Epigenetic Regulation Flashcards
What kind of transcription control is generally seen in eukaryotes?
Combinatorial control: Different regultory proteins can bind to the same regulatory sequence in DNA. The combination of regulatory proteins that bind to a regulatory element depends on the type of cell or the physiological state of the cell. Specific combinations of regultory proteins express or repress transcription.
Describe the structure of Myc, Max, and Mad
Family of bHLH-ZIP transcription factors that can acts as homodimers or heterodimers. Have a helix-loop-helix structure and interact noncovalently through their leucine zippers. Max is constituitively expressed.
Mad and Myc have have opposing functions in transcription and Max plays a central role
When is Myc only expressed
G1 to S transition of the cell cycle
Max-Max
ebox gene not transcribed
Myc-Max
Cell proliferation. Synthesis of genes required for entering into S phase
Mad-Max
Inhibit proliferation and initiate differentiation
Ebox
Gene elements required for cell division
Max-Max : silences
Myc-Max : Expression
Mad-Max : Repression
Describe the ways in which the activity of gene regulatory proteins is regulated in eukaryotic cells
1) The protein is synthesized only when needed and is rapidly degraded by proteolysis so that it does not accumulate
2) Activation by ligand binding
3) Activation by phosphorylation
4) Formation of a complex between a DNA-binding protein and a seperate protein with a transcription activating domain ( addition of a second subunit)
5) unmasking of an activation domain by phosphylation of an inhibitor protein
6) Stimulatoin of nuclear entry by removal of an inhibitory protein that otherwise prevents entry
7) Releasing a regulatory protein from a membrane bilayer by regulated proteolysis.
***each of these mechanisms is typically controlled by extracellular signal which are communicated across the plasma membrane to the gene regulatory proteins in a cell*
Describe how different signal transduction pathways activate kinases that regulate the AP-1 transcription factors Jun and Fos
ERK phophorylates Fos and JNK phosphorylates Jun. Jun and Fos then dimerize to form AP-1 and along with Ets. These activate transcription of genes that control proliferation and anti-apoptotic signals
Jun and Fos are bZIP proteins that heterodimerize through leucine zippers and bind with the scissor motif to the AP-1 element in the gene regulatory region.
Describe ways in which chromatin structure regulates gene expression
- positioning a gene in condensed or heterchromatin inhibits gene expression
- Histone acetylation opens chromatin and de-acetylation condenses chromatin
- histone methyltion regultes chromstin structure in a manner that depends on the histone residue modified. generally de-methylation regulates the chromatin in a way opposite of the signal that the original methylation sends. so if methylation reduces transcription than de-methylation will increase trancription and vice-versa
Why does X-inactivation occur in females?
Because if there was no X inactivation then the dosage of X gene products in females would be twice that of males and would be toxic to the female.
How does X inactivation occur in females
During embryogenesis the placenta sends a signal to the embryo cells. This causes non coding RNA to coat the maternal X chromosome in some cells and the paternal X in others. Next the X chromosome marked or inactivation undergoes de-acetylation and methylation by which it is silenced. This epigenetic modification is inherited by future somatic cells and females are a mosaic of cells that contain either an actice maternal or active paternal X
Explain the role of the locus control region (LCR) in regulating ß-globin gene expression in red blood cells
The ß-globin gene is part of a cluster of globin genes. The LCR is located upstream of this cluster and is shared by all the globin genes. Each globin gene has it’s own set of regultory sequences, but the LCR is like the master “on” switch. Gene regulatory proteins bind to the LCR and through DNA looping interact with proteins bound to the the individual gene control regions for each globin gene. The importance of the LCR is seen in patients with a certain thalassemia where all or part of the LCR sequence is deleted. Even though the ß-globin gene has it’s own regulatory sequences it will remain transcriptionally silent when the LCR is deleted.
Why is the LCR important?
The importance of the LCR is seen in patients with a certain thalassemia where all or part of the LCR sequence is deleted. Even though the ß-globin gene has it’s own regulatory sequences it will remain transcriptionally silent when the LCR is deleted. patents with this deletion suffer from severe anemia. The LCR also contains a barrier sequence that prevents heterochromatin from spreading to the ß-globin gene.
What does epigenetic mean?
Epigenetic refers to the inheritance or passage of information from parental cells to progeny cells through a mechanism other than the “instructions” present in the nucleic acid sequence of the copied DNA.
Two alleles can have the same genetic sequence but different inheritable genetic information
Epigenetic mechanisms occur through either modification of DNA or regulatory proteins
What are the types of epigenetic mechanism?
1) positive feedback transcription factor loops
2) DNA methylation
3) Acetylation and deacetylatyion of histones (interconvert between heterochromatin and euchromatin)
4) Histone phosphorylation and methylation
Explain how positive feedback transcription factor loops can generate cellular memory.
A gene that is transcriptionally silent will recieve a transient signal and become active. The product of that gene will bind to the gene regulatory region and continue to induce transcription of its own gene (positive feedback).
When the cell divides all of its progeny will remember that it recieved the “on” signal and will continue to transcribe that gene
What is the importance of combinatorial gene control in development?
When an embryonic cell divides one of its daughters makes a regulatory protein and the other does not. The daughter cells of the embryo sense the presence or abscence of these regulatory proteins which cause them to produce a unique combination of regulatory proteins within themselves. These combinations are inherited down the cell line and eventually lead to tissue differentiation based on the unique combination of regulatory proteins the cells in those tissues posess.
What usually results upon methylation of a promotor or an enhancer gene?
methylation of a promotor or enhancer usually inhibits expression of that gene
How is methylation of DNA inherited?
The methylated sequence is palindromic, and when the cell divides one strand of methylated DNA ends up in each daughter (hemi-methylation). A maintaintence methylation enzyme in the progeny cell finds the hemi-methylated sites and converts them to fully methylated palindromic sites. Progeny will have the same methylated C sites as the parental cell.
What is the theory for how DNA methylation may turn off genes?
Binding of gene regulatory proteins near an active promotor may prevent DNA methylation from occuring (not including denovo methylation). When a cell stops producing a protein the regulatory proteins will disassociatr since the activator proteins are no longer required. This allows the DNA to be methylated, which enables other proteins to bind, including chromatin remodeling complexes and histone deacetylases which shut down the gene.
What is the function of CG islands in maintaining the expression of housekeeping genes?
CG islands are dense regions of CG nucleotides, 1000-2000 nucleotide pairs longs. They crowd around promotors of housekeeping genes (genes that code for proteins essential to cell viability) and remain unmethylated. Since these regions are unmethylated in germ cells if a deamination occurs it is quickly recognized and repaired. These are selected for and passed on through the generations.
How can acetylation/methylation of histones be passed from parental cell to progeny
If a histone is acetylated/methylated half of the histones are passed to the daughter cell. maintainence HATs in the daughter cells acetylate the rest of the histones. Histone marks transfered to progeny cells are maintained the same way and signal for reduced expression of those genes
Describe genetic imprinting
Imprinting occurs when epigentic modifications (methylation) to DNA do not get removed during meiosis and are passed to the next generation. Genomic imprinting is known to occur in 50 human gene.
Usually hyper methylated genes do not get expressed and hypomethylated genes will still be expressed in the offspring.
