Lecture on RNA Transcription

Key Definitions

• Coding strand: DNA strand to be copied into RNA.
• Template strand: Complimentary base sequence to the coding strand, used to form RNA transcript.
• Transcription start site: Start of the coding sequence.
• Promoter region: Contains DNA sites called core promoter elements important for initiating transcription.
• Transcription initiation complex: Includes RNA Polymerase II (RNA Pol II) and various transcription factors.

Assembly of Transcription Initiation Complex

• TFIID binds to the TATA box within the core promoter elements.
  • Contains TATA-binding protein (TBP) which bends the DNA.
• TFIIA and TFIIB bind next.
  • TFIIB contacts TFIID and the core promoter element (BRE).
• RNA Pol II is recruited along with TFIIF.
• TFIIE and TFIIH complete the complex.
  • Forms the closed complex where DNA is still double-stranded.

Transition to Open Complex

• TFIIH: Uses ATP to unwind DNA, creating a transcription bubble exposing the template strand.
• RNA Pol II catalyzes addition of nucleotides in a 5' to 3' direction.

Abortive Initiation

• RNA Pol II synthesizes and releases short RNA fragments repeatedly.
• Eventually breaks free of the promoter in a phase called promoter clearance.
• TFIIH phosphorylates the C-terminal domain (CTD) of RNA Pol II, essential for RNA processing.

RNA Processing

• P-TEFb complex binds to phosphorylated CTD.
  • Adds a guanosine cap to the 5' end of RNA.
  • Further phosphorylates CTD, allowing elongation to resume.
  • Recruits additional RNA processing enzymes.

Elongation Phase

• RNA strand exits RNA Pol II as it elongates.
• DNA re-anneals behind the transcription bubble.
• Elongation factors can rescue stalled RNA Pol II enzymes.
• TFIIS rescues backtracked RNA Pol II by cleaving the unpaired 3' end.

Termination Phase

• RNA Pol II transcribes a polyadenylation signal.
• RNA processing proteins bind to CTD, cleave RNA transcript, and add a poly-A tail.
• RNA Pol II dissociates, releasing mature RNA transcript.