Genome Organization and Gene Expression Regulation in Prokaryotes and Eukaryotes: A Comparative Review

The genome is not merely a passive repository of genetic information; the way it is organized within the cell exerts a direct influence on gene expression, and gene expression in turn reshapes genome structure. This review examines and compares genome organization and the mechanisms of gene expression regulation in prokaryotes and eukaryotes. Prokaryotes possess a compact, largely circular genome, organize functionally related genes into operons, and rely on nucleoid-associated proteins and negative supercoiling for compaction; together with the direct coupling of transcription and translation, these features support a rapid response to environmental change. Eukaryotes, by contrast, package their larger, linear genomes into chromatin, employ extensive long-range regulatory elements such as enhancers, and rely on multiple layers of co-transcriptional and post-transcriptional RNA processing—including alternative splicing—to achieve precise, tissue- and context-specific control of gene expression. Recent evidence from chromosome conformation capture and related methods shows that the three-dimensional architecture of the genome, including topologically associating domains formed through loop extrusion, is not a passive structural feature but an active participant in gene regulation, and that transcription itself can reshape this architecture. A comparative, evolutionary perspective reveals that prokaryotic and eukaryotic systems reflect different evolutionary solutions to a shared trade-off between the speed of environmental response and the complexity of regulatory control, while retaining several conserved underlying principles, such as co-transcriptional regulation. Finally, this knowledge has practical significance for biotechnology and genetic engineering, from codon optimization and CRISPR-based genome editing to the choice of recombinant protein expression systems and the search for new disease-relevant targets within genome architecture itself

کلیدواژه ها:

Genome organization ، Gene expression regulation ، Prokaryotes ، Eukaryotes ، Chromatin ، Nucleoid ، Operon ، Enhancers ، Transcription factors ، Alternative splicing ، Topologically associating domains (TADs) ، Chromosome conformation ، CRISPR-Cas ، Comparative genomics