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.
Highlights
In eukaryotic cells, the genomes are packaged into the micron-sized nucleus with chromatin as the basic unit
We provide a detailed demonstration of the design of ChIA-paired-end tag (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
Summary
The genomes are packaged into the micron-sized nucleus with chromatin as the basic unit. Such packing of genomes into a three-dimensional structure with chromatin interactions is important for DNA replication, DNA damage repair, gene transcription, and other biological functions. Due to the significance of chromatin interactions in biology in general and transcription regulation in particular, the National Institute of Health (NIH) initiated the NIH Common Fund: 4D Nucleome (4DN) Program to study the three-dimensional (3D) genome structure and its spatiotemporal dynamics. Analysis with Paired-End Tag (ChIA-PET) sequencing method [1] is one of the high-throughput methods for generating chromatin interaction data with next-generation sequencing technology. The ChIA-PET experiment is based on the idea that the proximal DNA fragments from the same cross-linked molecular complexes can be ligated together [4], and it comprises a few basic steps (Figure 1): cross-linking of the molecules inside the nucleus, shearing the chromatin, precipitating molecules with
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