New & Noteworthy

Codependent Genes

May 16, 2013

When a gene is duplicated, one copy usually dies. It is battered by harmful mutations until it eventually just fades into background DNA.

But this isn’t the fate of all duplicated genes.  Sometimes they can survive by gaining new, useful functions.  The genes responsible for snake venom proteins are a great example of this.

Another way for a duplicated gene to live on is when both copies get different mutations that confer different functions, so that a cell needs both to survive.  Two examples of this type of codependent gene survival are highlighted in a new study by Marshall and coworkers.  They compared various fungal species and identified cases where two functions were carried out by either one gene or by two separate genes.  Surprisingly, these cases involve alternative mRNA splicing, which is a rare process in fungi.

The first gene pair they focused on was SKI7 and HBS1 from Saccharomyces cerevisiae.  In this yeast these two genes exist as separate entities, but in other yeasts like Lachancea kluyveri they exist as a single gene which the authors have called SKI7/HBS1. 

The SKI7/HBS1 gene makes two differently spliced mRNAs, each of which encodes a protein that matches up with either Ski7p or Hbs1p.  In addition, the SKI7/HBS1 gene can rescue a S. cerevisiae strain missing either or both the SKI7 and HBS1 genes.  Taken together, this is compelling evidence that SKI7 and HBS1 existed as a single gene in the ancestor of these two fungal species. In S. cerevisiae, after this gene was duplicated each copy lost the ability to produce one spliced form.

The second gene Marshall and coworkers looked at experienced the reverse situation during evolution.  PTC7 exists as a single gene that makes two mRNA isoforms in S. cerevisiae: an unspliced form that generates a nuclear-localized protein, and a spliced form that produces a mitochondrial protein. 

But in Tetrapisispara blattae, these two forms exist as separate genes.  The PTC7a gene is similar to the unspliced form in S. cerevisiae and the protein ends up in the nucleus, while the PTC7b gene is similar to the spliced S. cerevisiae version and its product is mitochondrial.  

Because an ancestor of S. cerevisiae had every one of its genes duplicated about 100 million years ago, yeasts have been a great system to study the fate of duplicated genes.  This study shows that even though gene duplication is widespread in fungi and alternative splicing is rare, these mechanisms are actually interrelated and each can increase the diversity of the proteins produced by a species.

Fun fact: 544 genes survived duplication in S. cerevisiae.  That is around 10%.

by D. Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics

Categories: Research Spotlight

Tags: alternative splicing, evolution, gene duplication, Saccharomyces cerevisiae

Keeping the Noise Down

May 08, 2013

When you get down to a single cell, things can get really noisy. Instead of the nice, smoothed over data that you see in populations, you see some variation from cell to cell. This is even if all the cells are identical genetically.

Of course this makes perfect sense if you think about it. Part of the variation comes from slightly different environments. Conditions at the bottom of the flask are bound to be different from those at the top! This goes by the name of extrinsic noise.

Another source of variation has to do with levels of reactants within the cell and the chances that they encounter each other so they can react. These effects can be especially pronounced when there aren’t a lot of reactants around. This goes by the name intrinsic noise.

One process with a lot of noise is gene regulation. It is often affected by minor fluctuations in the environment and there are usually just one or two copies of the gene itself. This is the perfect recipe for noise.

The noisiness of gene expression can be split into two steps. One, called burst frequency, reflects how often RNA polymerase sits down and starts transcribing a gene. The second, burst size, has to do with how many proteins are produced each time a gene is turned on.

Of these two processes, the most sensitive to noise is usually burst frequency. A transcription factor (TF) has to find the promoter of the gene it is supposed to turn on and then bring the polymerase over to that gene. This is dependent on the amount of TF in a cell and the number of TF binding sites on the DNA. What this means is that most of the time, genes with low levels of expression tend to be very noisy.

There are some situations, though, where it is very important to have low expression and low noise: for example, where a cell needs at least a few copies of a protein, but can’t tolerate too many. For most promoters, low levels of expression mean high noise, which in turn means there will be some cells that lack this key protein entirely. But a new study out in PLOS Biology shows one way that a promoter can have the best of both worlds.

