8.2 Transcription in Eukaryotes

Eukaryotic transcription is a complex process involving multiple RNA polymerases and regulatory elements. RNA polymerases I, II, and III transcribe different types of RNA, with RNA polymerase II responsible for mRNA production.

Transcription initiation requires general transcription factors and promoter elements like the TATA box. Enhancers and silencers regulate gene expression over long distances. The process involves chromatin remodeling and various protein complexes to control gene activity.

RNA Polymerases and Transcription Initiation

Types and Functions of RNA Polymerases

• RNA polymerase I transcribes ribosomal RNA genes (rRNA) in the nucleolus
  • Produces 28S, 18S, and 5.8S rRNAs
  • Essential for ribosome assembly and protein synthesis
• RNA polymerase II transcribes protein-coding genes and some small nuclear RNAs (snRNAs)
  • Responsible for producing messenger RNA (mRNA) and most small nuclear RNAs
  • Plays a crucial role in gene expression and regulation
• RNA polymerase III transcribes transfer RNA (tRNA) genes and other small RNAs
  • Produces 5S rRNA, tRNAs, and other small non-coding RNAs
  • Involved in protein synthesis and RNA processing

Transcription Initiation Complex Formation

• General transcription factors assist RNA polymerase II in initiating transcription
  • Include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIIH
  • Recognize and bind to specific DNA sequences in the promoter region
• TATA box serves as a core promoter element for many eukaryotic genes
  • Located approximately 25-30 base pairs upstream of the transcription start site
  • Recognized by TATA-binding protein (TBP), a subunit of TFIID
• Promoter elements consist of various DNA sequences that regulate gene expression
  • Include proximal promoter elements (CAAT box, GC box)
  • Influence transcription initiation and regulation
• Transcription initiation complex forms through stepwise assembly of components
  • TFIID binds to the TATA box, followed by TFIIB and RNA polymerase II
  • Remaining general transcription factors join to complete the pre-initiation complex
  • Complex formation leads to DNA melting and initiation of RNA synthesis

Transcriptional Regulation

Enhancers and Silencers

• Enhancers increase transcription rates of target genes
  • Located upstream, downstream, or within introns of the genes they regulate
  • Can function over long distances (up to 1 million base pairs)
  • Bind specific transcription factors to promote gene expression
• Silencers decrease transcription rates of target genes
  • Function similarly to enhancers but with opposite effects
  • Bind repressor proteins to inhibit gene expression
  • Can act over long distances and in orientation-independent manner
• Both enhancers and silencers interact with promoters through DNA looping
  • Facilitated by protein-protein interactions and chromatin remodeling
  • Allow distal regulatory elements to influence transcription initiation

Transcription Elongation and Termination

• C-terminal domain (CTD) of RNA polymerase II plays crucial role in transcription cycle
  • Consists of multiple repeats of a seven-amino-acid sequence
  • Undergoes phosphorylation and dephosphorylation during transcription
  • Serves as a platform for binding various factors involved in RNA processing
• Mediator complex acts as a bridge between regulatory proteins and RNA polymerase II
  • Large, multi-subunit protein complex
  • Transmits signals from transcription factors to the general transcription machinery
  • Facilitates pre-initiation complex assembly and stabilization
• Chromatin remodeling alters DNA accessibility for transcription factors
  • Involves ATP-dependent chromatin remodeling complexes (SWI/SNF, ISWI)
  • Modifies histone-DNA interactions to expose or conceal regulatory sequences
  • Includes histone modifications (acetylation, methylation, phosphorylation)
  • Plays crucial role in gene activation and repression