Notes on Transcription Process in Prokaryotic and Eukaryotic Systems

Overview of Transcription in Prokaryotes vs. Eukaryotes

• Conservation of Structure and Function
  • Although components differ between prokaryotic and eukaryotic systems, fundamental processes remain similar.

Key Enzymes in Transcription

• RNA Polymerase in Bacteria
  • Singular polymerase for transcription.
• RNA Polymerases in Eukaryotes
  • Three different polymerases:
  • RNA pol II: Main enzyme for mRNA transcription; also synthesizes snRNA and some other non-coding RNAs.
  • RNA pol I: Primarily synthesizes rRNA (ribosomal RNA).
  • RNA pol III: Synthetizes tRNA and other small RNA molecules.

DNA Elements and their Role in Transcription

• Core Promoter
  • Regions dictate where RNA polymerases initiate transcription.
• TATA Box
  • AT-rich region crucial for polymerase binding, influencing flexibility and recruitment.
• Core Promoter Structure
  • Consists of several elements including:
  • TATA element
  • BRE element
  • INR
  • DPE
• Specific Transcription Factors
  • Regulate the transcription process by interacting with the core promoter and recruited polymerase, influencing transcriptional activation.

Steps of Eukaryotic Transcription Initiation

• Recruitment Phase
  • Begin with the binding of TF IID, which interacts with the core promoter elements ensuring the correct positioning of RNA polymerase.
  • Phosphorylation
  • RNA pol II must undergo phosphorylation for activation and transcription initiation.
• Scanning Mode vs. Active Transcription Mode
  • Transition occurs after recruitment of RNA pol and dissociation of transcription factors such as TF II F.

Polymerase Differences: RNA pol I, II, III

• RNA pol I
  • Utilizes core promoter and an upstream control element (UCE) for rRNA synthesis; has unique binding dynamics with UBF (Upstream Binding Factor).
• RNA pol II
  • Most well-studied; does not utilize UCE but core elements for mRNA synthesis.
• RNA pol III
  • Lacks a core promoter; synthesizes tRNAs and some small nucleolar RNAs with box A and B binding sites.

Termination of Transcription

• RNA pol II Termination
  • Inaccurate end produced during transcription; relies on polyadenylation for the formation of stable mRNA.
• RNA pol I and III Termination
  • More structured and defined methods for ending transcription.
• Termination Mechanisms
  • Row-dependent (protein-mediated) and row-independent (sequence-dependent) mechanisms to stop transcription.

Gene Regulation Mechanisms

• Regulatory DNA Sequences
• Operons in Prokaryotes
  • Genes regulated in blocks allowing prokaryotes to efficiently manage expression levels with minimal genomic resources.
• Operon Examples
  • Lac Operon: Regulated by a repressor that binds operator, preventing transcription unless an inducer releases the repressor.
  • Tryptophan Operon: Repressed when tryptophan is abundant.

Enhancements in Eukaryotic Transcription

• Role of Transcription Factors
  • Fine-tune expression levels of specific genes, allowing more complex regulation than in prokaryotic systems.
• Gene Elements Upstream or Downstream
  • Facilitate or hinder polymerase recruitment and transcription; enables asynchronous activation of genes throughout the genome.

Riboswitches

• Function of Riboswitches
  • RNA structures can change shape in response to metabolite binding, influencing transcription termination or translation initiation.
  • Example of premature termination due to the formation of hairpin structures, affecting RNA stability and availability for translation.

Summary of Environmental Influences on Gene Expression

• Chromatin Structure
  • Active transcription leads to accessible DNA for repair mechanisms, suggesting an intertwined role of transcription and DNA maintenance.
• Key Transcriptional Events
  • Understanding the coordination of initiation and cessation of transcription allows for deeper insights into cellular control mechanisms and pathways involved in gene expression regulation.
• Overall Importance
  • Grasp of transcription mechanisms and their regulatory dimensions is crucial for studies in genetics, molecular biology, and biotechnology.