| Criteria | Prokaryotic RNA Polymerase | Eukaryotic RNA Polymerase | Remarks |
| Number of RNA Polymerases | Single type of RNA polymerase | Three main types: RNA Pol I, II, and III | Eukaryotes have compartmentalized transcription roles across polymerases |
| Subunit Composition | Core enzyme: α₂ββ′ω; Holoenzyme includes σ factor | Multiple subunits (12–17 subunits depending on polymerase type) | Eukaryotic polymerases are more complex and multi-subunit |
| Initiation Factors | σ factor is required for promoter recognition | Requires several general transcription factors (TFs) | Transcription initiation is more regulated and complex in eukaryotes |
| Promoter Recognition | Recognizes –10 and –35 promoter sequences | Recognizes TATA box and other upstream/downstream elements | Eukaryotic promoters are more diverse and often enhancer-dependent |
| Transcription Location | Cytoplasm | Nucleus | Separation of transcription and translation occurs in eukaryotes |
| Transcripts Produced | mRNA, rRNA, and tRNA by a single polymerase | RNA Pol I: rRNA; RNA Pol II: mRNA, snRNA; RNA Pol III: tRNA, 5S rRNA | Eukaryotic polymerases have specialized functions |
| Transcription Termination | Uses rho-dependent or rho-independent mechanisms | Termination mechanisms vary with polymerase; often complex and involve cleavage signals | Termination in eukaryotes is polymerase-specific |
| Post-Transcriptional Modifications | Minimal or absent (no capping, splicing, or polyadenylation) | mRNA undergoes 5’ capping, splicing, 3’ polyadenylation | Eukaryotic mRNA processing is extensive and essential for translation |
| Coupling with Translation | Transcription and translation are coupled | Transcription occurs separately from translation | Only in prokaryotes can translation begin while transcription is ongoing |
| Sensitivity to Toxins | Inhibited by rifampicin | RNA Pol II is inhibited by α-amanitin | Specific inhibitors are useful tools for studying transcription |
