HiCDB: a sensitive and robust method for detecting contact domain boundaries

作者：Chen, Fengling; Li, Guipeng; Zhang, Michael Q.; Chen, Yang^*

来源：Nucleic Acids Research, 2018, 46(21): 11239-11250.

DOI：10.1093/nar/gky789

• 3D GENOME
• TOPOLOGICAL DOMAINS
• REVEALS
• IDENTIFICATION
• ORGANIZATION
• EXPRESSION
• PRINCIPLES
• PREDICTION
• REGULATOR
• PAX5

Contact domains are closely linked to gene regulation and lineage commitment, while current understanding of contact domains and their boundaries is still limited. Here, we present a novel method HiCDB, which is constructively based on local relative insulation metric and multi-scale aggregation approach to detect contact domain boundaries (CDBs) on Hi-C maps. Compared with other 'state-of-art' methods, HiCDB shows improved sensitivity and specificity in determining CDBs at various Hi-C resolutions. The superiority of HiCDB enabled us to study the epigenetic features of detected CDBs and showed enrichment of architectural proteins and cell-type-specific transcription factor binding sites at CDBs. The further comparison of GM12878 and IMR90 Hi-C datasets suggested that cell-type-specific CDBs are marked by active regulatory signals and correlate with activation of nearby cell identity genes.

• 出版日期2018-11-30
• 单位清华大学