In this study, Carey and coworkers examined the noisiness of sixteen different naturally occurring promoters in the yeast S. cerevisiae, controlled by the TF Zap1p. This is a great system because the activity of Zap1p is determined by the concentration of zinc in the medium. This means the authors were able to look at the noisiness of these promoters under a broad range of gene activities.

Their research yields a treasure trove of information about the noisiness of these promoters at varying levels of expression. As we might predict, noise decreased at most (11/13) of the reporter genes as more active Zap1p was around. This makes sense, as cell to cell variability will decrease as genes are turned on more often. Higher burst frequency means less noise.

The opposite was true for most (2/3) of the reporters repressed by Zap1p. As more Zap1p was around, transcription of the reporter gene became less frequent, which meant that the noise effects became more prominent.

One of the more interesting findings in this study focused on an exception to this rule. The ZRT2 promoter showed a bimodal expression pattern, as it was activated at low levels of zinc and repressed at high levels. What makes it so interesting is that its noise level stays fairly constant.

As the zinc concentration increases and activity goes up, the noise goes down. This is what we would expect. But when zinc levels get high enough so that the gene is repressed, the noise levels do not increase. They stay similar to the levels seen with the activated gene.

The authors show that this promoter is repressed differently than the other two repressed promoters, ADH1 and ADH3. These promoters are repressed by decreasing the burst frequency: they fire less often when repressed. In contrast, the ZRT2 promoter fires at the same activated rate when repressed, but yields less protein with each firing: repression decreases burst size.

So this is how a cell can manage to get a gene turned on at low levels more or less uniformly through a cell’s population. If it can create a situation where the gene fires a lot but very little protein is made with each firing, then the cell will have relatively constant but low levels of that protein.

This study also provides a new tool for dissecting how a TF affects the expression of a gene. If a repressor decreases expression without an increase in noise, then it is probably affecting burst size. If on the other hand the noise goes up as expression goes down, then the repressor is affecting burst frequency.

by D. Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics

Categories: Research Spotlight

Tags: cellular noise, RNA polymerase II, Saccharomyces cerevisiae, transcription

Breaking Up is Hard to Do

May 01, 2013

When a cell goes cancerous, its chromosomes get seriously messed up. Pieces get deleted, duplicated, mixed and matched. One of the worst things that can happen, in terms of a cell keeping its chromosomes together, is that a chromosome ends up with two centromeres.

A centromere is the part of a chromosome that gets attached to the spindle so it can be moved to the right place during cell division. When there are two centromeres, both get attached and something has to give if the chromosome is pulled in two different directions. Often this means that the DNA of the chromosome breaks between the two centromeres.

This isn’t as simple as the rope breaking during a tug-of-war, though. A chromosome can withstand around 480 piconewtons of force before breaking, but the force exerted by the spindle that breaks the chromosome between the centromeres is just one piconewton or less. Clearly something else is going on to create those breaks!

In a new study out in GENETICS, Song and coworkers looked more closely at what happens when a dicentric chromosome breaks. They used a diploid strain of S. cerevisiae to show that where the DNA breaks is not random. In their experiments, the break tended to happen within 10 kilobases (kb) of the “foreign” centromere.

They used a previously described system where a conditional centromere was placed 50 kb from the normal centromere on chromosome III. This conditional centromere is only turned on in the absence of galactose. They then mated this strain to an unrelated one, resulting in a diploid with a high degree of heterozygosity. In other words, the chromosomes from each strain were different at lots of different places.

Song and coworkers streaked diploids from isolated colonies to a plate lacking galactose and then investigated how the yeast managed to resolve its double centromere issue. Two key ways that the yeast could eliminate the additional centromere involve crossing over between sister chromatids or break-induced repair. They focused on these as it is relatively easy to identify the DNA breakpoint. Because the two chromosomes in each pair are so different, they just needed to look for a loss of heterozygosity. In other words, where did the chromosomes become the same?

When they looked through 27 colonies, they found that the breaks weren’t randomly spread between the centromeres. Surprisingly, about half of them happened very near the conditional centromere. To make sure that there wasn’t something special about these sequences, they looked at two different strains with the conditional centromere located in different places on chromosome V instead of III. They obtained similar results.

