220 - lecture 18/19

Control of Gene Expression Study Notes

Overview of the Lecture

  • Course: BMSC 220 - Fall 2025

  • Date: November 20, 2025

  • Lecture Objectives:

    • The major levels of gene regulation in eukaryotic cells

    • Activation, repression, and chromatin shaping of transcription

    • Impact of mRNA processing on nuclear export

    • Control of translation through various mechanisms

    • Regulation of protein post-translation including degradation

    • Mention of small RNA-mediated silencing and nuclear export (referenced in the Panopto video)

Key Terminology

  • Transcription Regulator:

    • Any molecule that influences the transcription of a gene.

  • Transcription Factor:

    • A protein that influences transcription of a gene.

  • Repressor:

    • A protein that turns genes off.

  • Activator:

    • A protein that turns genes on.

Gene Regulation in Bacteria

  • Bacterial DNA Characteristics:

    • Circular, double-stranded DNA.

    • Nearly all DNA encodes RNAs or proteins.

  • Operons:

    • Groups of genes involved in the same biological processes, co-regulated.

    • Allow for coordinated regulation of transcription and translation:

    • Start/stop of transcription/translation is precisely regulated.

Bacterial Operon Structure

  • Components of a Bacterial Operon:

    • Polycistronic RNA:

    • Structural genes collectively transcribed into a single mRNA.

    • Promoter:

    • Site where RNA polymerase binds to initiate transcription.

    • Operator:

    • Regulatory sequence that interaction with repressor proteins occurs at.

    • Regulatory Gene:

    • Gene that encodes transcription regulators.

Specific Examples of Bacterial Operons

  • Trp Operon:

    • A repressible operon that regulates genes involved in tryptophan synthesis.

    • Mechanism:

    • High levels of tryptophan lead to the formation of a tryptophan-repressor complex.

      • This complex binds to the operator, blocking transcription.

    • Conversely, low tryptophan levels prevent the complex from forming, allowing transcription to proceed.

  • Lac Operon:

    • An inducible operon that regulates lactose metabolism.

    • Mechanism:

    • High lactose levels cause lactose to bind the repressor, resulting in a conformational change preventing repressor binding to the operator.

      • Thus, the lac operon is transcribed.

    • Low lactose levels allow the repressor to bind to the operator, blocking transcription.

Summary: Types of Operons

  • Repressible Operon:

    • Usually ON, turned OFF by corepressor (often involved in biosynthetic processes).

  • Inducible Operon:

    • Usually OFF, turned ON by inducer (often involved in catabolic processes).

Gene Regulation in Eukaryotes

  • Introduction:

    • Eukaryotic cells have more than 200 different cell types, each with unique functions.

    • Approximately 20,000 to 25,000 genes present.

    • Variability in gene expression among cells despite identical DNA.

Levels of Gene Expression Regulation

  1. Transcriptional Control: Regulation of which genes are transcribed into RNA.

  2. Processing Control: Regulation regarding mRNA processing steps.

  3. Translational Control: Regulation of how translation occurs.

  4. Post-translational Control: Regulation after proteins are produced.

Transcriptional Control

  • Differential Transcription and Regulation:

    • Refers to differential gene expression based on several factors:

    • Embryonic development stages.

    • Different tissues present.

    • Exposure to different stimuli.

Promoter Elements

  • Core Promoter:

    • Main region where RNA polymerase and general transcription factors assemble.

  • Proximal and Distal Promoters:

    • Proximal: Close regulatory sequences fine-tuning transcription.

    • Distal: Farther upstream regulatory sequences affecting transcription levels.

  • Enhancers:

    • Distinct from promoters, can be located far away yet facilitate increased transcription rates.

Combinatorial Control of Transcription

  • Mechanism:

    • The extent of transcription of a specific gene is contingent upon unique combinations of transcription factors (TFs) that bind regulatory sequences.

    • The combination can differ based on cell type, tissue type, developmental stage, or physiological state.

    • Approximately 5-10% of genes encode TFs, allowing for a multitude of interaction combinations.

Role of Enhancers in Transcription Activation

  • Characteristics of Enhancers:

    • Typically located far away from the target gene, yet influence transcription rates.

    • They may be inverted yet still functional.

  • Mechanism of Action:

    • DNA looping mechanisms bring enhancers closer to the promoter, often requiring additional proteins such as the Mediator complex.

Regulation of Chromatin Structure

  • Chromatin Remodeling Complexes:

    • Utilize ATP to adjust nucleosome positioning, which modulates DNA accessibility for transcription factors.

