National Key Laboratory of Crop Genetic Improvement, Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, No. 1, Shizishan Street, Hongshan District, Wuhan 430070, China.
Genes (Basel). 2019 Jul 22;10(7):554. doi: 10.3390/genes10070554.
Understanding chromatin interactions is important because they create chromosome conformation and link the cis- and trans- regulatory elements to their target genes for transcriptional regulation. Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing is a genome-wide high-throughput technology that detects chromatin interactions associated with a specific protein of interest. We developed ChIA-PET Tool for ChIA-PET data analysis in 2010. Here, we present the updated version of ChIA-PET Tool (V3) as a computational package to process the next-generation sequence data generated from ChIA-PET experiments. It processes short-read and long-read ChIA-PET data with multithreading and generates statistics of results in an HTML file. In this paper, we provide a detailed demonstration of the design of ChIA-PET Tool V3 and how to install it and analyze RNA polymerase II (RNAPII) ChIA-PET data from human K562 cells with it. We compared our tool with existing tools, including ChiaSig, MICC, Mango and ChIA-PET2, by using the same public data set in the same computer. Most peaks detected by the ChIA-PET Tool V3 overlap with those of other tools. There is higher enrichment for significant chromatin interactions from ChIA-PET Tool V3 in aggregate peak analysis (APA) plots. The ChIA-PET Tool V3 is publicly available at GitHub.
了解染色质相互作用很重要，因为它们可以形成染色体构象，并将顺式和反式调控元件与它们的靶基因连接起来，进行转录调控。染色质互作分析与末端配对标签（ChIA-PET）测序是一种全基因组高通量技术，可检测与特定感兴趣的蛋白质相关的染色质相互作用。我们于 2010 年开发了 ChIA-PET 工具，用于 ChIA-PET 数据分析。在这里，我们展示了 ChIA-PET 工具的更新版本（V3），作为一个计算软件包，用于处理来自 ChIA-PET 实验的下一代测序数据。它可以处理短读和长读 ChIA-PET 数据，并使用多线程生成 HTML 文件中的结果统计信息。在本文中，我们详细演示了 ChIA-PET Tool V3 的设计，以及如何安装它，并使用它分析来自人类 K562 细胞的 RNA 聚合酶 II（RNAPII）ChIA-PET 数据。我们使用相同的公共数据集和同一台计算机，将我们的工具与包括 ChiaSig、MICC、Mango 和 ChIA-PET2 在内的现有工具进行了比较。ChIA-PET Tool V3 检测到的大多数峰与其他工具的峰重叠。在总峰分析（APA）图中，ChIA-PET Tool V3 检测到的显著染色质相互作用的富集程度更高。ChIA-PET Tool V3 可在 GitHub 上公开获取。