Since the force exerted by the spindle isn’t enough to break the chromosome, there must be enzymes involved in creating the DNA breaks. But why do they prefer the region near the conditional centromere? One possibility is that the DNA there is stretched and is more open to enzymes. As the chromosome is being pulled apart, an enzyme gets into this region and manages to cut the DNA.

Although we don’t have time to go into it here, the paper also has a lot to say about the variety of ways that a diploid cell resolves its extra centromere in a way that allows it to survive. And that will inform the study of chromosome dynamics in all kinds of cells.

by D. Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics

Categories: Research Spotlight

Tags: cancer, DNA repair, Saccharomyces cerevisiae

Finally, Microbes Get the Recognition They Deserve

April 15, 2013

Anyone reading the SGD blog knows that the yeast Saccharomyces cerevisiae is an amazing little organism. Not only does it give us bread, wine and beer, but it also is an invaluable tool in understanding human biology. It has helped us better understand cancer, Alzheimer’s, and lots of other diseases, not to mention basic biological processes like gene regulation and cell cycle control. This little one celled beast is the rock star of biology!

And now, finally, government is starting to take notice. In a 58-0 vote, the Oregon House recently decided that yeast should be the official state microbe. If the Senate and the governor agree, then yeast will be getting the recognition it deserves. Take that, C. elegans, Drosophila, and all of you other model organisms!

Unfortunately, this recognition is not for yeast’s scientific value. Craft beer making is huge in Oregon, and designating yeast as the official state microbe is a way of celebrating this important state industry. Given all of yeast’s other important contributions to the well-being of us all, this feels a bit like celebrating Hugh Jackman for his role as Wolverine in X-Men while ignoring his roles on Broadway or his role as Jean Valjean in Les Miserables. Yes, he was great in X-Men, but that is an incomplete picture of him as an actor. Same thing with yeast.

Yeast should be celebrated for wine and bread, for medicines like anti-malarials and antifungals, for the deep biological understanding it has given us, and even for its possible future as a source for biofuels. Still, this honor is way better than nothing, and at least yeast will be the first microbe officially recognized by a state. Well, it will be if Oregon hurries.

Hawaii is voting on an official state microbe too, Flavobacterium akiainvivens. This bacterium was discovered by a high school student during a science fair project and is only found in the state of Hawaii. The Oregon senate should vote soon, or yeast will be the second officially recognized microbe.

Of course, the bill could die in the Senate. This is what happened in Wisconsin back in 2009 when their House passed a bill making Lactococcus lactis the official state microbe. This bacterium is important for making Wisconsin’s famous cheese but it wasn’t important enough for the Senate to approve it as Wisconsin’s official state microbe. Hopefully Oregon won’t make the same mistake with yeast.

by D. Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics

Categories: Research Spotlight

Tags: beer, Saccharomyces cerevisiae

The Indulgent Chaperone

April 01, 2013

When you think of a chaperone, you probably think of a strict adult at the prom who keeps a tight rein on the kids’ behavior.  Well, in nature, a chaperone sometimes has to do the opposite to help new genes form more quickly.  Sometimes the chaperone has to give the gene a longer leash to explore lots of different possibilities.

See, in theory, it is pretty easy to make a new gene.  A cell accidentally makes an extra copy of an existing gene and this gene is then free to mutate into something new.  A few mutations later and you have a new gene.

Turns out this is probably trickier than it sounds.  First off, having an extra copy of a gene can cause problems.  And second, getting to a new function is no walk in the park either.  It usually takes a few sequential mutations to get there and, with proteins being such persnickety things, many of the intermediates along the way end up being unstable. 

One way a cell might deal with these issues is to bring in a chaperone that lets the gene tolerate more mutations.  Chaperones are proteins that help stabilize other proteins, often under trying conditions like high temperature.  They coddle the protein and keep it stable so that it can still do its job.  In addition, chaperones can also cause a protein to relocate to different parts of the cell.

So the idea is that if a duplicated gene gains a mutation that lets its protein interact with a chaperone, the protein may get more stability from that interaction or may be rerouted to where it won’t do any harm. Because the chaperone buffers the possible harmful effects for the cell, the gene is free to explore more different intermediates on the way to its new function.

