7.3 Transcription

4 min read•august 22, 2024

Transcription is the first step in gene expression, where DNA is used as a template to create RNA. This process involves three main stages: initiation, elongation, and termination. RNA polymerase and various transcription factors play crucial roles in making it happen.

Different types of RNA are produced during transcription, including mRNA, rRNA, and tRNA. Each type serves a specific purpose in protein synthesis. Promoters and regulatory elements control when and how much transcription occurs, allowing cells to fine-tune gene expression.

Transcription Process

Initiation

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  • Transcription is the process of synthesizing RNA from a DNA template, which occurs in the 5' to 3' direction
  • Initiation of transcription begins when RNA polymerase binds to a specific promoter sequence on the DNA template strand, forming a closed promoter complex
  • The DNA then unwinds, forming an open promoter complex, and RNA polymerase begins synthesizing the RNA transcript

Elongation and Termination

  • During elongation, RNA polymerase moves along the DNA template strand, catalyzing the addition of complementary ribonucleotides to the growing RNA strand
    • The RNA transcript is synthesized in the 5' to 3' direction
    • The DNA template is read in the 3' to 5' direction
  • Termination of transcription occurs when RNA polymerase encounters a specific termination signal on the DNA template
    • In prokaryotes, termination can be either Rho-dependent or Rho-independent
    • In eukaryotes, termination is typically triggered by specific sequences and involves additional factors (transcription termination factors)

Transcription Enzymes and Factors

RNA Polymerase

  • RNA polymerase is the main enzyme responsible for catalyzing the synthesis of RNA during transcription
    • In prokaryotes, there is a single type of RNA polymerase
    • Eukaryotes have three types of RNA polymerase (RNA polymerase I, II, and III), each transcribing different classes of RNA
      • RNA polymerase I transcribes rRNA (except 5S rRNA)
      • RNA polymerase II transcribes mRNA and some snRNAs
      • RNA polymerase III transcribes tRNA, 5S rRNA, and some snRNAs

Transcription Factors

  • Sigma factors are proteins that bind to prokaryotic RNA polymerase and help recognize specific promoter sequences, facilitating the initiation of transcription
  • General transcription factors (GTFs) are proteins that assist eukaryotic RNA polymerases in initiating transcription
    • They help position RNA polymerase at the promoter and facilitate the unwinding of DNA
    • Examples of GTFs include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIIH
  • Transcription activators and repressors are proteins that bind to specific regulatory sequences on the DNA and can enhance or inhibit transcription, respectively
    • Activators can recruit RNA polymerase and GTFs to the promoter, increasing transcription rates (Sp1, CREB)
    • Repressors can block the binding of RNA polymerase or activators, reducing transcription rates (REST, YY1)

mRNA, rRNA, and tRNA Transcription

mRNA Transcription

  • Messenger RNA (mRNA) is transcribed from protein-coding genes and serves as a template for protein synthesis
    • In eukaryotes, mRNA is transcribed by RNA polymerase II
    • Eukaryotic mRNA undergoes post-transcriptional modifications, such as 5' capping, 3' polyadenylation, and splicing
      • 5' capping adds a 7-methylguanosine cap to the 5' end, protecting mRNA from degradation and facilitating translation
      • 3' polyadenylation adds a poly(A) tail to the 3' end, enhancing mRNA stability and translation efficiency
      • Splicing removes introns and joins exons to form a mature mRNA

rRNA and tRNA Transcription

  • Ribosomal RNA (rRNA) is a component of ribosomes and is transcribed from specific genes
    • In eukaryotes, rRNA is transcribed by RNA polymerase I (28S, 18S, and 5.8S rRNA) and RNA polymerase III (5S rRNA)
    • rRNA does not undergo extensive post-transcriptional modifications
  • Transfer RNA (tRNA) is transcribed from tRNA genes and plays a crucial role in protein synthesis by carrying amino acids to the ribosome
    • In eukaryotes, tRNA is transcribed by RNA polymerase III
    • tRNA undergoes post-transcriptional modifications, such as the addition of CCA at the 3' end and base modifications (pseudouridine, dihydrouridine)

Promoters and Transcriptional Regulation

Promoter Structure

  • Promoters are specific DNA sequences located upstream of the transcription start site that serve as binding sites for RNA polymerase and transcription factors
  • Core promoters are the minimal sequences required for the initiation of transcription and typically include:
    • The TATA box (in some eukaryotic genes), a consensus sequence (TATAAA) located ~25-30 base pairs upstream of the transcription start site
    • The transcription start site, where RNA polymerase begins synthesizing the RNA transcript
  • Regulatory promoters are sequences that bind transcription factors and can enhance or repress transcription
    • Proximal promoter elements, such as the CAAT box and GC box, are located close to the core promoter
    • Distal regulatory elements, such as enhancers and silencers, can be located far from the core promoter

Transcriptional Regulation

  • The binding of transcription factors to regulatory promoter elements can affect the recruitment and activity of RNA polymerase, thus modulating the rate of transcription initiation
    • Activators can increase transcription rates by stabilizing the binding of RNA polymerase and GTFs to the promoter (Sp1 binding to GC box)
    • Repressors can decrease transcription rates by blocking the binding of activators or RNA polymerase to the promoter (REST binding to NRSE)
  • Promoter strength, which is influenced by the sequence and arrangement of core and regulatory promoter elements, determines the basal level of transcription for a given gene
    • Strong promoters have a higher affinity for RNA polymerase and transcription factors, resulting in higher transcription rates (CMV promoter)
    • Weak promoters have a lower affinity for RNA polymerase and transcription factors, resulting in lower transcription rates (HSV-TK promoter)
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