Abstract
The genome of a eukaryotic organism is comprised of a supra-molecular complex of chromatin fibers and intricately folded three-dimensional (3D) structures. Chromosomal interactions and topological changes in response to the developmental and/or environmental stimuli affect gene expression. Chromatin architecture plays important roles in DNA replication, gene expression, and genome integrity. Higher-order chromatin organizations like chromosome territories (CTs), A/B compartments, topologically associating domains (TADs), and chromatin loops vary among cells, tissues, and species depending on the developmental stage and/or environmental conditions (4D genomics). Every chromosome occupies a separate territory in the interphase nucleus and forms the top layer of hierarchical structure (CTs) in most of the eukaryotes. While the A and B compartments are associated with active (euchromatic) and inactive (heterochromatic) chromatin, respectively, having well-defined genomic/epigenomic features, TADs are the structural units of chromatin. Chromatin architecture like TADs as well as the local interactions between promoter and regulatory elements correlates with the chromatin activity, which alters during environmental stresses due to relocalization of the architectural proteins. Moreover, chromatin looping brings the gene and regulatory elements in close proximity for interactions. The intricate relationship between nucleotide sequence and chromatin architecture requires a more comprehensive understanding to unravel the genome organization and genetic plasticity. During the last decade, advances in chromatin conformation capture techniques for unravelling 3D genome organizations have improved our understanding of genome biology. However, the recent advances, such as Hi-C and ChIA-PET, have substantially increased the resolution, throughput as well our interest in analysing genome organizations. The present review provides an overview of the historical and contemporary perspectives of chromosome conformation capture technologies, their applications in functional genomics, and the constraints in predicting 3D genome organization. We also discuss the future perspectives of understanding high-order chromatin organizations in deciphering transcriptional regulation of gene expression under environmental stress (4D genomics). These might help design the climate-smart crop to meet the ever-growing demands of food, feed, and fodder.
Highlights
A eukaryotic genome comprises several chromosomes, which vary along their length, contain supra-molecular complexes of chromatin fibers, and are intricately folded in a threedimensional (3D) structure
ChIA-PET study in rice demonstrated coordinated expression of the active genes connected by the formation of chromatin loops (Zhao et al, 2019). These findings suggest that active chromatin domains in nuclei form extensive physical contacts, and associate with gene expression as well as certain essential cellular processes
After preparing the draft genome for the model organisms, the scientific attention moved to annotate and decipher the biological functions of protein-coding genes to get the answer to many relevant biological questions
Summary
A eukaryotic genome comprises several chromosomes, which vary along their length, contain supra-molecular complexes of chromatin fibers, and are intricately folded in a threedimensional (3D) structure. Eukaryotic genome organization can be observed at three levels i) linear genome: the nucleotide sequence deciphered by DNA sequencing, ii) epigenome: representing the additional information added due to the modified bases and/or histone proteins which help regulate gene expression, and iii) 3D structure of the genome: representing the arrangement of chromatins/chromosomes in the nucleus (Bonev and Cavalli, 2016). It is evident that the information and function of a genome are modulated under varying environmental conditions by the epigenetic modifications in the linear DNA sequence and by altering the 3D chromatin organization within the nucleus (Dogan and Liu, 2018; Grob, 2020). Future perspectives of 3D genomics, with special reference to its application in plant/crop improvement, and the constraints currently being faced are discussed
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