Lecture 3: Transcriptional regulation – cis- and trans-acting elements

Week Two: Gene Expression and Maintenance

Overview of Gene Expression Control

• Focus on the regulation of transcription in gene expression.

• Importance of efficient transcription; RNA production is energetically unfavorable.

• Aim to understand how cells switch genes on and off to respond to cellular needs.

Key Definitions

• Gene Expression: A combination of processes including transcription, translation, and RNA modification culminating in protein production.

  • Do not generalize; specify which aspect of gene expression is affected in examinations.

• Regulate: Changing the amount of gene expression in response to cellular signals.

  • Positive Regulation: Increases transcription.

  • Negative Regulation: Reduces transcription.

Need for Gene Regulation

• Both prokaryotes and eukaryotes require transcription regulation to optimize energy usage.

  • Uncontrolled transcription leads to unnecessary RNA and protein synthesis.

• Regulation allows cells to accommodate varying protein needs efficiently.

Approach to Gene Regulation

• Focus on two types of elements:

  • Cis Elements: DNA sequences including promoters and operators that facilitate transcription.

  • Trans Elements: Proteins such as transcription factors that interact with cis elements to regulate transcription.

Mechanisms of Transcription Regulation

Prokaryotic Transcription Regulation

• Study of transcriptional units: Promoter, gene encoding protein, terminator, and the operator sequence.

• Operator Sequence:

  • Type of cis element recognized by proteins (transcription factors).

  • Acts as a binding site for activators and repressors.

Role of Repressors and Activators

• Repressor Proteins:

  • Bind to the operator, blocking RNA polymerase's access to the promoter, thus turning transcription off.

• Activator Proteins:

  • Bind to the operator to enhance RNA polymerase's ability to bind to the promoter, thus turning transcription on.

Eukaryotic Transcription Regulation

• Core Promoter: Region where basal transcription occurs. Minimal transcription occurs without regulatory elements.

• Regulatory Regions:

  • Multiple sequence elements controlling transcription intensity. Can be located at various distances (upstream/downstream) from the coding gene.

  • Enhancers:

  • Cis elements that can be located far from their corresponding promoter and may interact with transcription factors.

Identifying Cis Elements in Eukaryotes

• Gender approach through mutational studies of segments like the beta globin promoter to understand regulatory sequences.

• Identified elements include:

  • TATA Box: Part of the core promoter.

  • CAT Box and GC Box: Essential enhancer elements found in many genes.

Enhancers and Transcription Factors

• Transcription Factors: Modular proteins with specific domains for DNA binding (e.g.,

  • Zinc Finger; Helix-turn-helix; Leucine Zipper).

  • Two key domains:

  1. DNA Binding Domain: Binds to specific DNA sequences (cis elements).

  2. Activation Domain: Interacts with general transcription factors to regulate transcription efficiently.

• Interaction with the pre-initiation complex stabilizes the process leading to successful transcription initiation.

Role of Mediators

• Mediators: Complexes that bind RNA polymerase and transcription factors but do not bind DNA directly. They optimally position transcriptional machinery.

Influence of Chromatin Structure

Chromatin Remodeling in Transcription

• Nucleosomes: DNA wrapped around histone proteins; access to DNA is often limited due to this tight packaging.

• Chromatin Remodeling Complexes: Utilize ATP to modify nucleosome positioning.

  • Two methods of action:

  1. Nucleosome Sliding: Moves nucleosomes to expose cis elements for transcription factor binding.

  2. Nucleosome Removal: Fully removes chromatin to allow transcription factor access.

• Histone Modifications: Modify histone tails to change chromatin structure.

  • Acetylation: Generally activates transcription by loosening histone-DNA interactions.

  • Methylation: Typically represses transcription, tightening interactions.

Combination and Interplay of Modifications

• Histone Acetyltransferases (HATs): Add acetyl groups to histone tails, enabling transcription.

• Histone Deacetylases (HDACs): Remove acetyl groups, often leading to transcriptional repression.

• Histone Methyltransferases: Add methyl groups, whereas Demethylases remove methyl groups.

Effect of Phosphorylation

• Phosphorylation generally relaxes chromatin, particularly during DNA replication, facilitating access to transcription machinery.

• Phosphorylation enhances ease of binding for both RNA polymerase and DNA polymerase, indicating a relaxed chromatin state during replication.

Conclusion: Overview of Eukaryotic vs Prokaryotic Gene Regulation

• Eukaryotic transcription regulation is more complex than in prokaryotes, primarily occurring at the initiation stage.

• Focus is on activating transcription through the use of multiple cis elements and the action of various transcription factors, along with chromatin remodeling and modifications to histones.

• Control over elongation and termination is less common; instead, primary modulation occurs during initiation.