Chapter Three Flashcards
What is meant by “cancer cells display altered gene expression”
They mess with the quantity, timing, or localization of oncogenes and tumor suppressor genes.
Could be the result of transcription factors
How much of the entire genome is is transcribed vs. turned into proteins?
70 percent is transcribed, but only 2% codes for proteins.
What type of RNA is important for gene regulation?
non coding RNA
Where are most single nucleotide polymorphisms found in cancer?
non-coding regions
What is epigenetics?
They are heritable changes in the gene expression that are encoded by changes in the genome and chromatin components (histones) BUT NOT actual changes in the DNA sequence
How is gene expression altered?
By regulating:
- Transcription
- Chromatic structure
- Post transitional mechanisms
What are transcription factors?
They are proteins that bind to the promoter region and regulate transcription.
They can regulate signaling involved in apoptosis, differentiation and cell growth.
What are domains?
They are distinct, independent structural / functional units of a protein.
How do we regulate transcription?
- Synthesis - regulating the genes for TFs (regulate regulators)
- Covalent modulation (turn protein on/off
- Ligand bonding (flex, weaker bonding)
- Cell localization - where is the factor at in the cytoplasm?
- Dimerization - need a pair to work
What does AP-1 transcription factor regulate?
What is it activated by?
What does it bind to on the DNA sequence?
It regulates the expression of genes involved in differentiation, growth, and death.
It is activated by growth factors, ROS, and radiation
It binds on what is called the TPA response element
What do steroid hormones regulate?
They can also regulate transcription. Here’s how:
These lipid-soluble signaling molecules will bind to what are called steroid hormone receptor superfamily, which act as ligand-dependent transcription factors.
Once a steroid hormone binds to them it will be able to bind to DNA using its Zn finger binding domain.
Where do steroids come from? How does the receptor get to the DNA?
They pass through the cell membrane and bind to intracellular receptors.
The receptors may be within the cytoplasm or on the nucleus.
Then the receptor gets to the nucleus if it is not already there and binds to DNA response element to activate transcription.
What is the histone core?
It is an octomer of histone proteins 2x (H2A, H2B, H3, and H4) that are the protein that is the bead of the “bead on the string”.
What is the secondary and tertiary structure of the chromatin that you know so well?
Secondary - 30nm fibers
Tertiary - radial loops
How does chromatin structure facilitate the regulation of gene expression?
Well, chromatin cannot just be read / transcribed if it is compacted.
The conformation that chromatin takes on is dependent on the epigenetic modifications that have been passed on.
Explain in more detail the epigenetic alterations that alter transcription and the possible consequences.
Histones may be modified as well as the DNA itself (being methylated)
These modifications will determine whether or not the chromatin is loose or tight.
Important example: if there is epigenetic silencing of the genes involved in differentiation, cells may remain as stem cells.
What are the ways that histones may be modified in post transcriptional regulation?
- Methylation
- Acetylation
- Phosphorylation
- Ubiquitination
What in the heck are HAT’s?
What do they do?
They are known as Histone acetyltransferases
They transfer the addition of an acetyl group to specific histone-tail lysines. Adding them will will neutralize the charge on lysine and relax the chromatin folding.
The point of these is to turn on transcription.
What are HDACs?
They are called Histone De-acetylases. They do the opposite of HATs and they remove acetyl group, functioning to do the opposite, which is compact the chromatin and not allow for DNA transcription.
How does DNA Methylation work in post transcriptional regulation?
It adds a methyl group to the fifth spot on cytosine.
This only occurs at rare places in the genome and they are called CpGs (cytosine next to guanine)
Upon binding, the methyl-cytosine will spontaneously convert to thymine resulting in a C to T transition.
What are the enzymes that are involved in the transfer of methyl group to DNA?
What is so special about DNMT 1?
DNMT1, DNMT 3a, and DNMT3b
DNMT1 converts DNA that is half methylated to DNA that is fully methylated, making it heritable.
How does methylation silence the chromatin and turn off transcription?
The methyl recruits proteins that interact with HDAC and other chromatin remodeling enzymes.
What is common of the parts of chromatin that are loose in cancer cells?