A new study out in GENETICS by Lachowiec and coworkers lends support to this “capacitor hypothesis.”  The authors used both Arabidopsis and Saccharomyces cerevisiae to show that genes whose proteins interact with the chaperone Hsp90 evolved more quickly than closely related genes that did not.  This strongly supports the idea that chaperones can encourage new functions in duplicated genes.

The authors first looked at a couple of closely related transcription factors from Arabidopsis, BES1 and BZR1.  Using a specific inhibitor of HSP90 called geldanamycin (GdA), they were able to show that BES1 was a client of HSP90 but BZR1 was not.  They then created a phylogenetic tree of Arabidopsis BZR/BEH gene family and, by determining the ratio of non-synonymous to synonymous changes, found that BES1 had a higher rate of mutation.  One explanation is that the stabilizing/relocalizing influence of HSP90 allowed BES1 to tolerate more mutations.

This result was an excellent first step in showing that the capacitor hypothesis may be true in some cases, but it is limited by being based on a single pair of proteins.  To broaden their findings, Lachowiec and coworkers took advantage of the vast knowledge about Hsp90 interactions in Saccharomyces cerevisiae to look at many more genes.

At first this didn’t work out that well.  The authors looked at a data set of yeast proteins that interacted with Hsp90 (encoded in yeast by the HSP82 and HSC82 genes) and, after removing any co-chaperones from the set, found no difference in the rate of evolution between those proteins that interacted with Hsp90 and those that did not.  But as the authors note, this isn’t surprising as so many other factors play a role in the rate of evolution too.

To refine their analysis, they mimicked their BES1/BZR1 study and focused on pairs of closely related proteins where one interacted with Hsp90 and the other did not.  They found that proteins that interacted with Hsp90 had a “longer branch length” than did their close relatives that did not interact.  In other words, Hsp90 appeared to help along the formation of a new gene.

The authors then went back to Arabidopsis and showed that BZR and BES1 were found in distinct but overlapping parts of the cell.  This lends credence to the idea that chaperones cause proteins to localize to different parts of the cell. 

So it looks like an important function of chaperones may be to shepherd new gene formation.  They are more like a 1960’s version of a chaperone…they let duplicated genes make lots of mistakes on their way to discovering who they really are.

by D. Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics

Categories: Research Spotlight

Tags: chaperones, evolution, Saccharomyces cerevisiae

Thinking Inside the Box (or Mitochondrion)

March 28, 2013

The mantra in real estate is that location is everything. The same may be true for some cases of bioengineering. You may not get the best yield unless a whole pathway is in the right cellular compartment.

This is what Avalos and coworkers found for synthesizing branched chain alcohols in the yeast Saccharomyces cerevisiae. These scientists were able to increase yield by 260% by putting the whole pathway of enzymes into the mitochondrion. This is way better than anything anyone else has been able to achieve.

This matters because branched alcohols like isobutanol may prove to be better biofuels than ethanol. We can get more energy out of isobutanol than we can out of ethanol…it has more bang for the buck. Good idea in theory, but producing large quantities of isobutanol has not worked too well in practice.

Yeast is just not very good at making these alcohols, and efforts to improve yields have been anything but inspiring so far. Overexpressing the enzymes in the metabolic pathways that generate isobutanol increased yield by only about 10%. Unfortunately, 10% of almost nothing is still pretty close to nothing.

One of the key metabolic pathways involved in generating isobutanol and other branched chain alcohols is split between the mitochondria and the cytoplasm. Normally, the valine biosynthesis pathway converts pyruvate to valine and alpha-ketoisovalerate in the mitochondria; then those two intermediates, after transport to the cytoplasm, are further converted to isobutanol by the Erlich pathway for valine degradation. Avalos and coworkers reasoned that the failure to increase yield might be because of some rate limiting step in getting the intermediates from the mitochondria to the cytoplasm. And it looks like they may have been right.

They compared the effects of overexpressing the pathway enzymes in the cytoplasm and mitochondria and found the mitochondrial approach won hands down. Overexpression in the cytoplasm bumped yield up 10% while overexpression bumped it up 260%. And this increase wasn’t just for isobutanol. Yields of two other energy rich alcohols, isopentanol and 2-methyl-1-butanol, also went up significantly.

