Control of Gene Expression 

  • Controlling gene expression is often accomplished by controlling transcription initiation. 

  • Gene expression is often controlled by regulatory proteins binding to specific DNA sequences. 

  • Regulatory proteins bind to DNA to either block or stimulate transcription, depending on how they interact with RNA polymerase. 

  • Regulatory proteins gain access to the bases of DNA at the major groove.

  • Regulatory proteins possess DNA-binding motifs

Prokaryotic Regulation 

  • Prokaryotic organisms regulate gene expression in response to their environment. 

  • Eukaryotic cells regulate gene expression to maintain homeostasis in the organism. 

  • Sometimes regulation means that a cell induces apoptosis 

  • Programmed cell death 

  • Prokaryotes use operons 

  • Sequence of DNA containing a cluster of genes under the control of a single promoter

  • Control of transcription initiation can be:

  • Positive control: increases transcription when activators bind DNA 

  • Negative control: reduces transcription when repressors bind to DNA regulatory regions called operators 

  • The promoters positions and orients the polymerase correctly 

  • The operator is where the repressor binds

  • RNA polymerase binds to a region that is immediately upstream from the region of DNA that codes for a protein. The binding region is termed the operator. The promoter acts to position the polymerase correctly, so that the molecules can then begin to move along the DNA, interpreting the genetic information as it moves along. 

  • Operons can regulate genes negatively or positively 

→ Negative regulation 

  • Uses a repressor protein

  • Can be inducible (EX: lac operon)

  • Can be repressible (EX: trp operon)

→ Positive regulation 

  • Uses an activator protein

  • Activators: glucose, cAMP, and CAP 

  • The trp operon 

  • Encondes genes for the biosynthesis of tryptophan 

  • The operon is not expressed when the cell contains sufficient amounts of tryptophan 

  • The operon is expressed when levels of tryptophan are low 

  • It is negatively regulated by the trp repressor protein 

  • The presence of tryptophan causes the activation of the repressor, the repressor stops the production of tryptophan = repressed 

→ trp repressor binds to the operator to block transcription

→ Binding the repressor to the operator required a co-repressor which is tryptophan 

→ low levels of tryptophan prevent the repressor from binding to the operator 

  • The lac operon

  • Contains genes to breakdown lactose as an energy source 

  • Regulatory regions of the operon include the CAP binding site, promoter, and the operator 

  • The lac operator is negatively regulated by a repressor protein

  • The action is induction 

→ the lac repressor binds to the operator to block transcription in the presence of lactose, an inducer molecule binds to the repressor protein, so the repressor can no longer bind to the operator 

→ now transcription can proceed

  • If glucose is present 

  • RNA pol poorly binds to the lac operon promoter

  • The operon needs extra help from catabolite activators protein (CAP)

  • If no glucose is around, cAMP goes up 

  • cAMP binds with and activates CAP 

  • CAP binds to a region of DNA just before the lac operon promoter and helps RNA pol attach to the promoter, driving high levels of transcription 

  • Glucose, because the CAP site activation increases operon activity end, because it promotes the activity in response to the CAP/cAMP activations, it is said to be positively regulated. CAP/cAMP is an activator 

  • Positive control - the control of lac by cAMP and CRP


Eukaryotic regulation

  • Controlling the expression of eukaryotic genes requires transcription factors 

  • General transcription factors are required for transcription initiation and required for proper binding of RNA pol to the DNA

  • Specific transcription factors increase transcription in certain cells or in response to signals 

  • Coactivators and mediators are also required for the function of transcription factors

  • Coactivators and mediators bind to transcription factors and bind to other parts of the transcription apparatus 

  • The entire thing together is the TRANSCRIPTION COMPLEX 

  • General transcription factors bind to the promoter region of the gene 

  • RNA pol II then binds to the promoter to begin transcription at the start site (+1)

  • Enhancers are DNA sequences to which specific transcription factors (activators) bind to increase the rate of transcription 

  • Are often far upstream of the gene. When bound, it will fold DNA until it is close to the gene causing the activation of transcription and increasing it beyond basal levels. 

Eukaryotic Chromosome Structure 

  • Methylation (addition of CH3) of DNA or histone proteins is associated with the control of gene expression 

  • Clusters of methylated cytosine nucleotides binds to a protein that prevents activators from binding to DNA 

  • Methylated histone proteins are associated with inactive regions of chromatin. 

  • Acetylated histones make DNA more accessible for transcription 

  • Chromatin-remodeling complexes 

  • Modify histones, DNA, and chromatin

→ ATP dependent remodeling factors 

→ nucleosome sliding 

→ Remodeled nucleosome 

→ nucleosome displacement 

→ histone replacement 

Posttranscriptional Regulation 

  • Gene expression can be controlled after transcription, with mechanisms such as:

  • Alternative splicing 

  • RNA editing 

  • mRNA degradation 

  • RNA interference RNAi 

  • Alternative splicing 

  • Introns are spliced out of pre-mRNAs to produce the mature mRNA  that is translated 

  • Alternative splicing recognized different splice sites in different tissue types

  • The mature mRNAs in each tissue possess different exons, resulting in different polypeptide products from the same gene 

  • RNA editing creates mature mRNA that are not truly encoded by the genome 

  • Ex: apolipoprotein B exists in 2 isoforms 

→ one isoform is produced by editing the mRNA to create a stop codon

→ this RNA editing is tissue-specific 

  • Other means of control:

  • Transportation: movement of the mRNA may be interfered with 

  • Translation Repressor Proteins: interfere with translation 

  • Degradation of mRNA: loss of poly A tail 

→ mature mRNA molecules have various half lives depending on the gene and the location (tissue) of expression 

→ the amount of polypeptide produced from a particular gene can be influenced by the half life of the mRNA molecules 


  • Small RNAs act after transcription has occurred 

  • miRNA (micro RNA)

→ 22 nucleotides in length 

→ involved in repression of a gene

  • siRNA (small interfering RNA)

→ dsRNA

→ 20-24 nucleotides

  • circRNA (small circular RNA)

→ degrade miRNA and siRNA

  • snRNA (small nuclear RNA)

  • snoRNA (small nucleolar RNA)

  • piRNA (piwi-interacting RNA)

→ largest non-coding RNAs

→ help to form RNA-protein complexes 

→ many sub-types 

  • RNA interference (RNAi): a biological process in which RNA molecules inhibit gene expression or translation, by neutralizing targeted mRNA molecules 

  • Two types of small RNA molecules - miRNA and siRNA - are central to RNAi

CRISPR 

  • Clustered regularly interspaced short palindromic repeats 

  • Development of the genome editing technique was discovered by Emmanuelle Charpentier and Jennifer Doudna (2020 Nobel prize recipients) 

  • DNA sequences found in the genomes of prokaryotes 

  • Derived form DNA fragments of bacteriophages that had previously infected the cell 

  • Foreign DNA recognized by a cell 

  • Cas enzymes (such as Cas9 - CRISPR associated protein) and RNA become precision-guided weapons

  • Together, the viral RNA and the Cas enzymes drift through the cell 

  • If they encounter genetic material from a virus that matches the CRISPR RNA, the RNA latches on tightly 

  • The Cas enzymes then chop the DNA in two, preventing the virus from replicating 

  • Protein Degradation 

  • Proteins are produced and degraded continually in the cell 

  • Proteins to be degraded are tagged with ubiquitin

  • Degradation of proteins marked with ubiquitin occurs at the proteasome