Genetics Ch.17- Transcriptional Regulation in Eukaryotes:

Organization of the Eukaryotic Cell Facilitates Gene Regulation at Several Levels

  • Eukaryotic gene regulation is more complex than prokaryotes due to several factors:
  • Presence of a greater amount of DNA associated with histones and other proteins.
  • mRNAs must be processed (spliced, capped, and polyadenylated) before moving from the nucleus to the cytoplasm.
  • Genes are located on multiple chromosomes contained within a double membrane nucleus.
  • mRNA stability can vary widely, leading to modulation of translation, processing, and degradation.

Eukaryotic Gene Expression Influenced by Chromatin Modifications

Structural Features of Eukaryotic Genes

  • Chromosome Location: Eukaryotic genes reside on chromosomes that occupy specific locations in the nucleus.
  • Chromatin Structure: DNA interacts with histones to form chromatin, which can compact and inhibit functions such as transcription and repair.

Chromosome Territory

  • Discrete Domains: Each chromosome occupies a specific territory within the interphase nucleus, separated by interchromosomal domains that contain minimal DNA.
  • Transcriptional Activity: Active genes can relocate to the edges of these territories, changing their accessibility for transcription.

Transcription Factories

  • Active Sites: Areas within the nucleus where active RNA polymerases and transcription regulatory molecules aggregate, essential for successful gene expression.
  • Dynamic Structures: These can form and disassemble based on transcriptional needs, reflecting a responsive gene regulation environment.

Eukaryotic Transcription Initiation Requires Specific Cis-Acting Sites

Cis-Acting Sequences

  • Located on the same chromosome as the regulated gene and essential for controlled transcription.
  • Examples:
    • Promoters: Sites for transcription initiation.
    • Enhancers: Enhance transcription levels from a distance.
    • Silencers: Repress transcription initiation.

Promoters

  • Core Promoter: Essential for transcription initiation; determines where RNA polymerase binds.
  • Proximal Promoter Elements: Affect the efficiency of basal transcription levels.
  • Diversity in Promoters: Includes focused (one transcript) and dispersed (multiple transcripts) promoters supporting varied gene expression.

Eukaryotic Transcription Initiation Regulation by Transcription Factors

Transcription Factors

  • Definition: Regulatory proteins that target cis-acting sites, modulating expression.
  • Activators vs. Repressors: Activators increase transcription while repressors inhibit it, enabling fine-tuning through multiple factor interactions.

Example: Human Metallothionein IIA Gene (hMTIIA)

  • Responds to heavy metal exposure, featuring varied transcription activation influenced by its regulatory elements.

Activators and Repressors Interact with General Transcription Factors

RNA Polymerase II Initiation Complex

  • General Transcription Factors (GTF): Required for transcription initiation; assemble to form a pre-initiation complex (PIC) that stabilizes RNA polymerase at the promoter.
  • GTFs include TFIIA, TFIIB, and TATA-binding protein essential for accurate transcription initiation.

Mechanism of Activation

  • DNA Looping: Activators and repressors adjust the spatial organization of the transcription machinery, enhancing or inhibiting interaction with promoters
  • Coactivators and Enhancer Function: Coactivators like the enhanceosome facilitate effective transcription through interaction with promoter-bound factors.

ENCODE Data and Its Impact on Gene Regulation Understanding

ENCODE Overview

  • ENCODE Project: Aims to identify functional elements within the human genome; has revealed that over 80% of the genome contains regulatory elements, many previously thought to be non-functional.
  • Disease Association: Genome-wide association studies (GWAS) have identified numerous variations within regulatory regions, linking them to disease susceptibility, providing a new understanding of genetic regulation beyond classical genes.