User:Helmse

Discussion Question for PMCB Journal Club

Paper: "Does bad luck cause cancer?"

1. As more information becomes available in the heritable and environmental factors what affects will occur to this model?

2. What about the affects of the immune system, as random mutation is occurring constantly and cancer in the body occurs frequently, the immune system can in part take care of some cancers. Is another factor the immune system? Has that been taken out of the equation? Or what factor would it fit in?

3. So men continue to make gametes and say a mutation that happens randomly in the men is heritable is passed to children. This would affect those level potentially making them appear random ( if he doesn't get the cancer but passes down the mutation). Would this impact the model variables and if so how?

Paper: "Identifiers for the 21st Century..."

1. Is there a universal way to limit the deletion/ modification of identifiers, in order to create a more permittly accessable research field?

2. Who is responsible for the identifiers staying up to date currently, does this need to change, should there be a department for this?

3. Is it feasible to potentially require those in charge of the paper/ source in question to leave the site/identifier open for a certain time with a notice stating it will be deleted or moved and where it is being moved. who then is responsible for the changing of situations after the move, those who sited? Is there a way to right a code that could update or does that lead to hacking issues? Maureen 13:29, 10 October 2017 (PDT)Nice Qs. Will be a good discussion with these

Paper: TZAP and telomeres

Presenter 2

Paper:"A heterochromatin-dependent transcription machinery drives piRNA expression"

1. Is the TRF2 that Moonshiner recruits, the same TRF2 that is a part of the Shelterin complex that binds telomere sequences? Answer: No, flies don't have telemores, it isn't the same TRF2.

2. Being that microRNAs are incorporated into a RISC complex is the mechanism of microRNAs in humans similar to the piRNAs? Do they preform the same function? Has this been studied?

3. Being that TRF2 is used in two completely different contexts, and are separate things? Is there regulation on the naming of these factors? Sort of Answer: It appears there isn't much regulation to make sure there isn't overlap, which can confuse things quite a bit.

4. In genetics we saw the amount of heterochromatin in the 4 chromosomes of flies. Is this area (which is quite large on some) all a result of the transposon defense system discovered in this article? If viral transposons continue to be incorporated into the fly genome and this defense mechanism continues, how much of this can occur before the heterochromatin reaches critical mass (hypothetically)

5. What, if any, defense mechanism exist in responds to transposons?

Paper: "Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions"

1.What are the evoltionary mechanisms for having enhancers so far away from the promoters? Could inactive transposons push them farther apart? What are the evolutionary implications for skipping genes (if there are any)?

2. The ESC Crispr heterozygous and homozygous pups, why did they die, and why did the authors simply state they don't know why, and have no explanation? Is this okay to leave out investigating, is it unethical to leave out this information? Could this affect their results or conclusions? Why do you think they left out investigating this?

Further Questions brought up From Discussion More of a comment this is a great start at a potentially new way of diagnosing diseases that are harder to diagnose. I didn't realize until we talked in discussion how applicable this is to translational medicine. The idea that you could take the section suspected of the issue, and put it into a embryo of another species and see the change in developement. Then a partient can more specific know what is changed leading to the phenotype they have. That's simply amazing, and potentially groundbreaking for people with diseases of unknown cause.

3. With TADs being evolutionarily conserved, and are important for survival, what regulates TADs? What makes sure they are conserved? How do you get new TADs? Do TAD changes have anything to do with regulation of changes as a result of stress? Does altering TADs have any potential for response to stress?

Paper: "Cohesion Loss Eliminates All Loop Domains"

1. Is the recovery after reintroduction of cohesion a complete recovery or are there consequences, mislooped, misformation of sections?

2. What are other members of the cohesion complex?

ANSWER: I found a cool paper on this. Peters, Jan-Michael, et al. "The cohesion complex and its roles in chromosomebiology." Genes & Developement, Cold Springs Harbor Lab, 1 Jan 1970, genes Dee.cshlp.org/content/22/22/3089. It is long so Table 1. Has all of the subunits common names and function (this is from 1970 so not all are known so a bit vague.

3. How do they tell when there is a false positive? They may have discussed this I either missed it, or I don't really understand what they are saying.

4. Are there any known patients with mutations in either the CTCF or cohesion (the complexes with in baring the mutations)? If there aren't is it because these are vital of appropriate interactions, are they lethal? Would you have to knock out both copies for lethality (Probably Right)? How many copies are in the genome for these complexes? Fundamentally does the genome contain more than two copies for anything that is particularly vital for life or is the rule just two?

Partial ANSWER: The last question my quest if there can be multiple I remember a lecture talking about p53 having multiple copies (If I am wrong would someone kindly set me straight?).

5. Does the inactive X chromosome (actually both because either can be inactived) have any superenhancers? If so are they enhancers for genes that when not there are what result in the phenotype seen in turners and klinefielters (this was just on a test though less detail was taught, and I am more curious about the specifics of why the phenotype, such as which genes are on that inactive X)? On that note does the Y have any superenhancers, most of it is heterochromatin, but males don't have some of the symptoms turners do, so logic would mean that the Y has to have some important genes, would they need superenhancers to work even in highly compacted regions? Are superenhancers there for really important genes (evolution would select for important genes not being silenced so superenhancers to me logically would fit in to help keep them that way. Am I on the right track do we know?)

