Open AccessHigh resolution discovery of chromatin interactions
Author(s) -
Yuchun Guo,
Konstantin Krismer,
Michael Closser,
Hynek Wichterle,
David K. Gifford
Publication year - 2019
Publication title -
nucleic acids research
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 9.008
H-Index - 537
eISSN - 1362-4954
pISSN - 0305-1048
DOI - 10.1093/nar/gkz051
Subject(s) - chromatin , biology , computational biology , chia pet , genome , chromosome conformation capture , cluster analysis , consistency (knowledge bases) , genetics , computer science , chromatin remodeling , dna , machine learning , artificial intelligence , gene , transcription factor , enhancer
Chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) is a method for the genome-wide de novo discovery of chromatin interactions. Existing computational methods typically fail to detect weak or dynamic interactions because they use a peak-calling step that ignores paired-end linkage information. We have developed a novel computational method called Chromatin Interaction Discovery (CID) to overcome this limitation with an unbiased clustering approach for interaction discovery. CID outperforms existing chromatin interaction detection methods with improved sensitivity, replicate consistency, and concordance with other chromatin interaction datasets. In addition, CID also outperforms other methods in discovering chromatin interactions from HiChIP data. We expect that the CID method will be valuable in characterizing 3D chromatin interactions and in understanding the functional consequences of disease-associated distal genetic variations.