New & Noteworthy

Friends with Benefits

August 10, 2016

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A 2013 poll identified the top 20 modern necessities British people couldn’t live without. Some we can all relate to like smartphones, daily showers, and the internet, while others are more British-specific like a cup of tea or a full English breakfast.

Of course none of these are true necessities like food, water or air. We wouldn’t be as happy, nor as competitive, without some of these modern necessities, but we’d obviously still be alive. (But is life without the Internet really living?)

It turns out that the GCN5 gene is more like water or air for most eukaryotes—they can’t live without it. But our old friend Saccharomyces cerevisiae is different. This yeast isn’t as happy without GCN5, but it soldiers on nonetheless.

This nonessentiality, combined with its powerful genetics, makes yeast a great system for exploring what GCN5 does. And this is just what Petty and coworkers did with this important member of the histone acetyltransferase (HAT) family in a new study in GENETICS.

GCN5, like other HATs, transfers an acetyl group to histones, which results in increased activity of nearby genes. Consistent with this, previous work has shown that GCN5 acetylates histone H3 in the promoters of active genes.

HATs, along with their countervailing proteins histone deacetylases, as well as kinases, phosphatases, methyltransferases and so on, all work together to change gene expression on the fly in response to all sorts of different stimuli. These can include environmental signals, entering the cell cycle, or whatever.

Understanding how HATs work is critical for understanding how we (and other beasts) change gene expression in response to these signals. Which is what makes GCN5 in yeast such a great system. A strain deleted for GCN5 is sick, but alive, so we can study what happens when it is gone. And we can explore what we can do to fix its problems.

One of the many problems that yeast lacking GCN5 have is that they grow more poorly at high temperature than do yeast with GCN5. These researchers took advantage of this and looked for high copy suppressors of this temperature sensitivity. They found multiple genes, but the most common was RTS1, one of two regulatory subunits of the PP2A phosphatase complex.

Deleting GCN5 causes more problems than temperature-sensitivity, and overexpressing RTS1 restored some, but not all, of them. For example, RTS1 overexpression helped make the Δgcn5 strain less sensitive to DNA damage, less susceptible to microtubule disruption, better able to grow on nonfermentable carbon sources like glycerol or ethanol, and more able to progress into S phase during mitosis. But lots of PP2A^Rts1 could not rescue the abnormal buds nor the sporulation problems seen in a diploid lacking GCN5.

When the researchers deleted RTS1 or some of the genes that code for other critical components of the PP2A^Rts1 complex in a Δgcn5 strain, the strain died. The same was not true of a second regulatory subunit that can be part of the PP2A complex, CDC55—its deletion was not lethal, nor did it rescue the temperature sensitivity of the Δgcn5 strain.

Petty and coworkers provided evidence that the phosphatase activity of the PP2A^Rts1 complex was important by showing that okadaic acid, an inhibitor of this family of phosphatases, prevented Rts1p from rescuing the Δgcn5 strain’s temperature sensitivity. The easiest explanation is that the rescue happens because of the phosphatase activity of PP2A^Rts1, but it is also possible that a different member of the family might be providing the phosphatase activity.

So it looks like there is something important happening between PP2A and GCN5. Petty and coworkers next set out to find out what that might be.

First they showed that deleting GCN5 causes a decrease in the levels of core histones in the cell and that RTS1 overexpression fixed this problem. This happened at the transcription level as the RNA levels of the yeast histone genes (with the exception of HTA1) all showed reduced expression in the absence of GCN5, which again was restored when RTS1 was overexpressed.

Histone genes are normally turned on at the end of G1, then shut off at the end of S phase. This makes sense, as a cell needs to make more histones when it makes a new copy of its genome and this happens during S phase!

Consistent with the reduced histone gene expression seen earlier, the Δgcn5 strain failed to increase histone gene activity at the end of G1. Overexpressing RTS1 restored this induction. So it looks like GCN5 is involved in turning on all the histone genes, except maybe HTA1, at the right time, and that RTS1 can compensate if there is a lot of it around.

As a final set of experiments, the authors looked at what PP2A^Rts1 might be doing to rescue histone gene expression when GCN5 was deleted. They decided to look at histone modifications.

For this they used the SHIMA (Scanning HIstone Mutagenesis with Alanine) library, in which all key serine and threonine residues were individually mutagenized to alanine. Even though PP2A^Rts1 is thought to be primarily a serine/threonine phosphatase, they also looked at three tyrosine residues (Y40, Y43, and Y45) on H2B by mutating each individually to phenylalanine.

