Design And Implementation Of Chromatin Interaction Analysis Tools

It is important for DNA replication,repair,gene transcription,and other biological functions with three-dimensional structure of genome in nucleus.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,which makes it possible to identify transcriptional binding sites involved in long-range chromatin interactions at a genome-wide level.In 2010,ChIA-PET Tool was published to process the next-generation sequence data generated from ChIA-PET wet-lab experiments.In order to improve the efficiency of data analysis and use tools more conveniently,we updated ChIA-PET Tool package and developed ChIA-PET Tool V3.In this paper,we provide a detailed demonstration of how to install the ChIA-PET Tool V3 and analyze a specific ChIA-PET data set with it.At present,other ChIA-PET data analysis tools have developed.We compared our tool with other tools using the same public data set in the same machine.Most of peaks detected by ChIA-PET Tool V3 overlap with other tools.And we can get a large number of chromatin interactions from ChIA-PET Tool V3.There is higher enrichment for significant chromatin interactions of ChIA-PET Tool in APA plot.ChIA-Drop was developed by the team of the Jackson Laboratory for Genomic Medicine recently.The method is adapted for chromatin interaction analysis via droplet-based and barcode-linked sequencing to capture the multiplex chromatin interactions at the single molecule level.We developed ChIA-Drop Tool for ChIADrop data process and generate.hic file for visualization.We used it to process ChIADrop RNAP II(RNA polymerase II)rep1 and rep2 data,and used ChIA-PET Tool V3 to get chromatin interactions from BEDPE file.Then rep1 and rep2 were combined to get chromatin interactions,and compared with ChIA-PET RNAP II data.The overlap of the interactions between them was smaller than expected.