Part of the explanation almost certainly has to do with transport of intermediates between the mitochondrion and the cytoplasm, but that may not be the whole story. The mitochondrion might be a useful environment for other reasons too. For example, its smaller volume means an increase in the concentration of reactants, and its higher pH, lower oxygen content, and more reducing redox potential may be better for certain reactions. It also contains many key intermediates like heme, steroids, biotin and so on.

On the way to improving isobutanol yield, these scientists made it easier for others to test whether moving their pathway to the mitochondria can help increase the yield of their favorite metabolite. Avalos and coworkers created a system of plasmids that easily allows researchers to attach the N-terminal mitochondrial localization signal from Cox4p, subunit IV of the yeast cytochrome c oxidase, to genes of their choice. This will make it much simpler to test whether a pathway’s yield is enhanced by moving it into the mitochondrion.

These results show there is more to increasing yield than overexpression or codon optimization. Sometimes scientists need to take a good hard look at their particular pathway and think outside of the box for new ways to optimize yield. Or sometimes they just need to think within the box that is the mitochondrion.

by D. Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics

Categories: Research Spotlight

Tags: biofuel, mitochondria, Saccharomyces cerevisiae

Hate the CIN, Love the CINner

March 21, 2013

At first our favorite small eukaryote, S. cerevisiae, might not seem like a great model for cancer studies. After all, budding yeast can’t tell us anything about some of the pathways that go wrong in cancer, like growth factor signaling. And it clearly can’t help explain what happens in specific tissues of the human body. But in other ways, it actually turns out to be a great model.

For example, all the details of cell cycle control were originally worked out in yeast.  And now a whole new batch of genes has been found that influence a phenomenon, chromosome instability (CIN), that is important in both yeast and cancer cells.

As the name implies, chromosomes are unstable in cells suffering from CIN. Big chunks of DNA are lost, or break off and fuse to different chromosomes, turning the genome into an aneuploid mess. And this mess has consequences.

CIN can cause new mutations or make old ones have a stronger effect.  Eventually these mutations can affect genes that are important for keeping a cell’s growth in line.  Once these are compromised, a tumor cell is born. 

Since CIN is pretty common in yeast, we might be able to better understand it in cancer cells by studying it in yeast. The Hieter lab at the University of British Columbia has come up with a powerful screen to get yeast to confess why it CINs. 

A previous study from the group set the stage by finding a large group of mutants that have CIN phenotypes, implying that those genes are involved in keeping chromosome structure stable. In a new paper in G3: Genes, Genomes, Genetics, van Pel et al. uncovered the network of interactions among the genes in this set, using synthetic genetic array (SGA) technology. And they confirmed that the human homologs of some of these genes interact in the same way as in yeast, making them potential targets for cancer therapies.

The idea behind SGA studies is that if two proteins are involved in the same process, then a strain carrying mutations in both of their genes will be much worse off than a strain carrying either single mutation. In the worst case, the double mutant will be dead. This is known as a synthetic lethal interaction.

Yeast is a great model for doing these sorts of studies on a very large scale.  We can construct networks showing how lots of different genes interact, and most importantly, find the genes that are central to many interactions.   These “hubs” are likely to be the key players in those processes.

The researchers looked specifically for interactions between genes that are involved with CIN in yeast and are also similar to human cancer-related genes. They came up with various interaction hubs that will be interesting research subjects for a long time to come. In this study, they focused on one of these: genes involved with the DNA replication fork.

One of these in particular, CTF4, is a hub for both physical and genetic interactions. Unfortunately, Ctf4p doesn’t look like a good target for chemotherapy. It’s thought to act as a scaffold, and lacks any known activity that could potentially be inhibited by a drug. However, the interaction network around CTF4 that van Pel et al. uncovered suggests another way to target this hub. If a gene that interacts with CTF4 itself has a synthetic lethal interaction with another gene, and we could re-create the synthetic lethal phenotype in a cancer cell, we might be able to knock out the whole process. And that is just what they found in human cells.

