Measurement of differential chromatin interactions with absolute quantification of architecture (AQuA-HiChIP).

ABSTRACT: Methods developed to capture protein-anchored chromatin interactions (chromatin interaction analysis by paired-end tag sequencing and HiChIP) have yielded tremendous insights into the 3D folding principles of the genome, but are normalized by sequencing depth and therefore unable to accurately measure global changes in chromatin interactions and contact domain organization. We herein describe the protocol for absolute quantification of chromatin architecture (AQuA)-HiChIP, an advance that allows the absolute differences in protein-anchored chromatin interactions between samples to be determined. With our method, defined ratios of mouse and human fixed nuclei are mixed and subjected to endonuclease digestion. Chromatin contacts are captured by biotin-dATP incorporation and proximity ligatio

SUBMITTER: Gryder BE 

PROVIDER: S-EPMC10763690 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature