Systematic evaluation of chromosome conformation capture assays.

Abstract

Chromosome conformation capture (3C) assays are used to map chromatin interactions genome-wide. Chromatin interaction maps provide insights into the spatial organization of chromosomes and the mechanisms by which they fold. Hi-C and Micro-C are widely used 3C protocols that differ in key experimental parameters including cross-linking chemistry and chromatin fragmentation strategy. To understand how the choice of experimental protocol determines the ability to detect and quantify aspects of chromosome folding we have performed a systematic evaluation of 3C experimental parameters. We identified optimal protocol variants for either loop or compartment detection, optimizing fragment size and cross-linking chemistry. We used this knowledge to develop a greatly improved Hi-C protocol (Hi-C 3.0) that can detect both loops and compartments relatively effectively. In addition to providing benchmarked protocols, this work produced ultra-deep chromatin interaction maps using Micro-C, conventional Hi-C and Hi-C 3.0 for key cell lines used by the 4D Nucleome project.

Authors

Akgol Oksuz B  •  Yang L  •  Abraham S  •  Venev SV  •  Krietenstein N  •  Parsi KM  •  Ozadam H  •  Oomen ME  •  Nand A  •  Mao H  •  Genga RMJ  •  Maehr R  •  Rando OJ  •  Mirny LA  •  Gibcus JH  •  Dekker J

Link

https://www.ncbi.nlm.nih.gov/pubmed/34480151