lecture 11 lecture

Transcriptional Regulation and Epigenetics

Introduction

  • Coupled transcription/translation: In bacteria, mRNA translation occurs simultaneously with transcription.

  • Operon: A unit of bacterial gene expression and regulation, comprising structural genes and control elements recognized by regulatory gene products.

Mechanisms of Transcription Regulation

Trans-acting vs. Cis-acting Elements

  • Trans-acting: Products (proteins or RNAs) that can function on any DNA copy.

  • Cis-acting: A site affecting activity only for sequences on its own DNA (or RNA); does not code for protein.

Regulator and Structural Genes

  • Regulator gene: Encodes products that control expression of other genes, typically at the transcription level.

  • Structural gene: Encodes RNA or protein products other than regulators.

Control Mechanisms

Negative Regulation

  • Repressor proteins bind to operators to inhibit gene expression.

  • Example: In negative control, a trans-acting repressor binds to the cis-acting operator to halt transcription.

Positive Regulation

  • Transcription factors are required to bind at the promoter, allowing RNA polymerase to initiate transcription.

  • A trans-acting factor must bind to a cis-acting site to enable RNA polymerase at the promoter.

Types of Gene Regulation

  • Inducible regulation: The gene's expression is activated by the presence of a substrate (inducer).

  • Repressible regulation: The gene's expression is inhibited by the product of its pathway (corepressor).

  • Possible mechanisms: Negative inducible, negative repressible, positive inducible, positive repressible.

Structural Gene Clusters

  • Genes that perform similar functions may cluster together and are transcribed as a single polycistronic mRNA.

  • Example: The lac operon spans ~6000 bp of DNA.

The Lac Operon

Negative Inducible Control

  • Controlled by the lac repressor protein that binds an operator overlapping the promoter.

  • Constitutive expression: Continuous expression of a gene.

  • In the absence of β-galactosides, lac operon is expressed at a low level.

Induction Mechanism

  • The lac repressor is a tetramer encoded by the lacI gene.

  • β-galactoside sugars serve as inducers, facilitating transcription of lac operon genes.

  • The lac mRNA is unstable; induction can be reversed quickly.

Operator Mutations

  • Cis-acting mutations in the operator cause constitutive expression of lac structural genes.

  • Trans-acting mutations in the lacI gene affect all lacZYA clusters and may lead to constitutive expression.

  • Mutations that inactivate lacI prevent repressor action, allowing operon expression.

Operator Competition and Catabolite Repression

Repressor Binding and Competition

  • Repressor proteins bind to high-affinity operator sites, being released by inducers.

  • Low-affinity DNA sites serve as starting points for repressor binding.

Catabolite Repression in the Lac Operon

  • Catabolite repression: Glucose inhibits expression of genes (positive control in bacteria).

  • cAMP activates CRP (catabolite repressor protein), promoting RNA polymerase binding.

The Trp Operon

Repressive Control Mechanisms

  • Controlled by the amino acid tryptophan which activates an inactive repressor encoded by trpR.

  • Attenuation: Control of transcription termination before the first structural gene.

Eukaryotic Gene Regulation

Chromatin Structure Influences Gene Expression

  • Gene expression in eukaryotes is mainly regulated during transcription initiation by opening chromatin.

  • Transcription factors can alter or displace nucleosomes, enabling gene activation.

Histone and DNA Modifications

  • Histone acetylation marks sites for transcription activation; done by HAT enzymes.

  • Histone deacetylases (HDACs) remove acetyl groups, associated with gene repression.

  • Methylation of DNA and histones typically correlates with inactive chromatin.

Epigenetics and Inheritance

  • Epigenetic effects may arise from nucleic acid modifications or protein structural perpetuation.

  • Prions: Infectious agents that can propagate traits without nucleic acids; examples include PrPSc.

  • Mechanisms like dosage compensation balance expression between X chromosomes.

Summary of Genetic Control

  • Eukaryotic gene activation involves protein interactions across domains and chromatin remodeling processes.

  • Understanding the interplay of all these regulatory mechanisms sheds light on gene expression intricacies.