Gene Expression II: Mechanisms of Regulation Flashcards
Explain the concept of combinatorial gene control
It is the norm for eukaryotes. Multiple different regulatory proteins can bind to the identical regulatory element in a gene. The particular combination of proteins that bind to an element is dependent on the cell type or the physiological state of the cell. Some combinations will activate and some will repress gene expression. It is likely a “competition” of activators and repressors. The overall outcome is the net effect of these.
Describe how the combinatorial regulation of Myc, Max, and Mad binding to the E-box element can regulate the switch between cell division and cell differentiation
Myc, Max and Mad are bHLH (basic HLH zip) transcription factors that are involved in promoting the expression of genes associated with cell division.
Max is constitutively expressed, meaning it is always expressed and max will dimerize with itself to form Max-Max. When it dimerizes it binds to the E-box element but it will not turn on transcription in this case, transcription will simply occur at the basal level of ongoing expression of this gene but we aren’t doing anything to promote or inhibit it.
If the cell wants to DIVIDE, it will upregulate Myc. When Myc is expressed in high enough levels, it will displace Max from the Max-homodimer and form a Myc-Max heterodimer. This gives a strong signal to produce proteins that are involved in cell division. My binds to the E-box and we turn on or activate transcription.
If the cell wants to DIFFERENTIATE, we can’t have genes involved in cell division expressed. Differentiation is an opposing force of division, they are opposite. In this case, Mad will be produced and replace Max from the Max-Max homodimer to form a Mad-Max heterodimer. It will then bind to the E-box element but now we get transcription turned OFF or silenced.
Repressing a gene is leaky, or it can still produce some mRNA and thus protein so we need to completely silence it! When we want activation, we get acetylation because if causes the TFIID to bind to the DNA because it is less tightly packed.
Max-Max homodimer
Max is constitutively expressed, meaning it is always expressed and max will dimerize with itself to form Max-Max. When it dimerizes it binds to the E-box element but it will not turn on transcription in this case, transcription will simply occur at the basal level of ongoing expression of this gene but we aren’t doing anything to promote or inhibit it.
Myc-Max Heterodimer
If the cell wants to DIVIDE, it will upregulate Myc. When Myc is expressed in high enough levels, it will displace Max from the Max-homodimer and form a Myc-Max heterodimer. This gives a strong signal to produce proteins that are involved in cell division. My binds to the E-box and we turn on or activate transcription
Mad-Max Heterodimer
If the cell wants to DIFFERENTIATE, we can’t have genes involved in cell division expressed. Differentiation is an opposing force of division, they are opposite. In this case, Mad will be produced and replace Max from the Max-Max homodimer to form a Mad-Max heterodimer. It will then bind to the E-box element but now we get transcription turned OFF or silenced.
Myc, Max, and Mad Domains Characteristics
Myc heterodimerizes with other bHLH-ZIP proteins
Myc-Max dimers induce cell proliferation
Mad-Max dimers inhibit proliferation or cell division and initiate cell differentiation.
Myc-Max and Mad-Max complexes have opposing functions in transcription and Max plays the central role.
Max is constitutively expressed, meaning it is always expressed.
Myc is ONLY expressed in the G1 and S transition of the cell cycle because this is when we need cell division after replication.
When Max is bound, it doesn’t really have an activation domain so it won’t really be doing anything! This is where the leakiness comes from, we get the basal level of expression. Myc, however, has a very large activation domain, so we get this large activation signal when it binds to the E-box.
Mad is in-between, it has an activation domain but it is not “activating” it has repression activity. Its function is to repress. This is so we don’t get any expression
Transcription factors can be activated in 7 ways
1) Protein Synthesis
2) Ligand Binding
3) Covalent Modifications
4) Addition of second subunit
5) Unmasking
6) Stimulation of nuclear energy
7) Release from membrane
Protein Synthesis
The transcription factor didn’t previously exist so it will be synthesized as an active protein that can signal
Ligand Binding
There is a ligand that will interact with the transcription factor and activate it
Covalent Modifications
The transcription factor is expressed but it only becomes active when it is phosphorylated by a KINASE
Addition of second subunit
There is an addition of a second subunit that is necessary for the activation of this transcription factor
Unmasking
There is an inhibitor bound to the transcription factor and when its phosphorylated (the inhibitor) it will leave.
