In the nucleus of eutherian mammals, string-like genomic DNA macromolecule of each chromosome is folded into sub-compartments, forming chromosome territories (CT) that occupy discrete regions. Elucidating the organizational pattern of the genome in the nucleus has been a prominent subject, as it is crucially related to its functional implications, such as DNA modification, repair, and transcriptional activity. The rapid expansion of chromosome conformation capture technologies has permitted achieving deep insights into the hierarchy of genome architecture. Despite the remarkable progression of fine-mapping genome 3D organizations, the challenges of comprehending the genome architecture still remain. One is the molecular mechanism underlying how these higher-order non-random structures are organized; and the other is to decipher how the genome architecture relates to its functions.
A recent study published in Cell Research, a research team led by Prof. LI Jinsong from the Center for Excellence in Molecular Cell Science (Shanghai Institute of Biochemistry and Cell Biology) of the Chinese Academy of Sciences created mouse haploid ESCs (haESCs) and stable mouse strains with fused chromosomes by CRISPR-Cas9-induced cleavage at minor satellites of centromere. They demonstrated that fused chromosomes occupy adjacent territories in the nucleus, however, the overall chromosome territories, compartment distributions, and transcriptomes are largely unchanged. Moreover, they found inter-chromosomal interactions between fused chromosomes are elevated, and inter-chromosomal hubs are affected by the fusion events, especially in chr11 which is not involved in fusion events.
In this study published in Nature Communications, the research team led by Prof. LI Jinsong extended their research on chromosome fusion, in order to comprehend how the genome achieves such a robust and flexible architecture in the nucleus. However, due to the probabilistic property of the chromosome localization, mFISH, bulk Hi-C and single-cell Hi-C all have limitations on investigating how chromosomes are reorganized after chromosome fusions. So, they developed a new method to convert bulk Hi-C dataset to Genome Khimaira Matrix (K-matrix) mimicking single-cell Hi-C characteristics, which preserves not only the main features of the original dataset, but also displays model-to-model variations. More importantly, genome 3D models generated from those K-matrix displayed approaching of fused chromosomes and radial A/B compartment distribution.
By investigating the chromosome distance in calculated genome 3D models, the research team found chromosome fusion events can only induce minor chromosome location changes between fused chromosomes and non-fused chromosomes, and supporting the probabilistic model of proximity patterns. To decipher the radial shifts of chromosome, the research team also developed Layered Positional Decomposition analysis method to calculate the radial position of each chromosome segments. In general, chromosome fusions do not cause dramatic chromosomal radial shifts, implying that the reorganization of chromosomes after chromosome fusion might be parallel but not perpendicular to the circumference, which in turn could preserve radial A/B compartment distribution. Also, cell type-specific chromosome configurations may affect radial position shifts.
Further in the genome models of multiple chromosomes fused cells (mROB-O48 cells), even in cells with five pairs of fused chromosomes, the research team found genome structure could correctly predict the approaching of each fused chromosome pair and diminished chromosome distances between fused chromosomes. Strikingly, although the number of DEGs increased with more chromosomes fused, the overall A/B compartment distribution and expression pattern in the nucleus maintained the radial distribution profile across all the mROB-O48 cells. Nevertheless, the research team observed dramatic radial shifts of several chromosomes, especially chr6 and chr18 in fibroblast cells of mice with naturally occurring Rb fusions (BRbS mice). Taken together, their results suggest that 3D genome organization adjustments induced by Rb fusions might be preserved and aggregated during long-term natural evolution.
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