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Chromatin Interaction Analysis with Updated ChIA-PET Tool (V3)

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
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Genes 2019, 10(7), 554; https://doi.org/10.3390/genes10070554
Received: 23 June 2019 / Revised: 16 July 2019 / Accepted: 16 July 2019 / Published: 22 July 2019
(This article belongs to the Special Issue 3D Genomics)
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Abstract

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. View Full-Text
Keywords: chromatin interactions; genome-wide; high-throughput; chromatin interaction analysis with paired-end tag data analysis; ChIA-PET chromatin interactions; genome-wide; high-throughput; chromatin interaction analysis with paired-end tag data analysis; ChIA-PET
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Li, G.; Sun, T.; Chang, H.; Cai, L.; Hong, P.; Zhou, Q. Chromatin Interaction Analysis with Updated ChIA-PET Tool (V3). Genes 2019, 10, 554.

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