High resolution discovery of chromatin interactions
Name
gkz051.pdf
Description
Published version
Size
2.24 MB
Format
Adobe PDF
Checksum (MD5)
00370a7c73bdfb7710ed406ca9a191e1
Author(s)
Guo, Yuchun
Krismer, Konstantin
Closser, Michael
Wichterle, Hynek
Gifford, David K
Date Issued
2019
Journal
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Version
Final published version
Abstract
© 2019 The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. 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.
MIT Department
Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory
Massachusetts Institute of Technology. Department of Biological Engineering
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science
Terms of Use
Creative Commons Attribution 4.0 International license
Persistent DSpace Link
DOI of Published Version
https://doi.org/10.1093/nar/gkz051