They found that two residues on histone H2B, Y40 and T91, were required for RTS1 to be able to rescue the temperature sensitivity of a Δgcn5 strain. And mimicking the permanent phosphorylation of T91, by mutating it to either aspartic or glutamic acid, slowed the growth of wild type yeast and killed the deletion strain.

This tells us a lot about what GCN5 is doing in yeast, and it might also help us better understand certain human cancers. Turns out that the residue equivalent to T91 in mammals is phosphorylated in these cancers.

Petty and coworkers were able to learn all of this because of yeast’s powerful genetic tools, and because GCN5 is not essential in yeast. Once again, the awesome power of yeast genetics (#APOYG!) can help us understand human cell biology.

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

Categories: Research Spotlight, Yeast and Human Disease

New SGD Help Video: Exploring Expression Datasets with SPELL

August 09, 2016

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Trying to find relevant expression datasets or genes with similar expression profiles for your favorite genes? Look no further than SPELL – the Serial Pattern of Expression Levels Locator. Given a set of genes, SGD’s instance of SPELL locates informative expression datasets from over 270 published studies and pairs the genes in your query with additional coexpressed genes.

To learn the basics of SPELL and find out how to run a query, check out our help video:

For more SGD Help Videos, visit our YouTube channel, and be sure to subscribe so you don’t miss anything!

Categories: Tutorial

Sign Up Now for the Next SGD Webinar: August 3, 2016

July 28, 2016

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SGD’s Variant Viewer is an easy-to-learn web application that allows visualization of differences in both gene and protein sequences. With Variant Viewer, you can compare the nucleotide and amino acid sequences of your favorite genes in twelve widely-used S. cerevisiae strains. Our upcoming webinar on August 3rd, 9:30 AM PDT will provide a quick 10 minute tutorial on how to use Variant Viewer. We will demonstrate how to compare nucleotide and amino acid sequences of different S. cerevisiae genomes, and how to visualize strain-specific single nucleotide polymorphisms, insertions, and deletions contained within a given open reading frame.

If you are interested in attending this event, please register using this online form: http://bit.ly/SGDwebinar4

This is the fourth episode in the SGD Webinar Series. For more information on the SGD Webinar Series, please visit our wiki page: SGD Webinar Series.

Categories: Announcements, Sequence, Tutorial

Alliance of Genome Resources – Survey

July 21, 2016

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Please help the Alliance by completing the short survey at: http://bit.ly/SGD-AllianceSurvey

Six of the founding members of the Alliance of Genome Resources (Saccharomyces Genome Database, WormBase, FlyBase, ZFIN, MGI, and the Gene Ontology Consortium) attended the GSA’s The Allied Genetics Conference in Orlando from July 13-17. It was a great opportunity for staff of each of these individual resources to talk about their new collaboration to integrate their content and software into a single resource that benefits biologists, educators, and clinicians alike.

The model organism databases all have a long history of reaching out to their respective communities for feedback on new developments and input on future directions. Carrying on this tradition, the Alliance has created a short survey to obtain feedback on how best to provide human disease information in relation to model organisms. In addition, the Alliance is asking for input on the prioritization of website visualizations, tools, and curation of specific data types.

We appreciate your continued support!

Categories: Announcements

Keep Only What You Need

July 13, 2016

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In the Lord of the Rings trilogy, the evacuees from Edoras are warned to take only what they need. Aragorn, Gimli and Legolas do the same thing when they chase down the orcs who kidnapped Merry and Pippin. And Sam and Frodo get rid of all nonessentials so they can make it to Mount Doom.

They all need to do this because if they are weighed down they won’t make it to their goal or maybe even die. If Sam and Frodo had kept all of their equipment, they would have died on the Plateau of Gorgoroth before reaching Mount Doom and saving Middle Earth.

In some ways, the hurly burly world of yeast is a bit like these characters in Middle Earth. If yeast cells are weighed down by slightly deleterious or even nonessential items, they will not survive. They will be outcompeted by their leaner, less burdened peers. The orcs would have made it to Isengard if Aragorn, Gimli, and Legolas had been slowed down by too much extra stuff.

One place where we can see this is with introns. Unlike many other eukaryotes, S. cerevisiae has gotten rid of almost all of its introns—only around 5% of its genes have them. This suggests that the ones that have stuck around are doing something important.

In a new study out in GENETICS, Hooks and coworkers explore the idea that at least some of the remaining introns have hung around because they play an important role as untranslated RNAs with specific secondary structures. In fact, they provide evidence that the secondary RNA structure of an intron in the GLC7 gene in critical for the cell’s ability to respond to salt stress.

The first step was to identify introns with a conserved secondary structure. They compared 36 fungal genomes using three different RNA structure prediction tools and found that all three programs were able to identify structures for 14 of the introns. They also found 3 introns that scored very well with at least two of the programs. With the exception of known snoRNAs, none of these matched any other noncoding RNAs.

Next, Hooks and coworkers used RT-PCR as well as re-analysis of deep sequencing data of total RNA to figure out which of these introns might actually be a real noncoding RNA. They found that six of the introns remained intact in the cell much longer than is typical for excised introns and that noncoding RNAs were further processed in two of them, an intron from GLC7 and one from RPL7B.

They set out to determine if the predicted secondary structure of the RNA of the intron in GLC7 really did anything important in the cell. GLC7 was a good choice as it has been previously reported that this intron is involved in a cell’s response to high salt. So if the structure is important, than if it is disrupted, the cell should not respond as well to high salt.

They used a couple of different mutants to get at this question. The first mutant, the GLC7 ncRNA deletion mutant, simply deleted the predicted noncoding RNA from the intron. The second mutant, the GLC7 ncRNA insertion mutant, inserted 139 base pairs in the middle of the predicted noncoding sequence. The researchers found that neither responded as well to a high salt concentration, 0.9 M NaCl, as did a wild type or a negative control deletion that removed part of the intron that did not overlap with the predicted noncoding RNA sequence.

They also found that this loss in response could not be rescued with the noncoding RNA being expressed in trans from a separate, constitutive promoter. The secondary structure of this intron plays an important role in dealing with the stress of high salt in cis.

While deletion of the predicted noncoding RNA had little effect on GLC7 expression at low salt, the same was not true at higher salt. At 0.9 M NaCl, GLC7 mRNA levels were about half of that of the wild type or the negative control deletion mutant. It looks like under high salt conditions, this intron is important for getting enough GLC7 made to deal with the stress.

So, like Gimli’s axe or Sam’s water bottle, yeast has maintained this intron because it plays an important role in survival. It will be interesting to see why other introns have been maintained and if they too play their roles as noncoding RNAs.

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

Categories: Research Spotlight

Tags: introns, ncRNA, RNA structure

Look for SGD at TAGC 2016!

July 05, 2016

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SGD staff will be attending The Allied Genetics Conference 2016 (TAGC) on July 13-17, 2016, in Orlando, Florida. We will be hosting a Workshop, Posters, and an Exhibit Booth. We’ll be available during the entire conference to hear your comments or suggestions about SGD and answer your questions.

Five different model organism databases – SGD, WormBase, FlyBase, MGI, and ZFIN – will also be doing open demonstrations and tutorials in the Demo Room (Palms Ballroom Canary 3-4). There will be scheduled group presentations, one-on-one tutorials, troubleshooting and discussions.

Follow @yeastgenome and #TAGC16 on Twitter for the latest research being presented at TAGC.

Workshop: “Getting Even More out of SGD”

Saturday, July 16, 4:00pm – 6:00pm, Crystal Ballroom G2

We’ll be discussing our curation efforts in capturing yeast-human functional complementation data, the new sequence Variant Viewer, new genome browser, new data in YeastMine, and more. Bring your questions and comments – we love feedback!

Exhibit Booth

SGD will also have an exhibit booth at the conference, in conjunction with WormBase and FlyBase! Come by booth #530 (right across from the GSA booth) to take a spin on our site, learn about various features of the databases, and provide us with feedback as to what we can do to improve your SGD experience. You might even receive a prize for a good question or suggestion!

…and Psst! Be sure to ask about the newly-formed Alliance of Genome Resources…

Posters

In addition to the Workshop, SGD staff will present five posters – please stop by and chat with us.

