| Criteria | Prokaryotic Gene | Eukaryotic Gene | Remarks |
| Gene Organization | Typically organized in operons (polycistronic); multiple genes under one promoter | Mostly monocistronic; one promoter per gene | Operon-based regulation allows efficient co-expression of functionally related genes in prokaryotes |
| Presence of Introns | Rare; genes are generally uninterrupted (no introns) | Common; genes often contain multiple introns and exons | Eukaryotic genes undergo splicing to remove introns before translation |
| Regulatory Elements | Promoters, operators, and simple regulatory sequences | Complex promoters, enhancers, silencers, and insulators | Eukaryotic regulation involves multiple cis-elements and trans-acting factors |
| Transcription-Translation Coupling | Transcription and translation occur simultaneously in the cytoplasm | Transcription in nucleus; translation in cytoplasm | Spatial separation allows more elaborate post-transcriptional control in eukaryotes |
| mRNA Processing | Minimal; mRNA is usually mature and ready for translation | Extensive; includes 5’ capping, splicing, and 3’ polyadenylation | Eukaryotic gene expression is regulated at multiple levels, including mRNA processing |
| Gene Density | High; genes are closely packed | Low; genes are separated by large non-coding regions | Prokaryotic genomes are more compact with fewer non-coding sequences |
| Chromatin Structure | Lacks histones and nucleosomes; DNA is supercoiled | Packaged with histones into chromatin; nucleosome-based organization | Chromatin structure adds another layer of gene regulation in eukaryotes |