6. What mediators are responsible for the domains around superenhancers that keep the domain still there even if cohesion is missing? Missing cohesion would create some stress I would postulate, would changes in the domain when no cohesion is present activate any genes that would respond to this stress?

Paper: "HSP90 shapes the consequences of human genetic variation."

1. The paper talks about the effects charpeone folding has on variable expressivity, could this also contribute to Penetrance, and the idea that one generation could have a phenotype while the next does despite both having the mutation? What about the affects this could have on anticipation? Or even diseases where the homozygous has the most pronounced phenotype, but the heterzygotes has some symptoms?

2. Do organisms that live in extremes, like Archaea, have they evolved different chaperones that function in higher temperatures or higher stress environments? For that matter do eukaryotes have some chaperones that are at lower levels but function in higher stress environments?

3. What about mutations in the heat shock proteins themselves, does this cause disease? Can other chaperones compensate, or are the mutations homozygous lethal? Is one copy sufficient?

4. Is this system truly relavent across diseases, are other chaperones more important to other diseases, or is the HSP conserved? Could this system play a role in CF where the mutation leads to misfolding, which results in increased degradation of the mutant protein itself? Proteins have a native confirmation, but there are other ways for them to fold, if chaperones like HSP are recognizing this does the ranking on severity of misfold matter, does one misfold do better than another misfold? Is this what contributes to the variable expressivity?

5. Does the type of mutation, or type of aa change matter? Missense, nonsense, what about frame shift? Silent mutations don't change the aa, would HSP have a variable chaperoning for them?

Paper: "Competing memories of mitogen and p53 signaling control cell-cycle entry"

1. Why specifically use an inhibitor of MEK, it is in the middle of the pathway is that important to the study? Was it simply the easiest inhibitor (or cheapest)? Mostly just a curiosity question of why they choose MEK and not ERK, MYC, RAS, RAF.

2. Is it know how many phosphorylation sites Rb has? what amount of phosphorylation constitutes hyper-phosphorylation? Hypo? Put another way how many sites have to be phosphorylated so that E2F is able to be no longer repressed by RB? How much phosphorylation is need for a conformational change ( assuming it is a conformational change that decreases binding affinity of RB to E2F? Could it possibly be tissue or cell type specific or dependent?

3. Are there any known cancer cells lines with mutations in the genes that encode p21 or cyclin D1? Is it also possible that the Ras and P53 mutations know to occur in cancer are just tipping the balance between p21 and cyclin D? What I'm asking is it mutation in p21 or cyclin D resulting in an imbalance and downstream proliferation (cancer) or is it Ras and p53 mutations? Is it a combination? Is it cancer specific?

Answer: All of the above could be true? My best guess is that it is cancer dependent on what it tipping the cell cycle to proliferation.

Paper: “5’ UTR m6A promotes Cap-Independent Translation” If you want it independent don’t methylate it

1.Other bases can be methylated, what are the possible roles for these other methylated bases? What about other groups added to bases like hydroxymethyl which is an addition to cytosine that impacts histone specifically in the neurons? Do you think that every modification is a signaling mechanism?

2.Why is it important that the m6A is in the 5’UTR? what is preventing the m6As in the gene body from signaling the same as the m6A in the UTR? What does this mean in an evolutionary sense, in other words why would this be selected?

3.Could this cap independent translation play a role in cancer development and progression? Just slightly wild thought if a base in the 5’ UTR of an already activated oncogene was methylated and was an A could this result in increased synthesis as the complex is no longer dependent upon a 5’ cap? What about a methylation of an A in the 5’ UTR of a tumor suppressor or even the demethylation of a A in the 5’ UTR which make the gene more dependent on say a cap it does not have potentially. This gene would then not be as a active in regulation and preventing inappropriate proliferation?

4.Is it more likely for this cap independent to be found in the 5’ UTR of important genes? Could m6A be implicated in penetrance of disease? Such that if the gene has no cap but has a m6A in the 5’ UTR it can function but lose of both is worse? Can the sequence have this 5’ UTR m6A and get a cap added or are they mutually exclusive?

5.Do all eukaryotes have this mechanism, what about prokaryotes? Could this mechanism be from before the divergence of eukaryotes, who potentially then evolved to have another mechanism through a 5’ cap that could potentially be more advantageous then just a 5’ UTR m6A in these complicated system?

Paper: "sherlock investigating pathogens"

1.How long did it take them to come up with SHERLOCK, and how much finagling did it take to make the acronym spell out Sherlock?

2.How many other Cas’ are there? Do bacteria only have one or can they have multiple? How are they numbered?

3.What is the standard detection rate? How much of a pathogen is need to cause an illness? Are we saying that this system could allow for detection prior to illness?

4.One the topic of specificity I wonder how different do virus/pathogen particles have to be to constitute a separate virus? For example the flu virus mutates but at what point does it become a separate strain? Is the detection capability discussed in this paper based on what is stated to be that viruses particles? What happens when it mutates, can it mutate to be only detected as an unknown?

5.What is the time frame on this detection method? What is the false positive, false negative rate?

I think this is a really neat paper on a new diagnostic approach these are just my questions, some fairly random and more to do with curiosity.

• • • I like them. Maureen 11:05, 14 December 2017 (PST)