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http://dx.doi.org/10.14348/molcells.2021.0014

HiCORE: Hi-C Analysis for Identification of Core Chromatin Looping Regions with Higher Resolution  

Lee, Hongwoo (Department of Chemistry, Seoul National University)
Seo, Pil Joon (Department of Chemistry, Seoul National University)
Publication Information
Molecules and Cells / v.44, no.12, 2021 , pp. 883-892 More about this Journal
Abstract
Genome-wide chromosome conformation capture (3C)-based high-throughput sequencing (Hi-C) has enabled identification of genome-wide chromatin loops. Because the Hi-C map with restriction fragment resolution is intrinsically associated with sparsity and stochastic noise, Hi-C data are usually binned at particular intervals; however, the binning method has limited reliability, especially at high resolution. Here, we describe a new method called HiCORE, which provides simple pipelines and algorithms to overcome the limitations of single-layered binning and predict core chromatin regions with three-dimensional physical interactions. In this approach, multiple layers of binning with slightly shifted genome coverage are generated, and interacting bins at each layer are integrated to infer narrower regions of chromatin interactions. HiCORE predicts chromatin looping regions with higher resolution, both in human and Arabidopsis genomes, and contributes to the identification of the precise positions of potential genomic elements in an unbiased manner.
Keywords
3D genome; binning method; CCCTC-binding factor; chromatin loop; CTCF; Hi-C;
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