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bioRxiv · 10.1101/2022.04.28.489957

MCIBox: A Toolkit for Single-molecule Multi-way Chromatin Interaction Visualization and Micro-Domains Identification

Tian, S. Z.·Li, G.·Ning, D.·Jing, K.·Xu, Y.·Yang, Y.·Fullwood, M. J.·Yin, P.·Huang, G.·Plewczynski, D.·Wang, W.·Zhai, J.·Wang, Z.·Dai, Z.·Lin, Y.·Chen, W.·Zheng, M.
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Abstract

The emerging ligation-free three-dimensional (3D) genome mapping technologies can identify multiplex chromatin interactions with single-molecule precision. These technologies offer new insight into high-dimensional chromatin organization and gene regulation, but also introduce new challenges in data visualization and analysis. To overcome these challenges, we developed MCIBox, a toolkit for Multi-way Chromatin Interaction (MCI) analysis, including a visualization tool and a platform for identifying micro-domains with clustered single-molecule chromatin complexes. MCIBox is based on various clustering algorithms integrated with dimensionality reduction methods that can display multiplex chromatin interactions at single-molecule level, allowing users to explore chromatin extrusion patterns and super-enhancers regulation modes in transcription, and to identify single-molecule chromatin complexes that are clustered into micro-domains. Furthermore, MCIBox incorporates a two-dimensional kernel density estimation algorithm to identify micro-domains boundaries automatically. These micro-domains were stratified with distinctive signatures of transcription activity and contained different cell cycle associated genes. MCIBox could potentially distinguish the specificity of single-molecule chromatin interaction patterns in various phases of a cell cycle or cell types.

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Tian, S. Z., Li, G., Ning, D., Jing, K., Xu, Y., Yang, Y., Fullwood, M. J., Yin, P., Huang, G., Plewczynski, D., Wang, W., Zhai, J., Wang, Z., Dai, Z., Lin, Y., Chen, W., Zheng, M.. 2022-04-30. MCIBox: A Toolkit for Single-molecule Multi-way Chromatin Interaction Visualization and Micro-Domains Identification. https://doi.org/10.1101/2022.04.28.489957

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