  • Histone-Modifying Enzymes:

    • Modify histone proteins to influence chromatin state and gene expression by adding/removing functional groups (e.g., acetyl, methyl, phosphate).

    • Acetylation typically leads to an open chromatin state, while certain methylation patterns lead to silencing or activation.

Transcriptional Activation Approaches

  • Paused Polymerase:

    • Some genes remain ready with RNA polymerase at the promoter but stalling shortly after initiation.

    • Release signals activate rapid transcription resumption, expediting gene expression when necessary (e.g., Hsp70).

Transcriptional Repression Mechanisms

  • Deacetylation:

    • Histone deacetylases (HDACs) remove acetyl groups, tightening chromatin and reducing transcription.

    • These enzymes are typically part of repressor complexes.

  • DNA Methylation:

    • Mediated by DNA methyltransferases adding methyl groups to cytosines, causing chromatin compaction and long-term gene silencing through recruitment of silencing proteins.

  • Long Noncoding RNAs (lncRNAs):

    • Nonprotein coding RNAs (~200 nucleotides) that can attract chromatin-silencing factors, effectively turning off specific genes (e.g., Xist for X chromosome inactivation).

Processing Control

  • Aspects of mRNA Processing:

    • Addition of 5' cap and Poly(A) tail.

    • Splicing and Alternative Splicing which are major regulatory points allowing for increased protein diversity.

    • Nuclear Export involving selective export of properly processed mRNAs from the nucleus.

Importance of Splicing

  • Protein Diversity:

    • Different proteins can be generated from a single gene through mRNA splicing pathways, exemplified through mRNA transcripts consisting of multiple exons.

Nuclear Export Mechanics

  • Only mRNAs that are properly capped, spliced, and polyadenylated are exported from the nucleus.

  • Incorrectly processed transcripts are retained in the nucleus (further detail in Panopto video).

Translational Control

  • Key Components of Translational Control:

    1. Initiation Control:

    • Protein interactions with untranslated regions (UTRs) influence translational initiation globally and for specific mRNAs.

    1. Cytoplasmic Localization:

    • Localization of mRNAs affects where translation occurs, impacting protein production patterns.

    1. mRNA Stability:

    • Variability in mRNA lifespan influences translation rates.

    1. miRNA Silencing:

    • A significant post-transcriptional regulation mechanism (detailed in Panopto video).

Example of Translational Control

  • Ferritin Mechanism:

    • Function: Stores iron in cells.

    • In low iron conditions, iron regulatory protein (IRP) binds to iron-response element (IRE) blocking translation.

    • In high iron conditions, iron binds to IRP, allowing translation to proceed due to conformational changes in IRP.

mRNA Localization in Translation

  • Developmental Significance:

    • In organisms like Drosophila, localized mRNAs lead to localized protein production essential for body patterning.

    • Key examples include Bicoid mRNA localized to the anterior and Oskar mRNA localized to the posterior.

mRNA Stability and Decay

  • P-Bodies:

    • Cytoplasmic structures involved in mRNA decay.

    • Mechanisms include deadenylation, decapping, and degradation of unstable mRNAs.

    • P-bodies can store mRNAs for later use.

Posttranslational Control

  • Protein Stability Mechanics:

    • Factors influencing a protein’s lifespan include its amino acid composition, particularly at the N-terminus.

    • Proteins undergo degradation in proteasomes, cylindrical structures that assist in controlled protein degradation.

Ubiquitin Pathway

  • Ubiquitination Process:

    • Proteins targeted for degradation are tagged with ubiquitin by ubiquitin ligases.

    • Polyubiquitinated proteins are recognized by the proteasome cap, leading to degradation and release of amino acids into the cytosol.

Check Your Understanding: Key Questions

  • Chromatin Structure Influence:

    • Describe how chromatin structure impacts transcription factor access to DNA.

  • Alternative Splicing Contribution:

    • Explain how alternative splicing increases protein diversity from a single gene.

  • Nuclear Export Requirement:

    • Recognize the necessity for mRNAs to be properly capped, spliced, and polyadenylated before leaving the nucleus.

  • Translational Control Mechanisms:

    • Compare mechanisms concerning translation initiation, mRNA localization, and mRNA stability.

  • Role of P-bodies:

    • Identify the function of P-bodies in regulating cytoplasmic mRNA fate.

  • Ubiquitination Direction:

    • Summarize the process by which ubiquitination channels proteins to proteasomes for degradation.