期刊
GENOME RESEARCH
卷 30, 期 1, 页码 72-84出版社
COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
DOI: 10.1101/gr.249367.119
关键词
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资金
- Russian Foundation for Basic Research (RFBR) [18-29-13021]
- Russian Science Foundation [17-74-10143]
- Computational Cluster of the Novosibirsk State University
- Computational Nodes of the Institute of Cytology and Genetics [0324-20190041]
- Russian Science Foundation [17-74-10143] Funding Source: Russian Science Foundation
Recent experimental and computational efforts have provided large data sets describing three-dimensional organization of mouse and human genomes and showed the interconnection between the expression profile, epigenetic state, and spatial interactions of loci. These interconnections were utilized to infer the spatial organization of chromatin, including enhancer-promoter contacts, from one-dimensional epigenetic marks. Here, we show that the predictive power of some of these algorithms is overestimated due to peculiar properties of the biological data. We propose an alternative approach, which provides high-quality predictions of chromatin interactions using information on gene expression and CTCF-binding alone. Using multiple metrics, we confirmed that our algorithm could efficiently predict the three-dimensional architecture of both normal and rearranged genomes.
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