Gene expression principles

Learning Objectives

  • Describe "differential gene expression"

    • Definition: The concept referring to the varying levels of expression of different genes in various cell types, developmental stages, or environmental conditions.
    • Involves identifying different possible regulatory regions of a gene and understanding their roles.
    • Types of regulation include:
    • Transcriptional Regulation: Controls the transcription of DNA to mRNA.
    • Post-transcriptional Regulation: Modifications that occur after transcription but before translation.
    • Translational Regulation: Controls the process of translation of mRNA to protein.

  • Predict effects of mutations in regulatory regions

    • Focus on how mutations can alter gene expression at various levels (transcription, post-transcription, and translation).

Gene Regulation General Principles

  • Genetic Similarity
    • Humans and chimpanzees share 96% identical DNA.
    • Differences in “regulatory sequences” account for most of the phenotypic differences between the two species.
    • QUIZ 1 Average Score: 85%.

Understanding Genes

  • Definition of a Gene:
    • A gene is defined as the DNA sequence located between the transcription initiation site and the transcription termination site.
    • The term “coding sequence” refers to the portion of the gene that is translated into a protein, which lies within the larger sequence considered a part of the gene.

Regulatory Regions of a Gene

  • Diagrams and Elements Analysis

    • Students will label various elements on a diagram of a gene, including:
    • Promoter: The region where RNA polymerase binds to initiate transcription.
    • Transcription Start Site (TSS): The specific location where transcription begins.
    • 5’-UTR (Untranslated Region): A segment of mRNA that is upstream of the coding sequence, involved in regulation and stability.
    • 3’-UTR: A similar region downstream of the coding sequence, also involved in regulation and stability, often contains signals for mRNA degradation.
    • 3’ Cleavage Site: The site where the poly-A tail is added.
    • Introns: Non-coding sequences within a gene that are removed during RNA splicing.
    • Exons: Coding sequences that are retained in the mRNA after splicing.
    • Transcription Termination Site: Marks the end of transcription.
    • Translation Initiation Codon: The start codon that represents the first amino acid in the translated protein.
    • Translation Termination Codons: Signals the end of translation.

  • 5’ and 3’ UTR Importance:

    • These regions are crucial for mRNA stability and are involved in regulatory processes.

Regulatory Mechanisms

  • Levels of Gene Regulation
    • Gene regulation can occur at many levels, including:
    • Chromatin Remodeling: Alterations in chromatin structure that affect gene accessibility.
    • Alternative Splicing: Producing different mRNA variants from a single gene, leading to diverse protein products.
    • mRNA Transport: Movement of mRNA from the nucleus to the cytoplasm.
    • mRNA Stability: Influences how long mRNA persists in the cell, affecting translation potential.
    • Transcriptional Regulation: The control of the initiation and rate of transcription.
    • Post-transcriptional Regulation: Control mechanisms that occur after transcription, including splicing and mRNA degradation.
    • Translational Control: Regulation of the translation process itself.
    • DNA Methylation: Chemical modification of DNA that may inhibit gene expression.
    • Transcription Factors: Proteins that regulate transcription by binding to specific DNA regions.
    • Post-translational Modifications: Chemical alterations to proteins after translation that can significantly impact their function and activity.

Transcriptional Control Regulatory Regions

  • RNA Polymerase II: Essential enzyme for mRNA transcription, binding to the core promoter region.
  • Transcription Factors:
    • Activators: Bind to enhancers to promote transcription.
    • Repressors: Bind to silencers to inhibit transcription.
  • Enhancers and Silencers:
    • Enhancers: DNA sequences that can enhance gene expression levels.
    • Silencers: DNA elements that, when bound by repressor proteins, decrease transcription levels.

Effects of Mutations on Gene Expression

  • Activity Question 2: Consider mutations at different regions and their impacts:

    • Affecting transcription and translation processes.
    • Evaluate impacts on the amount or sequence of the resulting products (mRNA and protein).

  • Single Base Deletion Mutations

    • Region A: Likely outcomes include:
    • No effect on transcription or mRNA.
    • Could prevent transcription initiation at the TATAA box.
    • May alter mRNA sequence.
    • Might lead to an increase or decrease in mRNA levels.
    • Region B: Possible outcomes encompass:
    • May change mRNA levels (increase, decrease, or remain unchanged).
    • Potentially generates longer or shorter mRNA sequences.
    • Could result in a single nucleotide change in mRNA but not change its length.
    • Possibly no effect on transcription or mRNA sequence.
    • Region C: Likely impacts include:
    • May prevent transcription altogether or prevent translation activities.
    • Can result in alteration of mRNA.
    • May also have no effect on transcription or resulting mRNA sequence.
    • Region D: Queries whether mutations cause frame shifts or changes in protein synthesis. Possible outcomes:
    • Yes, or No, with respect to frame shifts.
    • Likely to affect the amount of mRNA transcribed and protein translated.
    • Could also lead to variations in both mRNA and protein levels.

Anatomy of a Gene

  • Gene Composition

    • Regulatory elements (promoter, enhancers, silencers) typically constitute a significant portion of the genome (20%-35%).
    • Introns account for about 5% of the genome.
    • Expressed parts:
    • 5’UTR, 3’UTR, and exons constitute only 1%-2% of the genome.

  • Alternative Splicing: The traditional one gene-one protein hypothesis has evolved; a single gene can produce multiple proteins through alternative splicing.

Transcription Factor Dynamics

  • Transcription factors can exhibit variability between cell types, as demonstrated in neurons and muscle cells:
    • Neurons express specific transcription factors not present in muscle cells.
    • Transcription Factors “Blue” bind to blue-tinged enhancer regions; “Black” bind to black-enriched regions. Both factors generally present in most cell types, not limited to neurons.
    • Transcription Factor Red & Purple: Investigates potential changes in gene expression profiles should neurons express additional factors typically seen in muscle cells.

Activity on Single Nucleotide Deletion Consequences

  • Reflections on the implications of specific mutations (single nucleotide deletion) on gene expression.
  • Students are tasked to predict how these mutations can affect transcription, mRNA stability, and protein translation pathways.

Comprehensive Gene Illustration

  • A diagrammatic representation of a gene and its structure:
    • Showcasing components like the transcription initiation site, coding sequences, introns, and exons with respective positions marked clearly.
    • Illustrating regulatory elements and showcasing transitions from transcription to translation.