New & Noteworthy

Register for the 29th International Conference on Yeast Genetics and Molecular Biology (ICYGMB)

January 24, 2019


icygmb logo

The 29th International Conference on Yeast Genetics and Molecular Biology (ICYGMB) will be held at the the Swedish Exhibition & Congress Centre, Gothenburg, Sweden, from August 18-22, 2019.

The ICYGMB brings together scientists from all around the globe to present and discuss cutting-edge research on yeast. Described as the “most important event in yeast research“, the conference facilitates an environment where the international yeast community can freely exchange information, strike collaborations, and build new projects and alliances.

The 2019 meeting is enriched with over 50 speakers and a program that aims to provide an up-to-date overview of the most exciting topics in yeast research. The program includes lectures and workshops that discuss topics such as cell signaling, evolutionary genetics, aging and disease models, yeast biotechnology, and more.

Registration and abstract submission are now open. The early registration deadline is April 1. The abstract submission deadline for oral presentations is May 15, whereas July 31 is the deadline for abstracts that will be included in the Conference Abstract book.

Categories: Conferences

New Data Tracks added to JBrowse

January 15, 2019


SGD has updated our JBrowse genome browser with 157 new data tracks related to genome-wide experiments and omics data for you to explore. You can easily access these new tracks, which visualize data from the twenty publications listed below, by entering JBrowse and clicking on the left-hand “Select tracks” tab. Then, search for the PMID associated with the reference of interest.

Note that some references appear more than once, as they have multiple data tracks associated that belong to different categories in JBrowse.

For more information on using JBrowse, be sure to check out our playlist of JBrowse video tutorials on YouTube. If you have any questions or feedback about the new tracks or about our genome browser, please don’t hesitate to contact us.

Transcription & Transcriptional Regulation

Reference PMID Description in JBrowse
Baptista et al. (2017) 28918903 ChEC-seq to map the genome-wide binding of the SAGA coactivator complex in budding yeast.
Castelnuovo et al. (2014) 24497191 Genome-wide measurement of whole transcriptome versus histone modified mutants
El Hage et al. (2014) 25357144 Genome-wide distribution of RNA-DNA hybrids identifies RNase H targets in tRNA genes retrotransposons and mitochondria.
Freeberg et al. (2013) 23409723 Mapped regions of untranslated, polyadenylated transcriptome bound by RNA-binding proteins (RBPs)
Kang et al. (2015) 25213602 Genome-wide transcript profiling by paired-end ditag sequencing
Lee et al. (2018) 29339748 ChIP-Seq, mRNA-seq, ATAC-seq, and MNase-seq samples in wild-type (WT) and various mutants were prepared using Saccharomyces cerevisiae.
Park et al. (2014) 24413663 Simultaneous mapping of RNA ends by sequencing (SMORE-seq) to identify the strongest transcription start sites and polyadenylation sites genome-wide
Rossbach et al. (2017) 28924058 Authors utilized the Calling Cards Ty5 retrotransposon insertion method to identify binding sites of cdc7kd, cdc7kdΔcterm and Gal4 transcription factor within the yeast genome.
Schaughnency et al. (2014) 25299594 Genome-wide identification of transcription termination sites; pA pathway and non-polyadenylation pathway in strains missing Sen1p or Nrd1p

Histone Modification

Reference PMID Description in JBrowse
Castelnuovo et al. (2014) 24497191 Genome-wide measurement of whole transcriptome versus histone modified mutants
Hu J. et al. (2015) 26628362 ChIP-seq and MNase-seq to determine how histone modifications and chromatin structure directly regulate meiotic recombination. Identified acetylation of histone H4 at Lys44 (H4K44ac) as a new histone modification
Joo et al. (2017) 29203645 Next-Generation-Sequecing (NGS)-derived genome-wide occupancy of TAF (Taf1) compared with other basal initiation components (TBP and TFIIB), histones (H3, H4, Htz1 and H4 acetylation) and histone regulator complexes (Swr1, Bdf1) in S. cerevisiae
Kniewel et al. (2017) 28986445 ChIP-seq to determine the whole-genome enrichment of Mek1 targeted histone H3 threonine 11 phosphorylation (H3 T11ph) during Saccharomyces cerevisiae meiosis.
Lee et al. (2018) 29339748 ChIP-Seq, mRNA-seq, ATAC-seq, and MNase-seq samples in wild-type (WT) and various mutants were prepared using Saccharomyces cerevisiae.
Weiner et al. (2018) 25801168 Examining chromatin dynamics through genome-wide mapping of 26 histone modifications at 0 4 8 15 30 and 60 minutes after diamide addition using MNase-ChIP

