MCIBox: a toolkit for single-molecule multi-way chromatin interaction visualization and micro-domains identification. Issue 6 (12th September 2022)

• Record Type: Journal Article
• Authors: Tian, Simon Zhongyuan; Li, Guoliang; Ning, Duo; Jing, Kai; Xu, Yewen; Yang, Yang; Fullwood, Melissa J; Yin, Pengfei; Huang, Guangyu; Plewczynski, Dariusz; Zhai, Jixian; Dai, Ziwei; Chen, Wei; Zheng, Meizhen
• Is Part Of: Briefings in bioinformatics. Volume 23:Issue 6(2022)
• Publication Date: 2022-09-12
• Subjects: multi-way chromatin interactions -- single-molecule -- micro-domains -- visualization -- machine learning -- chromatin extrusion -- super-enhancers; Genetics -- Data processing -- Periodicals; Molecular biology -- Data processing -- Periodicals; Genomes -- Data processing -- Periodicals; 572.80285
• DOI: 10.1093/bib/bbac380
• Languages: English
• ISSNs: 1467-5463

Abstract

Abstract: The emerging ligation-free three-dimensional (3D) genome mapping technologies can identify multiplex chromatin interactions with single-molecule precision. These technologies not only 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. Taken together, MCIBox represents an invaluable tool for the study of multiple chromatin interactions and inaugurates a previously unappreciated view of 3D genome structure.