Eukaryotic Gene Regulation Notes 1

Eukaryotic Gene Regulation

Learning Goals

• Understand regulation of gene expression at different levels:
  • Chromatin
  • Transcription
  • Post-transcription/mRNA
  • Translation
  • Post-translation

Complexity of Eukaryotic Organisms

• Eukaryotic organisms exhibit higher complexity through:
  • Larger genomes
  • Extensive gene regulation
• All cells possess the same genome but exhibit different gene expression levels to:
  • Differentiate cell types
  • Respond to environmental changes

Levels of Gene Regulation

• Comparison between Bacteria and Eukaryotes:
  1. Chromatin
  2. Transcription
  3. mRNA Processing
  4. mRNA Degradation
  5. Translation
  6. Post-translational Modifications

Detailed Levels of Gene Regulation in Eukaryotes

1. Chromatin Regulation

   • Histone Modifications:
     • Affect gene expression through changes in their interaction with DNA
     • Acetylation: Increases gene expression (mediated by histone acetyltransferases)
     • Methylation & Phosphorylation: Can either increase or decrease gene expression (mediated by methyltransferases, kinases, and phosphatases)
   • DNA Methylation:
     • Occurs at CpG (C - phosphate – G) sites, where a methyl group is added to cytosine base adjacent to guanine
     • High density of CpG sites known as CpG islands often located in gene promoters
     • Methylated CpG sites keep histones tightly bound, affecting transcriptional activity

2. Transcription Regulation

   • Responsible for determining when, where, and how genes are expressed
   • Cis-acting Elements: Sequences regulating gene expression on the same chromosome
   • Trans-acting Factors: Gene products (RNA or proteins) that bind to cis-acting elements and regulate genes across all chromosomes

Promoter and Regulatory Elements in Transcription

• Promoters: Binding sites for transcription factors to recruit RNA polymerase (RNA Pol)
  • Located directly upstream of target gene
• Core promoter elements: Essential sequences for transcription (~50-100 bp of start site)
  • E.g., TATA box
• Proximal Elements: Non-essential but help regulate transcription (~250 bp from start site), includes elements like CAAT and GC boxes
• Distal Elements (Enhancers/Silencers):
  • Non-essential, can be located far from the gene, up to 1 Mb.

Transcription Factors

• General Transcription Factors (GTFs):
  • Required for transcription initiation, bind to core promoter elements
• Activators: Increase expression under specific conditions by binding to enhancer elements
• Repressors: Decrease expression under certain conditions by binding to silencer elements

Example: Human Metallothionein 2A Gene (MT2A) Regulation

• Normal Conditions: Low expression, depending on cell type
• Heavy Metal Presence: Increases transcription through activator MTF-1 that binds to regulatory elements
• Core Promoter Elements: Include TATA box and GC box, regulated by different activators
• Repression: Through factors like PZ120, affecting transcription levels

Responses to Environmental Factors

• Two main responses:
  • To heavy metals (increased expression via MTF-1)
  • To glucocorticoid hormones (increased expression via glucocorticoid receptors)
• If necessary transcription factors (like MTF-1) cannot bind to their sites, expression would diminish in response to stimuli (heavy metals/glucocorticoids).

Important Notes:

• Cis-acting vs. Trans-acting:
  • Cis: DNA sequences regulating the same gene
  • Trans: Proteins or RNAs that influence gene expression across different locations in the genome

Conclusion

• Understanding eukaryotic gene regulation involves studying the intricate interactions between chromatin structure, transcription machinery, and various regulatory elements. This is crucial for grasping how cells make distinct decisions about gene expression in response to internal and external signals.