Chromatin Organization

Reference PMID Description in JBrowse
Chereji et al. (2014) 29426353 Genome binding/occupancy profiling of single nucleosomes and linkers by high throughput sequencing
Gutierrez et al. (2017) 29212533 Authors sought to correct sequence bias of MNase-Seq with a method based on the digestion of naked DNA and the use of the bioinformatic tool DANPOS
Hu Z. et al. (2014) 24532716 Genome-wide measurement of nucleosome occupancy during cell aging
Hu J. et al. (2015) 26628362 ChIP-seq and MNase-seq to determine how histone modifications and chromatin structure directly regulate meiotic recombination. Identified acetylation of histone H4 at Lys44 (H4K44ac) as a new histone modification
Joo et al. (2017) 29203645 Next-Generation-Sequecing (NGS)-derived genome-wide occupancy of TAF (Taf1) compared with other basal initiation components (TBP and TFIIB), histones (H3, H4, Htz1 and H4 acetylation) and histone regulator complexes (Swr1, Bdf1) in S. cerevisiae
Lee et al. (2018) 29339748 ChIP-Seq, mRNA-seq, ATAC-seq, and MNase-seq samples in wild-type (WT) and various mutants were prepared using Saccharomyces cerevisiae.

RNA Catabolism

Reference PMID Description in JBrowse
Geisberg et al. (2014) 24529382 Half-lives of 21,248 mRNA 3_ isoforms in yeast were measured by rapidly depleting RNA polymerase II from the nucleus and performing direct RNA sequencing throughout the decay process.
Smith et al. (2014) 24931603 Identification of genome-wide transcripts; looking at nonsense-mediated RNA decay pathway

Transposons

Reference PMID Description in JBrowse
Lee et al. (2018) 29339748 ChIP-Seq, mRNA-seq, ATAC-seq, and MNase-seq samples in wild-type (WT) and various mutants were prepared using Saccharomyces cerevisiae.
Michel et al. (2017) 28481201 Genome-wide examination of protein function by using transposons for targeted gene disruption
Rossbach et al. (2017) 28924058 Authors utilized the Calling Cards Ty5 retrotransposon insertion method to identify binding sites of cdc7kd, cdc7kdΔcterm and Gal4 transcription factor within the yeast genome.

DNA Replication, Recombination, and Repair

Reference PMID Description in JBrowse
Mao et al. (2017) 28912372 Map of N-methylpurine (NMP) lesion alkalation damage across the yeast genome

 

Categories: New Data

Disease Pages at SGD: Linking Yeast Genetics and Human Disease

December 22, 2018


neurodegenerative_disease

SGD’s Disease Ontology page for neurodegenerative disease

To promote the use of yeast as a catalyst for biomedical research, SGD utilizes the Disease Ontology (DO) to describe human diseases that are associated with yeast homologs. Disease Ontology annotations to yeast genes are now available through SGD’s new Disease pages. Each page corresponds to a Disease Ontology term, such as amyotrophic lateral sclerosis, and lists out all yeast genes annotated to the term by SGD.

Yeast genes with one or more human disease associations will also have a new Disease Summary tab (example: MIP1), accessible from the genes’ respective locus pages. The Disease summary tab shows all manually curated, high-throughput, and computational disease annotations for the yeast gene. Additionally, these pages feature a network diagram that depicts shared disease annotations for other yeast genes and their human homologs.

network_diagram_disease

The shared disease annotations diagram for MIP1

For more information, check out SGD’s Disease Ontology help page. Explore the new Disease pages and features, and be sure to let us know if you have any feedback or questions.

Categories: New Data

Macromolecular Complex Pages Now Available

December 14, 2018


Macromolecular complexes, already retrievable from SGD’s YeastMine data warehouse, are now available on new pages on the SGD website. These new Complex pages (example: GAL3-GAL80 complex) provide manually curated information about the complex as well as helpful links and diagrams. Key features of Complex pages include:

  • Manually curated summaries of the complex’s function and biology
  • A list of all known subunits and other complex participants
  • A Complex Diagram that shows the physical interactions between each subunit
  • Gene Ontology (GO) terms annotated to the complex
  • Images of complex structure from the Protein Data Bank (PDB), if available
  • A network diagram that shows how the complex relates to other complexes in terms of function and shared subunits

Complex pages can be accessed by running a search for the complex, or by visiting the gene summary pages of its subunits. For example, to find the GAL3-GAL80 complex page, simply run a search for “GAL3-GAL80” and click on the Complexes category (symbolized by the gold dot). Or, go to the GAL3 or GAL80 gene page and locate the Complex section.

SGD curated these macromolecular complex data in collaboration with curators at EMBL-EBI’s Complex Portal. Be sure to check out the page for your favorite complex, and let us know if you have any feedback or questions.

Categories: New Data

SK1 Sequence Updated in SGD

November 20, 2018


The alternative reference strain SK1 is a rapid and synchronously sporulating diploid constructed by Kane and Roth in the early 1970’s to study carbohydrate metabolism under sporulation conditions. Whereas the reference strain S288C is notorious for being poor at sporulation, SK1 undergoes sporulation readily, and as such has been widely used to study the genetics of sporulation and meiosis.

