Mar 18, 2025 Intro To Gene Regulation

Gene Expression

• Refers to the transcription and translation of a gene 

Regulation of Gene Expression

• The ability of a cell to control how/when/where/if a particular in the DNA gets expressed

  • Why would regulating gene expression be important for all cells to be able to do?

    • All cells (single & multicellular) must be able to adjust which genes they are transcribing/translating (expressing) at any given moment to respond in real time to environmental factors (e.g., signals from other cells, nutrient availability, etc.) 

    • In multicellular organisms (eukaryotes), the regulation of gene expression also allows different cell to perform different (specialized) functions (in other words, become different cell types)

• For example: Us humans, are made up of many different cell types (neurons, epithelial cells, macrophages, osteocytes, fibroblasts) 

  • Each of your cells can independently decide which genes from the genome they’ll express in a given situation 

  • All of your cells in your body (with exceptions) contain the same genes 

    • And the same versions (alleles) of those genes 

    • But they make different proteins b/c they express different genes from the same “DNA library” 

  • In a multicellular organism, each cell has access to exact same library of genes, but certain cell types will only express a particular subset of those genes to make only particular proteins (and thus perform only particular functions) 

Points where gene expression may be regulated

• Gene regulation can occur at just about any step in the Central Dogma (this is true for both prokaryotes and eukaryotes)

• Transcriptional level (in MCB 181 will only discuss gene regulation at this level)

  • Epigenetic regulation* (make DNA sequences more/less accessible for transcription)

    • *only eukaryotes can regulate gene expression this way

  • Binding of regulatory proteins to non-coding sequences on DNA (e.g., TFs binding to enhancers in eukaryotes)

• Post-transcriptional level*

  • How mRNA is processed (e.g., splicing)

  • mRNA stability (e.g., 5’ cap & 3’ polyA tail)

    • *means only eukaryotes can regulate gene expression this way

• Translational level 

  • Whether initiation complex can assemble at 5’ cap

• Post-translational level 

  • How proteins are processed (which affects their activity/function) 

Negative and Positive Control of Transcription of a Gene

• In eukaryotes & prokaryotes, + and - regulation describes whether a gene is being transcribed more or less than before 

• Gene transcription can be positively regulated 

  • Transcription is stimulated (“turned on”)

• Gene transcription can be negatively regulated

  • Transcription is repressed (“turned off”)

Regulating Transcription in Prokaryotes 

• Regulating gene expression in general is simpler in prokaryotes than eukaryotes:

  • The organization of prokaryotic DNA is not complex as eukaryotic DNA (not packaged in chromatin)

  • Prokaryotic mRNA is not processed 

  • There is no nuclear membrane separating the processes of transcription and translation in prokaryotes 

• Positive regulation of prokaryotic transcription

  • The default of some genes is “don’t transcribe me.” For this kind of gene, RNA polymerase can’t bind well to its promoter and thus can’t start transcription on its own

  • When a situation arises in which the cell wants to express (“activate”) one of these genes, an activator protein specific for the gene will bind to a site near the gene’s promoter (activator sequence) to help RNA polymerase initiate transcription

• Negative regulation of prokaryotic transcription

  • The default for some other genes is always “on.” For this kind of gene, RNA polymerase binds easily to the gene’s promoter and can initiate transcription just fine on its own

• When the cell wants to inhibit the expression of this gene, a repressor protein specific to the gene binds to a DNA sequence near the beginning of the gene (usually in or after the promoter) called an operator

• This blocks RNA polymerase from transcribing the gene

Introducing the lac operon in E. coli bacteria 

• A classical model for understanding transcriptional regulation 

• First, why would a single-celled organism like a bacterium need to regulate gene expression?

  • ALL organisms (both single-celled and multicellular) must be able to respond flexibly to their environment if they want to live

• Bacterial gene regulation

  • E. coli’s (and all cells’) “favorite meal” is glucose

    • Metabolizing glucose provides greatest net energy “pay off”

  • If glucose isn’t available, E. coli will utilize other energy/carbon sources

    • If lactose is present, E. coli can import it into the cell and break it down into glucose and galactose (takes energy and materials to make necessary proteins, so net payoff is less)

    • To avoid wasting the energy and materials for making lactose metabolism proteins if they aren’t needed, E. coli regulate the expression of the genes encoding these proteins, which are located in the lac operon

• What’s an operon?

  • A set of multiple bacterial genes that are regulated together and are transcribed into a single mRNA (they share a promoter)

  • The part of the mRNA corresponding with each gene is translated into the protein encoded by that gene 

  • Operons usually contain multiple genes that functionality related proteins (they all contribute to the same biochemical/cellular process)

• Anatomy of the lac operon

  • The lac operon contains 3 genes that code for 3 proteins involved in lactose metabolism

    • lacZ: codes for B-gal, the enzyme that breaks down lactose into glucose and galactose 

    • lacY: codes for lactose permease, a transmembrane protein that transports lactose into the cell

    • lacA: codes for another protein you don’t have to worry about 

    • One promoter (lacP) controls the transcription lacZ, lacY, and lacA

      • A repressor binding site called an “operator” (lacO), which binds a repressor encoded by lacl, located outside the operon

Summary of what we covered

• Both prokaryotes and eukaryotes regulate gene expression to respond reflexively to their environments

• Additionally, in a multicellular organism, different cell types need different proteins at different times and in different amounts in order to perform their unique functions (despite all cell types having the exact same DNA) 

• Thus, the transcription and translation of specific genes in the DNA is precisely regulated in real-time, so a cell only makes those proteins it needs, when it needs them

• Regulation of gene expression can happen at any step of the Central Dogma - we will only focus on how transcription is regulated in this class

• The transcription of genes can be “positively” regulated or “negatively” regulated

• To study the regulation of gene expression at the transcription level, we will first look at how prokaryotes regulated transcription by looking at the way they regulate the transcription and translation (expression) of proteins that digest food (lactose)