Poster no.	Title	Presenter	Location	Time/Day
Y3076/A	The Saccharomyces Genome Database Variant Viewer	Olivia Lang	Cypress Ballroom	1:30pm – 2:30pm, Thursday, 7/14
Y3168/C	Saccharomyces Genome Database: How to find what you are looking for	Gail Binkley	Cypress Ballroom	1:30pm – 2:30pm, Thursday, 7/14
Y3170/B	Saccharomyces Genome Database: Outreach and online training services	Kevin MacPherson	Cypress Ballroom	1:30pm – 2:30pm, Thursday, 7/14
Y3191/B	Integrating Post-Translational Modification Data into the Saccharomyces Genome Database	Sage Hellerstedt	Cypress Ballroom	2:30pm – 3:30pm, Thursday, 7/14
Y3157/A	Homology curation at SGD: budding yeast as a model for eukaryotic biology	Stacia Engel	Cypress Ballroom	2:30pm – 3:30pm, Thursday, 7/14

Demo Room

SGD, WormBase, FlyBase, MGI, and ZFIN invite all Conference registrants to come to the Demo Room (Palms Ballroom Canary 3-4) to learn how to make the best use of MOD tools and features for your research and teaching.

All day on Thursday 7/14 and Friday 7/15, other than during scheduled group presentations from 12:45pm – 1:30pm and 6:15pm – 7:30pm, personnel are available in the demo room for one-on-one tutorials, troubleshooting and discussions. Make sure you don’t miss the SGD Demo Room presentations on Thursday 7/14 from 6:15pm – 6:30pm and Friday from 12:45pm – 1:00pm!

Find these SGD staff members at the conference:

Mike Cherry	Stacia Engel	Pedro Assis	Gail Binkley
Sage Hellerstedt	Kalpana Karra	Olivia Lang	Kevin MacPherson

Categories: Announcements, Conferences

Some Like it Hot

June 28, 2016

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According to an AFI poll, the best comedy of all time was the 1959 film “Some Like It Hot.” In this classic screwball comedy two men have to dress up as women to escape the mob and still make money as musicians. All sorts of hilarity ensues as one of them falls in love with a woman and a man falls in love with the other as a woman.

The key to this comedy is that the two actors, Tony Curtis and Jack Lemmon, have to play both the male and female parts. If they were played by separate actors and actresses, the movie would die at the box office. It would be a lethal mutation.

A new study by Solis and coworkers in Molecular Cell presents evidence that in yeast, the heat shock transcription factor Hsf1p is a bit like Tony Curtis and Jack Lemmon—it plays dual roles, both in maintaining basal levels of various heat shock proteins and in turning the appropriate genes up in response to a heat shock. This is different than in mammalian cells where HSF1 is only responsible for turning up heat shock genes in response to a spike in temperature. Something else maintains the levels of these proteins needed for survival.

So yeast is more like the comedy “Some Like it Hot,” or perhaps Tootsie, while mammalian cells are more conventional comedies where different actors play the male and female roles. Because Hsf1p plays a dual role in yeast, its deletion causes the cell to die. Mammalian cells can survive without HSF1 as long as it doesn’t encounter any temperature spikes.

Solis and coworkers started out by coming up with a way to dissociate the genes that Hsf1 regulates under normal conditions from those upregulated under heat shock conditions. For this they used the “Anchor-Away” approach to remove Hsf1p from the nucleus under normal conditions.

Basically, they co-expressed HSF1 fused to FRB, the FKBP rapamycin-binding domain, and a ribosomal protein L13A-FKBP12 fusion. When they add rapamycin to this strain, the two proteins heterodimerize and Hsf1p is dragged out of the nucleus. They confirmed that Hsf1p was gone from the nucleus within a few minutes.

Next, they used native elongating transcript sequencing (NET-seq) 15, 30, and 60 minutes after rapamycin addition to see which genes were affected when Hsf1p left the nucleus. They found that only 25 genes were repressed and five were induced at these time points. Using RNA-seq and ChIP of Hsf1p they showed that Hsf1p was probably responsible for the expression of 18 of the 25 repressed genes and none of the induced ones.

So yeast Hsf1p is involved in the basal expression of a number of chaperone genes. In a set of experiments that I don’t have time to go over here, they also showed that most of the heat shock response was independent of Hsf1p in yeast. Their data suggests that Msn2/4p may be the key player instead.

They next did a similar set of experiments in mammalian cells but with a couple of differences. First off, these cells can survive HSF1 deletion, meaning they didn’t need to do anything fancy—they just used CRISPR/Cas9 to delete the gene in mouse embryonic stem cells and mouse embryonic fibroblasts.

Under normal conditions they found that the deletion of this gene caused two genes to go up in expression and two to go down. This is what you might expect by chance suggesting that in mammalian cells, HSF1 isn’t involved in basal expression of any genes.

They next used RNA-seq to compare gene expression of these cells and their undeleted counterparts under normal and heat shock conditions. They found a set of nine genes that were induced in both wild type cells and repressed in the HSF1-deleted cells under heat shock conditions. Eight out of nine of these are involved in chaperone pathways and they overlap surprisingly well with the yeast genes that Hsf1p controls under basal conditions.