The genome of SK1, which was temporarily removed from SGD, is now available once again with an updated sequence provided by Scott Keeney from the Sloan Kettering Institute. You can access the updated SK1 sequence for your favorite genes from the Sequence tab, in the Alternative Reference Strains section (example: ECM22 Sequence page). To access the entire SK1 genome sequence, visit the SK1 Strain page. 

In addition, we have updated following Sequence and Analysis tools to utilize the latest SK1 sequence:

Variant Viewer will be updated in a future release. Be sure to check out these updated tools and resources and let us know if you have any questions or comments.

Categories: Data updates, Website changes

New Protein Localization Resource: YeastRGB

November 14, 2018


yeastRGB

Multiple display units in YeastRGB

YeastRGB is a new resource for exploring protein abundance and localization. Utilizing data from the classical C-terminally tagged GFP yeast library along with new-generation collections derived from SWAp Tag (SWAT) technology, YeastRGB enables simultaneous visualization of dozens of yeast strains imaged with multiple fluorescent tags.

From SGD, you can access YeastRGB through any Protein page (example: Atp12p). The YeastRGB link is located in the Resources section, under Localization. Alternatively, you can visit the YeastRGB website and search for your favorite genes or keywords.

For more information on YeastRGB, see the publication by Dubreuil et al. at Nucleic Acids Research: https://doi.org/10.1093/nar/gky941

Categories: Announcements

Registration Open for the 30th Fungal Genetics Conference

November 07, 2018


The 30th Fungal Genetics Conference takes place next year March 12-17, 2019 at Asilomar Conference Grounds in Pacific Grove, CA. The biennial Fungal Genetics Conference is a place where scientists working on any aspect of fungal genetics–such as gene regulation, evolutionary biology, cell development, fungal-host interactions and more–can come together in a common platform to share ideas and collaborate.

The schedule of events is now available. The conference features multiple workshops, Plenary Sessions with central themes on various aspects of fungal biology, and dozens of diverse Concurrent Sessions where you can attend talks on topics most relevant to your research. The 2019 Perkins/Metzenberg Lecture, which provides perspectives given by a leader in the field of fungal genetics, will be presented by John Taylor from the University of California, Berkeley.

Register soon! The abstract submission deadline and early registration deadline are both in one month, on December 5th 2018.

Categories: Announcements, Conferences

Apply Now for the 2019 Fungal Pathogen Genomics Course

October 30, 2018


Fungal Pathogen Genomics is an exciting week-long course that provides experimental biologists working on fungal organisms with hands-on experience in genomic-scale data analysis. Through a collaborative teaching effort between the web-based fungal data mining resources FungiDB, EnsemblFungi, PomBase, SGD/CGD, MycoCosm, and JGI, students will learn how to utilize the unique tools provided by each database, develop testable hypotheses, and analyze various ‘omics’ datasets across multiple databases.

Daily activities in Fungal Pathogen Genomics will include both individual and group exercises, lectures on the bioinformatics resources provided by various databases, and presentations by distinguished guest speakers. Examples of what you will learn at Fungal Pathogen Genomics include:

  • RNA-seq and SNP analysis and visualization via EuPathDB Galaxy workspace in FungiDB
  • Identification of secondary metabolite clusters in MycoCosm
  • Finding virulence genes and annotation in Ensembl
  • Accessing and analyzing genetic interactions in CGD/SGD
  • Discovering taxonomic conservation or phenotypes in PomBase

The application deadline for the Fungal Pathogen Genomics workshop to be held May 7-12, 2019 at the Wellcome Genome Campus in Hinxton, Cambridge, UK is February 7, 2019.

Don’t miss out – apply now!

Categories: Announcements

SGD Fall 2018 Newsletter

October 05, 2018

SGD periodically sends out its newsletter to colleagues designated as contacts in SGD. This Fall 2018 newsletter is also available on the community wiki. If you would like to receive the SGD newsletter in the future please use the Colleague Submission/Update form to let us know.

Categories: Newsletter

Resistance is Not Futile: How Yeasts Avoid Getting Ill from IILs

September 24, 2018


poison_ivy__batman__by_flo_moshi

In the Batman comics, Poison Ivy is resistant to all natural toxins and diseases (from deviantart)

Resistance to poisoning is a good thing in the cartoon world, where both good and bad guys and gals often have superpowers that render them resistant to all sorts of toxins and poisons. But does that happen in the “real” world that we live in?

Well, some people would say that Keith Richards and cockroaches are the ultimate examples of earthly organisms resistant to every known toxin! But there are other more mundane examples of humans that are resistant or tolerant to certain chemical or organic compounds.