Stimulation of nuclear energy
The translocation of the transcription factor into the nucleus causes an inhibitor to dissociate and the transcription factor to be active.
Release from membrane
A membrane-bound transcription factor is cleaved releasing the active portion into the cytoplasm.
Autocrine Pathway
The cell releases signals that will act on itself
Paracrine Pathway
Neighboring cells release a signal to act on a neighboring cell or cells
Kinase Cascade
A “cascade” in which one kinase phosphorylates another kinase which then phosphorylates another and then another and it is repeated as a cascade to get an end result like a kinase entering the nucleus and activating transcription via phosphorylating a transcription factor. Jun and Fos are an example of a kinase cascade.
Describe how different signal transduction pathways activate kinases that regulate the AP-1 transcription factors Jun and Fos
It is a kinase cascade that eventually leads to JNK being phosphorylated which will then phosphorylate Jun causing it to be able to bind to the AP-1 site now. ERK is also part of a kinase cascade that will phosphorylate Fos that will then be able to bind to the AP-1 element. Jun and Fos are bZIP heterodimers connected via a leucine zipper and bind with a scissor motif to the AP-1 element.
JNK
JNK is the kinase that phosphorylates and thus activates the Jun dimer
ERK
ERK is the kinase that phosphorylates and thus activates the Fos dimer
Describe models for how the position of a gene in the heterochromatin or euchromatin of a chromatid influences its expression
Positioning a gene in condensed or heterochromatin inhibits gene expression where placing it in euchromatin or less condensed regions increases gene expression. The chromatin structure can regulate cell phenotype. If the gene is positioned in heterochromatin it will not be expressed. If it is in euchromatin it will be expressed. An example is the inactivation of one X chromosome to form the Barr Body.
Describe how the X chromosome is inactivated in females
An example is the inactivation of one X chromosome to form the Barr Body. If both gene pairs in the X chromosomes were expressed in females, we would have a dosage problem. Basically, the chromosome undergoes extensive deacetylation to allow it to interact with the DNA and adjacent nucleosomes more and it also undergoes methylation that tells the cell to condense the DNA in a compact manner there. The cells are thus mosaic in females because this is done randomly. Some cells have the X from mom expressed, some the X from dad. The progeny cells will express the same X chromosome being condensed as was determined randomly by the parental cell. But, the condensing of one of the X chromosomes is done randomly.
Explain the role of the locus control region in regulating Beta-Globin gene expression in red blood cells
In this case, we are again looking at how heterochromatin can regulate gene expression. The hemoglobin gene is only expressed in young RBCs and it is not expressed in any other cell type. So the other cell types must have the region of chromosome 11 present as heterochromatin so that it will not be expressed. However, in early RBCs this region of chromosome 11 must be exposed in order to express the hemoglobin gene. Thus, it is present as euchromatin. The key is this locus control region because transcription factors will be produced by early RBCs and will bind to the locus control region and cause expression. In an embryo, the cells know to make the appropriate transcription factors to bind to the locus control region to express epsilon-globin. Then, when it reaches the fetal stage, it will produce gamma-globin instead of epsilon now. Then when the child is born it will switch to beta-globin. The locus control region is critical because it will bind all of these different transcription factors and say which globin to express. Heterochromatin structure regulates the hemoglobin gene expression.
Define the term epigenetic
Epigenetic refers to the inheritance or passage of information from parental cells to progeny cells by a mechanism other than from the “instructions” within the DNA sequence. Due to epigenetics, two alleles can have the same nucleotide sequence but give different inheritable genetic information. Epigenetic mechanisms occur through modifications of either DNA or gene regulatory proteins.
