Improved cohesin HiChIP protocol and bioinformatic analysis for robust detection of chromatin loops and stripes.

ABSTRACT: Chromosome Conformation Capture (3 C) methods, including Hi-C (a high-throughput variation of 3 C), detect pairwise interactions between DNA regions, enabling the reconstruction of chromatin architecture in the nucleus. HiChIP is a modification of the Hi-C experiment that includes a chromatin immunoprecipitation (ChIP) step, allowing genome-wide identification of chromatin contacts mediated by a protein of interest. In mammalian cells, cohesin protein complex is one of the major players in the establishment of chromatin loops. We present an improved cohesin HiChIP experimental protocol. Using comprehensive bioinformatic analysis, we show that a dual chromatin fixation method compared to the standard formaldehyde-only method, results in a substantially better signal-to-noise ratio, increase

SUBMITTER: Buka K 

PROVIDER: S-EPMC11906747 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature