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.