Taken together these experiments paint an interesting picture. In yeast, HSF1 is mostly responsible for the basal expression of chaperone genes, and in mouse cells it is a key player in the heat shock response of a similar set of genes. This suggests that deletion of HSF1 is lethal in yeast because the decreased expression of one or more of the genes it regulates under normal conditions.

They tested this by expressing 15 of the 18 genes (three are redundant to some of the others) on four different plasmids and saw that a yeast strain that is deleted for HSF1 now survives. So one or more of these genes is responsible for yeast death in the absence of HSF1.

Through a process of elimination, Solis and coworkers found that the key genes were SSA2, a member of the HSP70 family, and HSC82, an HSP90 family member. The decrease in expression of these two genes cause by the deletion of HSF1 results in a dead yeast cell.

These experiments are so cool. In yeast, HSF1 makes sure there is enough of these chaperones around in good times to fold proteins properly and has a minor role in the heat shock response, while in mouse cells, the same gene plays no real role in basal levels of expression of chaperone genes and instead is critical for responding to heat shock. The protein regulates similar genes, just under different conditions.

These neat science experiments can tell us more about diseases, like cancer too. Turns out that some cancer cells may be more like yeast cells in that deletion of HSF1 stops them from growing and causes an increase in poisonous protein aggregates which may give us a new way to target HSF1-dependent cancers. For example, it may be that targeting Hsp70 or Hsp90 could be useful for treating HSF1-dependent cancers.

In cancer cells then, HSF1, like Dustin Hoffman in Tootsie, Milton Berle in the Milton Berle Show, or Bugs Bunny in many different cartoon shorts, takes on dual roles in the cell. And as we learned from yeast, this could be these cancers’ Achilles heel.

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

Categories: Research Spotlight, Yeast and Human Disease

Support Model Organism Databases!

June 22, 2016

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Model Organisms such as yeast, worm, fly, fish, and mouse are key drivers of biological research, providing experimental systems that yield insights into human biology and health. Model Organism Databases (MODs) enable researchers all over the world to uncover basic, conserved biological mechanisms relevant to new medical therapies. These discoveries have been recognized by many Nobel Prizes over the last decades.

NHGRI/NIH has recently advanced a plan in which the MODs will be integrated into a single combined database, along with a 30% reduction in funding for each MOD (see also these Nature and Science news stories). While integration presents advantages, the funding cut will cripple core functions such as high quality literature curation and genome annotation, degrading the utility of the MODs.

Leaders of several Model Organism communities, working with the Genetics Society of America (GSA), have come together to write a Statement of Support for the MODs, and to urge the NIH to revise its proposal. We ask all scientists who value the community-specific nature of the MODs to sign this ‘open letter’. The letter, along with all signatures, will be presented to NIH Director Francis Collins at a GSA-organized meeting on July 14, 2016 during The Allied Genetics Conference in Orlando. We urge you to add your name, and to spread the word to all researchers who value the MODs.

In other words, sign this letter!

Categories: Announcements, News and Views, Yeast and Human Disease

Look Before You Leap…Into DNA Repair

June 09, 2016

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Sometimes in an emergency, it can be useful to take a pause before trying to fix a problem. If the ambulance is on the way you may not want to start removing someone’s appendix right then and there. Yes you may save them, but the ambulance and EMTs will do less damage to the patient once they get there.

The same sort of logic applies to cells too. For example, a double stranded break is a deadly emergency that can wreak havoc with a cell’s genome.

The cell can deal with this in a few ways; the big two being non-homologous end joining (NHEJ) and homologous recombination (HR). NHEJ is the simplest in that the broken ends are simply stuck back together. However, it often results in a bit of DNA damage as a few bases are added or lost at the ligation point.

The other option, homologous recombination (HR), involves using a homologous DNA region as a template to essentially resynthesize the broken area. There are two possible ways this can happen in a cell: gene conversion and break induced replication (BIR).

If both ends are available without too much of a gap and in the right orientation, the cell opts for gene conversion, the safer of the two options. Only a small section of DNA is resynthesized, keeping most of the original DNA intact.

It is a different story for BIR, the second approach. Here, a large swath of DNA gets resynthesized, meaning a big loss of heterozygosity (LOH)—two sections of DNA are now identical over a large region. BIR only happens when there is only one end available or when there is a big gap of missing DNA.

Of the two HR possibilities, gene conversion is preferable over BIR. This is why the cell wisely waits to make sure there is no other option before starting down this path. This pause goes by the name of recombination execution checkpoint (REC).

A new study by Jain and coworkers out in GENETICS has identified two of the key players involved in this checkpoint—SGS1 and MPH1. Both are highly conserved 3’ to 5’ helicases.

These researchers found that when both are deleted, the REC disappears. And that isn’t all. In situations where the wild type cell would choose to repair its DNA by BIR, the double deletion strain no longer does. Instead, it now uses a process that is more similar to gene conversion.

Jain and coworkers found this using a reporter that contained an HO endonuclease site in the middle of the LEU2 gene. Once the HO endonuclease is activated, it makes a double strand DNA break, cutting the LEU2 gene in half.

The cell was provided with a variety of templates to be used in HR. One of these only provides the part of the LEU2 gene to the right of the HO endonuclease site. As only one of the ends has homology to the cleaved LEU2 gene, with this template, the cell can only use BIR to repair the break.

The researchers saw a huge increase in how fast the DNA was repaired using the BIR-only template in the strain deleted for both sgs1 and mph1 compared to the wild type strain. The double mutant repaired the DNA using BIR nearly as quickly as a wild type cell could using gene conversion. The pause before repair was essentially lost in the double mutant.

The double deletion strain wasn’t just faster with the BIR-specific template either. It repaired DNA via this pathway about 4 times better than the wild type strain did.

There are at least a couple of different reasons why the double mutant could be so much better at repairing DNA in BIR situations. In the first, the cell is just better at BIR—it can initiate the BIR pathway much more quickly than wild type. The second possibility is that this double mutant isn’t using the BIR pathway anymore and is using something closer to gene conversion.

Jain and coworkers found that the second option is the more likely of the two. The way they figured this out was to make a mutation in the POL30 gene, a gene required for DNA repair by BIR but not gene conversion. So, they tested what happens when POL30 is mutated in the wild type and the sgs1 mph1 double deletion strains.

They found that while a dominant negative mutant of pol30 had the predicted effect of severely compromising repair in wild type cells using their BIR-specific reporter, it had no effect in the double deletion mutant. Since Pol30p is needed for the BIR pathway, the strain deleted for sgs1 and mph1 must be using a different pathway to fix the DNA damage. So the pause is eliminated because the cell isn’t really using the BIR pathway anymore.

We don’t have time to go into it here, but there is a lot more research in this paper that looks at why the REC might be lost and that probes the differences in how MPH1 and SGS1 influence the BIR pathway that I encourage you to read. For example, deleting SGS1 is not identical to deleting MPH1 in terms of the BIR DNA repair pathway. And each single mutant still uses the BIR DNA pathway as the pol30 mutation severely compromises the ability of each to repair the BIR-specific reporter.

There is a lot more fascinating stuff like this in the study. The bottom line, though, is that MPH1 and SGS1 are the level-headed people urging folks not to panic and to wait for the EMTs to get to the accident scene to help. When MPH1 and SGS1 are gone, the cell dives right in and starts repairing breaks without waiting for the safest option—gene conversion. Who knows what havoc is wreaked in their absence!

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

Categories: Research Spotlight

New High-throughput GO Annotations Added to SGD

June 06, 2016

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We’ve added 1,400 high-throughput (HTP) cellular component GO annotations from a new paper published by Maya Schuldiner’s lab. In this paper, Yofe et al., 2016 devised and implemented a methodology, called SWAT (short for SWAp-Tag), creating a parental library containing 1,800 strains, all known or predicted to localize to the yeast endomembrane system. Once created, this novel acceptor library serves as a template that can be ’swapped’ into other libraries, thus facilitating the rapid interconversion to new libraries by simply replacing the acceptor module with a new tag or sequence of choice. As proof of principle, this paper describes the parental library (N’ SWAT-GFP), and its utility as a gateway to the construction of two additional libraries (N’ mCherry and N’ seamless GFP). A high-content screening platform was used to generate images that were then manually reviewed and used to assign subcellular locations for proteins in these collections. Based on these results, SGD has incorporated GO annotations for proteins when at least two of three tags gave the same cellular localization. In addition, Locus Summary page descriptions for genes within this collection that did not have a known cellular location prior to this study have been updated. Finally, this study also provides access to a list of proteins predicted to contain signal peptides using three different algorithms. We would like to thank Maya Schuldiner and members of her lab for help with the integration of this information into SGD.

Categories: New Data

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