Abstract
The genome is the most functional part of a cell, and genomic contents are organized in a compact three-dimensional (3D) structure. The genome contains millions of nucleotide bases organized in its proper frame. Rapid development in genome sequencing and advanced microscopy techniques have enabled us to understand the 3D spatial organization of the genome. Chromosome capture methods using a ligation approach and the visualization tool of a 3D genome browser have facilitated detailed exploration of the genome. Topologically associated domains (TADs), lamin-associated domains, CCCTC-binding factor domains, cohesin, and chromatin structures are the prominent identified components that encode the 3D structure of the genome. Although TADs are the major contributors to 3D genome organization, they are absent in Arabidopsis. However, a few research groups have reported the presence of TAD-like structures in the plant kingdom.
Highlights
The genome is the most functional part of a cell, and genomic contents are organized in a compact three-dimensional (3D) structure
A chromosome has a distinct status in the nucleus, known as a ‘chromosome territory’, which is further partitioned into chromosomal compartments (A/B), topologically associated domains (TADs), and chromatin loops, mediated by the CCCTC-binding factor (CTCF; Figure 1) [18,19,20]
lamin-associated domain (LAD) found in the nuclear periphery during one cell cycle can be found in the periphery of the nucleolus in the following cell cycle [202]. These dynamic LAD organizations in the lamina and nucleolar periphery suggest that both have the potential to organize a silent chromatin, it remains unclear whether a similar gene-silencing mechanism operates in both compartments [187]
Summary
Method to detect chromatin interaction between a specific locus and rest of the genome. It improves the sensitivity through replacement of inverse PCR with primer extension. Improved 4C variant for improved sensitivity and specificity. It uses molecular identifier to derive high-complexity quantitative chromatin contact profiles. Used to capture structural and regulatory chromatin interaction by restriction enzymes. Enables understanding of genome-wide detection of higher-order interactions within the nucleus. Mapping of multiplex chromatin interactions with single molecule precision. Allow mapping of chromatin interaction mediated by protein of interest
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