Gene Regulation in Eukaryotes

Gene Regulation in Eukaryotes

Gene Regulation Overview

  • Gene Expression: Refers to the process by which information from a gene is used to synthesize functional gene products, often proteins.

  • Constitutive Expression:

    • Certain genes are expressed continuously and at a constant rate.

    • Often referred to as Housekeeping Genes ( rRNA, some chaperons, actin) because they are required for maintaining basic cellular function.

    • Not subject to regulation.

  • Regulated Genes:

    • Many genes are only needed under certain conditions and thus must be able to be turned on or off (regulation can involve increasing or decreasing activity).

    • Effective gene expression requires the coordination of multiple genes due to many cellular processes depending on this coordination.

  • Mechanisms of Gene Regulation:

    • 1. Operons (found only in bacteria) same promoter, multiple ORFs per mRNA

    • 2. Shared Transcription Factors, different promoters

Stages of Gene Regulation

  • Transcriptional Regulation: Most gene regulation occurs at the stage of transcription initiation, but can happen at various levels:

    • At any stage of transcription:

      • Initiation

      • Elongation

      • Termination

    • Post-transcriptionally:

      • Involves mechanisms such as:

        • mRNA stability

        • Translation initiation

    • Post-translationally:

      • Concerns protein stability and activity

    • Altering DNA Structure:

      • Gene expression can also be regulated by modifying the physical structure of DNA, more complex in eukaryotes due to elements like histones, nucleosomes, and chromatin.

Levels of Gene Regulation in Eukaryotes

Transcription Regulation in Eukaryotes

  • Common Mechanisms:

    1. Specific Transcription Factors:

    • Activators:

      • Proteins that increase the likelihood of transcription of specific genes.

    • Repressors:

    • Proteins that inhibit gene transcription

    • .2. Chromatin Structure:

    • Alters the accessibility of the promoter to RNA polymerase and general transcription factors.

    • Influences the accessibility of regulatory elements for specific transcription factors.

Transcription Review

  • Gene Structure:

    • Similar in both bacteria and eukaryotes with key components:

    • Promoter

    • Transcribed region

    • 5’ UTR (Untranslated Region)

    • 3’ UTR

    • Protein-coding region (ORF)

  • Promoter Elements:

    • Bacterial Promoter Elements: Recognized by RNA polymerase are typically located at positions -10 and -35.

    • Eukaryotic Promoter Elements: More diverse and complex than bacterial promoters but share the same general function.

  • Transcription Process:

    • Overall process is similar but varies significantly in specifics between bacterial and eukaryotic transcription.

    • Eukaryotes:

      • Involve mRNA processing and require general transcription factors for initiation (RNA Polymerase + general transcription factors).

    • Bacteria:

      • Coupling of transcription and translation occurs, with distinct mechanisms for transcription termination.

    • Translation Process:

    • Similar but involves different physical structures:

      • In bacteria: Shine-Dalgarno sequence for ribosome binding.

      • In eukaryotes: Proteins interacting with the 5’ Cap and 3’ poly(A) tail.

    • Coupling of Transcription and Translation:

    • Coupled process in bacteria vs. spatially and temporally separated in eukaryotes due to nuclear organization.

    • Eukaryotic cells require mRNA to be exported for translation.

Regulatory Elements

  • Regulatory elements often involved in transcription regulation can be:

    • Proximal Regulatory Promoter: Located immediately upstream of the core promoter.

    • Enhancers: These can be located further upstream and can significantly influence transcription. (DISTAL)

  • Key Point:

    • DNA does not perform actions directly but serves as a binding site for proteins including transcription factors.

    • Elements on DNA include:

    • Promoter

    • Regulatory elements

    • Enhancers

  • Transcription Factors:

    • General Transcription Factors: Basal transcription apparatus that is necessary for minimal transcription levels.

    • Specific Transcription Factors: Includes both activators and repressors.

Specific Transcription Factors

Activators

  • Mechanism of action:

    • Activators work by interacting with general transcription factors at the core promoter, stabilizing the basal transcription apparatus and promoting transcription.

Repressors

  • Mechanisms of action include:

    1. Preventing activators from binding DNA.

    2. Preventing activators from interacting with the basal transcription apparatus.

    3. Destabilizing the basal transcription apparatus, inhibiting transcription.

Example: Galactose Metabolism in Yeast

  • Gene involved in the breakdown of galactose, primarily used in metabolism to produce energy.

  • Gal4:

    • A transcriptional activator (specific transcription factor).

    • Regulatory element: UAS (Upstream Activating Sequence) recognized as an enhancer by Gal4, helping it recruit general transcription factors.

  • Gal80:

    • A transcriptional repressor (specific transcription factor).

    • In the absence of galactose, Gal80 binds to Gal4, blocking its ability to activate transcription.

    • Post-translational regulation occurs here.

  • Gal3:

    • Activity is regulated in the presence of galactose. (post-translational regulation)

    • When galactose levels are high, Gal3 will bind to galactose and subsequently bind to Gal80, preventing it from interacting with Gal4. (post-translational regulation)

Mechanism of Galactose Regulation

  • Galactose Absence:

    • Gal4 binds to UAS enhancer.

    • Gal80 binds to Gal4, leading to an unstable basal transcription apparatus.

    • Results in low transcription levels.

  • Galactose Presence:

    • Galactose binds to Gal3, which then binds to Gal80.

    • This interaction allows Gal4 to bind with the basal transcription apparatus.

    • Results in a stable basal transcription apparatus, thereby increasing transcription levels.

Chromatin Structure and Gene Regulation

Learning Outcomes for Chromatin Structure

  • Understand chromatin remodeling complexes, the significance of histone modification, and DNA methylation in regulating gene expression.

Review of Chromatin Structure

  • Nucleosome Structure:

    • Composed of DNA wrapped around a histone octamer.

    • Histones have tails that can undergo post-translational modifications.

  • Impact of Chromatin Structure on Gene Expression:

    • Less compact (open) chromatin allows for increased transcription.

    • More compact (closed) chromatin represses transcription.

    • The dynamic nature of chromatin structure is vital for gene regulation.

Mechanisms Affecting Chromatin Structure

  1. Chromatin Remodeling:

    • Process where chromatin becomes accessible for the basal transcription apparatus.

    • Nucleosome positioning can be altered by remodelers, achieved by:

      • 1. Sliding along the DNA strand.

      • 2. Inducing conformational changes in the DNA or nucleosome structure.

  2. Histone Modification:

    • Modifications on amino acids in histone tails include acetylation, methylation, and phosphorylation.

    • Specific modifications can recruit other proteins involved in transcription regulation.

  3. DNA Methylation:

    • Involves adding methyl groups to specific cytosine bases in DNA.

    • Results in repressing transcription by recruiting enzymes that remove acetyl groups from histone tails, thereby inducing a closed chromatin configuration.