Inter-chromosomal Contact Properties in Live-Cell Imaging and in Hi-C

• Published in: Molecular cell Vol. 69; no. 6; pp. 1039 - 1045.e3
• Main Authors: Maass, Philipp G., Barutcu, A. Rasim, Weiner, Catherine L., Rinn, John L.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 15.03.2018
• Subjects: Animals; Cell Line; Chromosomes, Human - genetics; Chromosomes, Human - metabolism; CISTR-ACT; CLING; CRISPR live-cell imaging; CRISPR-Cas Systems; Female; FIRRE; Gene Editing - methods; Hi-C; Humans; Image Processing, Computer-Assisted - methods; inter-chromosomal interactions; Kinetics; lncRNA; loci dynamics; Male; Mice; Microscopy, Confocal - methods; Mouse Embryonic Stem Cells - metabolism; NHCCs; Nucleic Acid Conformation; Protein Conformation; Retinal Pigment Epithelium - metabolism; Time-Lapse Imaging - methods; CRISPR live-cell imaging; lncRNA; CISTR-ACT; NHCCs; Hi-C; loci dynamics; CLING; inter-chromosomal interactions; FIRRE
• ISSN: 1097-2765; 1097-4164
• DOI: 10.1016/j.molcel.2018.02.007

Imaging (fluorescence in situ hybridization [FISH]) and genome-wide chromosome conformation capture (Hi-C) are two major approaches to the study of higher-order genome organization in the nucleus. Intra-chromosomal and inter-chromosomal interactions (referred to as non-homologous chromosomal contacts [NHCCs]) have been observed by several FISH-based studies, but locus-specific NHCCs have not been detected by Hi-C. Due to crosslinking, neither of these approaches assesses spatiotemporal properties. Toward resolving the discrepancies between imaging and Hi-C, we sought to understand the spatiotemporal properties of NHCCs in living cells by CRISPR/Cas9 live-cell imaging (CLING). In mammalian cells, we find that NHCCs are stable and occur as frequently as intra-chromosomal interactions, but NHCCs occur at farther spatial distance that could explain their lack of detection in Hi-C. By revealing the spatiotemporal properties in living cells, our study provides fundamental insights into the biology of NHCCs. [Display omitted] •CRISPR live-cell imaging (4D-CLING) of non-homologous chromosomal contacts (NHCCs)•4D-CLING reveals the spatiotemporal dynamics and properties of NHCCs•NHCCs are as frequent and stable as intra-chromosomal contacts•NHCCs occur at larger distances, perhaps why they are not readily detected in Hi-C Comparing time-lapse live-cell imaging, Maass et al. characterize the spatiotemporal properties of genomic contacts between non-homologous chromosomes. They determined that these contacts occur frequently in mammalian cells, remain stably associated over time, and occur at spatial distances that are not readily captured in genome-wide chromosome conformation capture (Hi-C).