RT Journal Article SR Electronic T1 Cryomilling Tethered Chromatin Conformation Capture reveal new insights into inter-chromosomal interactions JF bioRxiv FD Cold Spring Harbor Laboratory SP 2022.02.03.478915 DO 10.1101/2022.02.03.478915 A1 Xu, Jiang A1 Kumar, Sanjeev A1 Hua, Nan A1 Kou, Yi A1 Lei, Xiao A1 Rout, Michael P. A1 Aitchison, John D. A1 Alber, Frank A1 Chen, Lin YR 2022 UL http://biorxiv.org/content/early/2022/02/12/2022.02.03.478915.abstract AB Traditional methods used to map the three-dimensional organization of chromatin in-situ generally involve chromatin conformation capture by formaldehyde crosslinking, followed by detergent solubilization and enzymatic digestion of DNA. Ligation of proximal DNA fragments followed by next generation sequencing (NGS) generates contact information that enables a global view of the chromatin conformation. Here, we explore the use of cryomilling to physically fragmentize the cells under cryogenic conditions to probe chromatin interactions in the cryomilled cell fragments by the tethered chromatin conformation capture (TCC). Our results show that cryomilling TCC (CTCC) can generate a global contact map similar to that obtained with in-situ Hi-C. This result suggests that summation of chromatin interactions mapped in individual subcellular fragments can reconstitute the global contact map of intact cells in an ensemble manner, paving the way for chromatin conformation analyses of solid tissue by CTCC. Compared with the conventional in-situ methods such as Hi-C, CTCC shows more uniform access to different subcompartments of the folded genome. On the other hand, most inter-chromosomal (trans) contacts are diminished or lost in CTCC except for a group of unique trans contacts that remain intact throughout the cryomilling and in- vitro crosslinking steps. These apparently ultra-stable trans interactions have much enhanced signal in CTCC due to the elimination of signals of most, presumably weak and transient trans interactions. Systematic and comparative analyses between CTCC and in-situ Hi-C provide further insights into the chromatin structure organization and reveal a generally unentangled chromosome interface and the existence of stable inter-chromosomal contacts that may represent intermingled inter-chromosomal interfaces.Competing Interest StatementThe authors have declared no competing interest.