University College London, UK.
Novosibirsk State University, Russia.
Brief Bioinform. 2021 Jul 20;22(4). doi: 10.1093/bib/bbaa352.
Chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) is recognized as an extremely powerful tool to study the interaction of numerous transcription factors and other chromatin-associated proteins with DNA. The core problem in the optimization of ChIP-seq protocol and the following computational data analysis is that a 'true' pattern of binding events for a given protein factor is unknown. Computer simulation of the ChIP-seq process based on 'a-priory known binding template' can contribute to a drastically reduce the number of wet lab experiments and finally help achieve radical optimization of the entire processing pipeline. We present a newly developed ChIP-sequencing simulation algorithm implemented in the novel software, in silico ChIP-seq (isChIP). We demonstrate that isChIP closely approximates real ChIP-seq protocols and is able to model data similar to those obtained from experimental sequencing. We validated isChIP using publicly available datasets generated for well-characterized transcription factors Oct4 and Sox2. Although the novel software is compatible with the Illumina protocols by default, it can also successfully perform simulations with a number of alternative sequencing platforms such as Roche454, Ion Torrent and SOLiD as well as model ChIP -Exo. The versatility of isChIP was demonstrated through modelling a wide range of binding events, including those of transcription factors and chromatin modifiers. We also performed a comparative analysis against a few existing ChIP-seq simulators and showed the fundamental superiority of our model. Due to its ability to utilize known binding templates, isChIP can potentially be employed to help investigators choose the most appropriate analytical software through benchmarking of available ChIP-seq programs and optimize the experimental parameters of ChIP-seq protocol. isChIP software is freely available at https://github.com/fnaumenko/isChIP.
染色质免疫沉淀结合高通量测序（ChIP-seq）被公认为是研究众多转录因子和其他与染色质相关蛋白与 DNA 相互作用的极其强大的工具。优化 ChIP-seq 方案和随后的计算数据分析的核心问题是，给定蛋白质因子的“真实”结合事件模式是未知的。基于“先验已知的结合模板”的 ChIP-seq 过程的计算机模拟可以大大减少湿实验室实验的数量，并最终有助于实现整个处理流水线的彻底优化。我们提出了一种新开发的 ChIP-seq 测序模拟算法，该算法在新型软件 in silico ChIP-seq（isChIP）中实现。我们证明了 isChIP 非常接近真实的 ChIP-seq 方案，并且能够对类似于从实验测序获得的数据进行建模。我们使用经过充分验证的转录因子 Oct4 和 Sox2 生成的公开可用数据集验证了 isChIP。虽然该新型软件默认与 Illumina 方案兼容，但它还可以成功地与 Roche454、Ion Torrent 和 SOLiD 等替代测序平台以及模型 ChIP-Exo 进行模拟。isChIP 的多功能性通过模拟广泛的结合事件得到了证明，包括转录因子和染色质修饰剂的结合事件。我们还与几个现有的 ChIP-seq 模拟器进行了比较分析，展示了我们模型的基本优势。由于其能够利用已知的结合模板，isChIP 可能被用于通过对可用的 ChIP-seq 程序进行基准测试来帮助研究人员选择最合适的分析软件，并优化 ChIP-seq 方案的实验参数。isChIP 软件可在 https://github.com/fnaumenko/isChIP 上免费获得。