First the authors identified a couple of human genes that were predicted from the yeast screen to be close to human CTF4 in the interaction network and to have a synthetic lethal interaction with each other. They then lowered the expression of one using small interfering RNA (siRNA), and reduced the activity of the other with a known inhibitor. Neither treatment alone had much effect, but combining them significantly reduced cell viability.

Since cancer cells frequently carry mutations in CIN genes, it should be possible to create a synthetic lethal interaction, guided by the yeast interaction network, where one partner is mutated in cancer cells (equivalent to using siRNA in this study) and the other partner is inhibited with a drug. Since it relies on a cancer-specific mutation, this approach has the potential to selectively target cancer cells while not disturbing normal cells, the ultimate goal for chemotherapy.

by Maria Costanzo, Ph.D., Senior Biocurator, SGD

Categories: Research Spotlight, Yeast and Human Disease

Tags: cancer, DNA replication, Saccharomyces cerevisiae, yeast model for human disease

Old Genes, New Tricks

March 14, 2013

You can’t teach an old dog new tricks, or so the saying goes. But imagine you found that your old dog knew a complicated trick and had been doing it all her life, right under your nose, without your ever noticing it! You’d be surprised – about as surprised as the Hinnebusch group at NIH when they discovered that some long-studied S. cerevisiae genes had an unexpected trick of their own.

They were working on the VPS* (vacuolar protein sorting) genes. While known for a very long time to be important in protein trafficking within the cell, Gaur and coworkers found that two of these genes, VPS15 and VPS34, play an important role in RNA polymerase II (pol II) transcription elongation too. Now there is an unexpected new trick…like your dog learning to use a litter box!

There had been a few hints in recent years that the VPS genes, especially VPS15 and VPS34, might have something to do with transcription. Following up on these, the researchers tested whether vps15 and vps34 null mutants were sensitive to the drugs 6-azauracil and mycophenolic acid. Sensitivity to these drugs is a hallmark of known transcription elongation factors. Sure enough, they were as sensitive as a mutant in SPT4, encoding a known transcription elongation factor. Further experiments with reporter genes and pol II occupancy studies showed that pol II had trouble getting all the way to the end of its transcripts in the vps mutant strains.

There was a bit of genetic interaction evidence that had suggested that there might be a connection between VPS15, VPS34, and the NuA4 histone acetyltransferase complex. This is important, since NuA4 is known to modify chromatin to help transcription elongation. Looking more closely, the researchers found that Vps34p and Vps15p were needed for recruitment of NuA4 to an actively transcribing reporter gene.

Other lines of investigation all pointed to the conclusion that these VPS proteins have a role in transcription. They were required for positioning of several transcribing genes at the nuclear pore, could be cross-linked to the coding sequences of transcribing genes, and could be seen localizing at nucleus-vacuole junctions near nuclear pores.

One appealing hypothesis to explain this has to do with what both genes actually do. Vps34p synthesizes phosphatidylinositol 3-phosphate (PI(3)P) in membranes, while Vps15p is a protein kinase required for Vps34p function. The idea is that when Vps15p and Vps34p produce PI(3)P at the nuclear pore near transcribing genes, this recruits the NuA4 complex and other transcription cofactors that can bind phosphoinositides like PI(3)P. There are hints that this mechanism may also be at work in mammalian and plant cells.

There’s a lot more work to be done to nail down the exact role of these proteins in transcription. But this story is a good reminder to researchers that new and interesting discoveries may always be hiding in plain sight.

* These genes were also called VPL for Vacuolar Protein Localization and VPT for Vacuolar Protein Targeting

by Maria Costanzo, Ph.D., Senior Biocurator, SGD

Categories: Research Spotlight

Tags: RNA polymerase II, Saccharomyces cerevisiae, transcription, VPS genes

Cancerous Avalanche

March 05, 2013

Cancer often gets going with chromosome instability.  Basically a cell gets a mutation that causes its chromosomes to mutate at a higher rate.  Now it and any cells that come from it build mutations faster and faster until they hit on the right combination to make the cell cancerous.  An accelerating avalanche of mutations has led to cancer.

There are plenty of obvious candidates for the genes that start these avalanches: genes like those involved in segregating chromosomes and repairing DNA, for example.  But there are undoubtedly sleeper genes that no one has really thought of.  In a new study out in GENETICS, Minaker and coworkers have used the yeast S. cerevisiae to identify three of these genes — GPN1 (previously named NPA3), GPN2, and GPN3.