They have fewer mutations compared to the condensed regions.
How can epigenetic regulation and mutations go hand in hand?
Mutations may inactivate genes that are important for epigenetic regulation
Explain how methylation may act as the second hit for a tumor suppressor.
Well, lets say that the tumor suppressor has a mutation on one allele but still produces protein in small amounts.
The methylation may alter the DNA promoter region turning off the gene for good, or it could epigenetically modify the histone and kill expression of the tumor suppressor.
What is true about histone modifications and cancer?
There is abnormal HAT or HADC activity.
What is true about methylation and cancer?
DNMT are observed in certain cancers.
The hypermethylation of certain genes
Generally, the genome of cancer cells is hypomethylated, but specific gene promoters are hypermethylated.
What are long non-coding RNAs?
What are lncRNAs responsible for generally?
They are RNA of 200 + nucleotides that lack start and stop codons, are highly adenylated and are transcribed from gene enhancers.
They are involved in epigenetic modifications and post transcriptional regulation.
What are microRNAs?
How do they facilitate in regulating gene expression?
They are small (non-protein coding) RNAs that regulate mRNA expression. 18-25 nucleotides long.
They will join the RISC (RNA-induced silencing complex) and hydrolyze with the 3’ UTR (right after stop codon) of the target mRNA which leads to the degradation of the mRNA and
What is an oncomir?
it is a microRNA that promotes cancer development by down regulating tumor suppressor genes or enhancing oncogenic pathways.
Can certain microRNAs be helpers against cancer?
Yes, some may act as tumor suppressors. Example could be that they down regulate or prevent the translation of oncogenic genes.
Why do cells in culture undergo senescence after a certain amount of divisions?
- due to length of telomeres (they get smaller after each replication)
- specialized protein complexes called shelterin complexes at the end of chromosomes
What do telomeres protect against?
- They protect against enzyme digestion
- DNA ds break mechanisms from being fired
Why do telomeres get shorter?
To fix the overlap at the end of the double strand in replication of the lagging strand, DNA Poly requires an RNA primer and eventual removal of the primer, which shortens the length of the telomeres each time.
This is, of course, without speaking of telomerase.
What does telomerase do?
How does it do it in basic terms?
It maintains the length of telomeres.
It uses hTERT (human telomerase reverse transcriptase) that synthesizes DNA from RNA
as well as human telomerase RNA (hTR) which contains bases that are complementary to the typical TTAGGG repeats, which acts as a template for the hTERT
in what percent of cancers is telomerase overexpressed?
90 percent
If you wanted to take normal cells and turn them into cancer cells in vitro, what would you NEED to have?
telomerase
What can speed up telomeric shortening?
ss breaks and ROS
How may telomere shortening act as a tumor suppression mechanism?
Well, replicative potential may be limited if the DNA gets damaged.
Why would shortening telomeres probably not be an effective cancer treatment?
Because it could act on other cells, and shortening takes time and typically, there isn’t time to wait around for replication to be haulted.
What is a treatment regarding DNA methylation that you learned about?
Because many genes that are involved in carcinogenesis are hypermethylated, we can target DNMT (DNA methyl transferases) to inhibit the methylation.
A drug called 5azaC will mimic Cytosine and be placed in the RNA and DNA and and covalently link will DNMT which results in much less methylation in the overall DNA
How do HDAC inhibitors work to treat cancer?
What effect do they have on normal cells?
Normally HDACs remove acetyl groups, which results in chromatin compaction and therefore gene silencing (potentially tumor suppressors - stuff that is involved in apoptosis or inhibiting the cell cycle).
Here, the inhibitors will bind to the HDACs which are often over-expressed in cancer cells, and reactivate important genes.
The have little to no effect on normal cells.
How can Long Non-Coding RNAs (lncRNAs) be helpful in identifying cancer?
Because it is known that the lncRNA PCA3 is highly over expressed in prostate cancer cells and they developed an RNA-based urine test for diagnosis of the cancer.
Are telomerase inhibitors very specific?
Why are they not really useful in treating cancer?
You think they would have to be.
Telomerase inhibitors take a lot of time to shorten enough to be effective, which is really not ideal for cancer therapies.
