据方面，spotter在单分子实验中收集的数据与细胞规模收集的数据之间提供了关键桥梁。重要的是，除了快速生成可以与下一代测序和蛋白质组学数据进行比较的输出外，spotter还可以生成残留水平的位置信息，这些信息可以用于详细可视化单个模拟轨迹。我们预计，spotter将是一个有用的工具，在探索的相互作用的过程是至关重要的原核生物。
Stochastic simulation models have played an important role in efforts to understand the mechanistic basis of prokaryotic transcription and translation. Despite the fundamental linkage of these processes in bacterial cells, however, most simulation models have been limited to representations of either transcription or translation. In addition, the available simulation models typically either attempt to recapitulate data from single-molecule experiments without considering cellular-scale high-throughput sequencing data or, conversely, seek to reproduce cellular-scale data without paying close attention to many of the mechanistic details. To address these limitations, we here present spotter (Simulation of Prokaryotic Operon Transcription & Translation Elongation Reactions), a flexible, user-friendly simulation model that offers highly-detailed combined representations of prokaryotic transcription, translation, and DNA supercoiling. In incorporating nascent transcript and ribosomal profiling sequencing data, spotter provides a critical bridge between data collected in single-molecule experiments and data collected at the cellular scale. Importantly, in addition to rapidly generating output that can be aggregated for comparison with next-generation sequencing and proteomics data, spotter produces residue-level positional information that can be used to visualize individual simulation trajectories in detail. We anticipate that spotter will be a useful tool in exploring the interplay of processes that are crucially linked in prokaryotes.
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影响因子：
16.8
作者：
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通讯作者：
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影响因子：
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作者：
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通讯作者：
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