A mutation in any one of these genes leads to chromosomal problems.  For example, mutations in GPN1 and GPN2 cause defects in sister chromatid cohesion and mutations in GPN3 confer a visible chromosome transmission defect.  All of the mutants also show increased sensitivity to hydroxyurea and ultraviolet light, two potent mutagens.  And if two of the genes are mutated at once, these defects become more severe.  Clearly, mutating GPN1, GPN2, and/or GPN3 leads to an increased risk for even more mutations!

What makes this surprising is what these genes actually do in a cell.  They are responsible for getting RNA polymerase II (RNAPII) and RNA polymerase III (RNAPIII) into the nucleus and assembled properly.  This was known before for GPN1, but here the authors show that in gpn2 and gpn3 mutants, RNAPII and RNAPIII subunits also fail to get into the nucleus. Genetic and physical interactions between all three GPN proteins suggest that they work together in overlapping ways to get enough RNAPII and RNAPIII chugging away in the nucleus.

So it looks like having too little RNAPII and RNAPIII in the nucleus causes chromosome instability. This is consistent with previous work that shows that mutations in many of the RNAPII subunits have similar effects.  Still, these genes would not be the first ones most scientists would look at when trying to find causes of chromosomal instability. Score another point for unbiased screens in yeast leading to a better understanding of human disease.

by D. Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics

Categories: Research Spotlight, Yeast and Human Disease

Tags: cancer, chromosome instability, RNA polymerase II, RNA polymerase III, Saccharomyces cerevisiae

Crowdsourcing Genetic Disease

February 28, 2013

Remember when sequencing the human genome was going to help us better understand and treat complex diseases like Type 2 diabetes or Parkinson’s? Well, ten years later, we’re still waiting.

Sure we’ve made some progress. Using genome wide association studies (GWAS), scientists have uncovered markers here and there that explain a bit about how a genetic disease is inherited. But despite a seemingly never-ending stream of these assays, scientists simply can’t explain all of the genetics behind most of these diseases.

So now scientists need to try to explain this missing heritability. If they can find out why they aren’t getting the answers they need from GWAS, then maybe they can restructure these assays to give better results.

As usual, when things get dicey genetically, scientists turn to the yeast Saccharomyces cerevisiae to help sort things out. And in a new study out in Nature, Bloom and coworkers have done just that.

In this study, they mated a laboratory and a wine strain of yeast to get 1,008 test subjects from their progeny. They extensively genotyped each of these 1008 and came up with a colony size assay that allowed them to determine how well each strain grew under various conditions. They settled on 46 different traits to study genetically.

What they found was that none of these traits was determined by a single gene. In fact, they found that each of the 46 different traits had between 5 and 29 different loci associated with it, with a median of 12 loci. This tells us that at least in yeast, many genetic loci each contribute a bit to the final phenotype. And if this is true in people, it could be a major factor behind the missing heritability in GWAS.

If a trait is dependent on many genetic loci that each have a small effect, then researchers need large populations in order to tease them out. In fact, when Bloom and coworkers restricted their population to 100 strains, they could only detect a subset of the genetic loci. For example, the number of loci went from 16 to 2 when they looked at growth in E6 berbamine.

So it may be that scientists are missing loci in GWAS because there are simply too few participants in their assays. If true, then the obvious answer is to increase the size of the populations being studied. Thank goodness DNA technologies get cheaper every year!

Of course as the authors themselves remind us, we do need to keep in mind that humans are a bit more complex than yeast. There may be other reasons that we aren’t turning up the genetic loci involved in various traits. It may be that we can’t as accurately measure the phenotypes in humans or that human traits are more complicated than the yeast ones studied. Another possibility is that in humans, there are more rare alleles that can contribute to a given trait. These would be very hard to find in any population studies like GWAS.

Still, this study at the very least tells us that larger populations will undoubtedly uncover more loci involved in human disease. Thank you again yeast.

by D. Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics

Categories: Research Spotlight, Yeast and Human Disease

Tags: GWAS, model organism, Saccharomyces cerevisiae

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