RNA transcription is the process of copying DNA into RNA. In prokaryotes and eukaryotes, it's similar but has key differences. Both use RNA polymerase to make RNA, but prokaryotes have one type while eukaryotes have three.

Prokaryotic transcription happens in the cytoplasm and is simpler. Eukaryotic transcription occurs in the nucleus and involves more steps. Eukaryotes also modify their RNA after transcription, adding caps and tails, while prokaryotes don't.

Transcription in Prokaryotes and Eukaryotes

Transcription in prokaryotes vs eukaryotes

• Similarities involve RNA synthesis from DNA template catalyzed by RNA polymerase forming phosphodiester bonds between ribonucleotides in 3 stages: initiation, elongation, termination
• Differences include location (prokaryotic in cytoplasm, eukaryotic in nucleus), number of RNA polymerase types (prokaryotes have 1, eukaryotes have 3 - I, II, III)
• Prokaryotic RNA polymerase initiates transcription independently while eukaryotic RNA polymerase II requires transcription factors
• Prokaryotic genes organized into operons allowing coordinated transcription of multiple genes while eukaryotic genes typically transcribed individually
• Eukaryotic transcripts undergo post-transcriptional modifications (5' capping, 3' polyadenylation, splicing) absent in prokaryotes

Role of RNA polymerase

• Initiation:
  • Binds promoter region of DNA template
  • In prokaryotes, σ factor recognizes and binds -35 and -10 regions
  • In eukaryotes, general transcription factors (GTFs) assist RNA polymerase II in promoter recognition and binding
  • Unwinds DNA double helix separating strands forming transcription bubble
• Elongation:
  • Catalyzes phosphodiester bond formation between ribonucleotides using DNA template strand to guide RNA sequence
  • Moves 5' to 3' along DNA template extending RNA transcript
  • Transcription bubble moves along DNA template with double helix re-forming behind enzyme
• Termination:
  • In prokaryotes, occurs through Rho-dependent involving Rho protein binding nascent RNA causing RNA polymerase dissociation or Rho-independent relying on stem-loop structure formation in nascent RNA followed by uracil residues causing stalling and dissociation
  • In eukaryotes, signals for RNA polymerase II include polyadenylation signal (AAUAAA) and downstream GU-rich sequence triggering cleavage, polyadenylation, and release of RNA polymerase II

Components of promoters

• Prokaryotic promoters:
  • -35 region: Consensus TTGACA, 35 bp upstream of transcription start site, recognized by σ factor
  • -10 region (Pribnow box): Consensus TATAAT, 10 bp upstream of transcription start site, facilitates DNA melting and transcription bubble formation
  • Spacer region: Typically 17 ± 1 bp between -35 and -10 regions, optimal spacing crucial for efficient promoter recognition and binding
• Eukaryotic promoters:
  • Core promoter: Minimal DNA sequence required for initiation by RNA polymerase II, includes TATA box, initiator (Inr), downstream promoter element (DPE)
    1. TATA box: Consensus TATAAA, 25-30 bp upstream of transcription start site, binding site for TATA-binding protein (TBP) subunit of TFIID
    2. Initiator (Inr): Consensus YYANWYY (Y = pyrimidine, N = any nucleotide, W = A or T), encompasses transcription start site, functions independently or with TATA box
    3. Downstream promoter element (DPE): Consensus RGWYV (R = purine, V = not T), 28-32 bp downstream of transcription start site, binding site for TAF6 and TAF9 subunits of TFIID
  • Proximal promoter elements: Regulatory sequences upstream of core promoter, binding sites for specific transcription factors that modulate expression
  • Enhancers and silencers: Distal regulatory elements located thousands of bp from promoter, binding sites for activators or repressors that fine-tune expression

Significance of transcription factors

• Proteins that bind specific DNA sequences and regulate transcription by promoting or repressing RNA polymerase recruitment and activity
• Activators:
  • Bind enhancer sequences stimulating expression
  • Promote transcription by recruiting coactivators that modify chromatin making promoter more accessible, interacting with general transcription factors or RNA polymerase to stabilize preinitiation complex enhancing initiation, facilitating transition from initiation to elongation by promoting RNA polymerase release from promoter
• Repressors:
  • Bind silencer sequences inhibiting expression
  • Repress transcription by competing with activators for binding sites preventing active transcription complex formation, recruiting corepressors that modify chromatin making promoter less accessible, interacting with general transcription factors or RNA polymerase to destabilize preinitiation complex reducing initiation
• Combinatorial control:
  • Multiple transcription factor binding sites allow integration of cellular signals to fine-tune expression
  • Different combinations lead to distinct cell-type-specific and condition-specific regulation (tissue development, stress response)
• Play crucial role in development, cell differentiation, and responses to environmental stimuli by modulating expression of specific gene sets