RT Journal Article
SR Electronic
T1 Systematic evaluation of chromosome conformation capture assays
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.12.26.424448
DO 10.1101/2020.12.26.424448
A1 Oksuz, Betul Akgol
A1 Yang, Liyan
A1 Abraham, Sameer
A1 Venev, Sergey V.
A1 Krietenstein, Nils
A1 Parsi, Krishna Mohan
A1 Ozadam, Hakan
A1 Oomen, Marlies E.
A1 Nand, Ankita
A1 Mao, Hui
A1 Genga, Ryan MJ
A1 Maehr, Rene
A1 Rando, Oliver J.
A1 Mirny, Leonid A.
A1 Gibcus, Johan Harmen
A1 Dekker, Job
YR 2020
UL http://biorxiv.org/content/early/2020/12/27/2020.12.26.424448.1.abstract
AB Chromosome conformation capture (3C)-based assays are used to map chromatin interactions genome-wide. Quantitative analyses of chromatin interaction maps can lead to insights into the spatial organization of chromosomes and the mechanisms by which they fold. A number of protocols such as in situ Hi-C and Micro-C are now widely used and these 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 experimental parameters of 3C-based protocols. We find that different protocols capture different 3D genome features with different efficiencies. First, the use of cross-linkers such as DSG in addition to formaldehyde improves signal-to-noise allowing detection of thousands of additional loops and strengthens the compartment signal. Second, fragmenting chromatin to the level of nucleosomes using MNase allows detection of more loops. On the other hand, protocols that generate larger multi-kb fragments produce stronger compartmentalization signals. We confirmed our results for multiple cell types and cell cycle stages. We find that cell type-specific quantitative differences in chromosome folding are not detected or underestimated by some protocols. Based on these insights we developed Hi-C 3.0, a single protocol that can be used to both efficiently detect chromatin loops and to quantify compartmentalization. Finally, this study produced ultra-deeply sequenced reference interaction maps using conventional Hi-C, Micro-C and Hi-C 3.0 for commonly used cell lines in the 4D Nucleome Project.Competing Interest StatementThe authors have declared no competing interest.