For example, almost everyone knows someone (or themselves) who can’t drink milk, because if they do, they feel really sick, with uncomfortable or even severe gastrointestinal symptoms. These people are said to be “lactose intolerant” (which is NOT an allergy to milk), because their gut can’t digest a sugar called lactose found only in milk and milk-based products.

Interestingly, all humans have the “lactase” gene that allows their body to digest lactose, but lactose intolerant folks have a particular “switch” sequence in their DNA that causes the gene to get totally turned off once they’re not babies anymore.

Hydrolysis_of_lactose

The lactase enzyme splits the disaccharide lactose into galactcose (1) plus glucose (2) (from wikimedia)

However, people who CAN drink milk as adults (“lactose tolerant” people) have a change in their DNA sequence that inactivates the switch. So these people have the lactose-digesting gene turned on and functioning for their whole lives and can consume milk and dairy products even as adults.

This is an example of genomic diversity among human beings, where people’s individual genome sequences have differences that can make them resistant to the negative effects of some foods or chemicals, while other people have little or no tolerance at all.

This type of DNA sequence variation across all the members of a species is called “standing genetic variation” and it’s a very good thing. Why? Because when a changing or novel environment challenges a population, standing genetic variation increases the chance that some individuals can adapt to new types of foods (like what happened with the lactase gene) or have other characteristics that make them better suited to survive in the new environment…or even be resistant to new diseases!

PlanetOfTheApes

In the Planet of the Apes series, “simian flu” kills almost all humans except for those few who are resistant (from deviantart)

But what does all of this have to do with yeast? Well, just like lactose intolerant humans, yeast can get sick when they try to “eat” certain things too, and will fail to grow well in the presence of such compounds. But could there be some yeast individuals somewhere in the world that have tolerance to certain normally-toxic compounds?

This is exactly the question that Higgins and co-workers asked, and in the September issue of Genetics they describe how they found naturally occurring yeast that can tolerate high levels of compounds called “ionic liquids.” And they also discovered the underlying naturally-occurring genetic variations in two genes that make the yeasts more tolerant to these compounds!

So what are ionic liquids and why were these investigators interested in them? Ionic liquids are a type of salt that can exist in a liquid state at temperatures under the boiling point of water or even at room temperature.

One type in particular, “imidizolium ionic liquids” (IILs) are often used in production of biofuels because they efficiently solubilize plant biomass cellulose and help turn it into glucose. The glucose can then be fermented (often by our yeast friend Saccharomyces cerevisiae) into bioethanol or other biofuels.

However, most commonly used S. cerevisiae strains, when grown in the presence of IILs, get very ill. But if IIL-tolerant yeasts could be found, they could help improve the production of cellulosic ethanol and other bioproducts.

Exxon_desert_tanker

Cellulosic biofuels may help decrease worldwide carbon emissions by reducing fossil fuel use (from wikimedia)

Higgins and co-workers decided to make use of the standing genetic variation within the S. cerevisiae species by taking hundreds of different strains of S. cerevisiae, isolated from around the world, and seeing if any of them could grow better in the presence of IILs.

And indeed they found some strains that were extremely IIL-tolerant compared to other S. cerevisiae strains such as beer, wine or lab strains, or even those commonly used in biofuel production! The yeast strain that was the most IIL-tolerant was, surprisingly, a clinical isolate from Newcastle, England.

The researchers then took genomic DNA from this IIL-tolerant strain and chopped it up into large pieces and put the pieces (carried on special plasmids called fosmids) into the common S288C lab strain (which is intolerant to high IILs) to see which regions could allow the lab strain to now grow in the presence of high levels of IILs.

They found two genes that conferred tolerance to the IILs: the SGE1 gene, plus a previously unnamed gene, YDR090C, which had not been studied very much. The proteins made from both genes appear to be located in the plasma membrane of the cell. The authors propose that the tolerant version of the SGE1 protein, already known to be a multidrug efflux pump that exports toxic cationic dyes out of the cytoplasm, is directly involved in the pumping the IILs out of the cells to help yeast tolerate these toxic compounds.

MDR_pump

The Sge1 protein is a multidrug transporter. Similar proteins in humans can cause resistance to anti-cancer drugs (from wikimedia)

The researchers were not able to exactly figure out what YDR090C is doing in the membrane to help cells be resistant to the bad effects of IILs, but they did find out that cells with a deletion of the gene were less tolerant to IILs. They thus named this gene “ILT1” for “Ionic Liquid Tolerant”.

The authors also found that the SGE1 gene from the IIL-resistant “wild” strain from England had a change in its protein sequence relative to the lab strain, but rather than making the protein more efficient at pumping, it looks like the changed protein is more abundant in the cell and thus can just pump out more of the obnoxious IILs.

Whenever they put this resistant gene version into an IIL-intolerant yeast, it did the trick of allowing the strain to grow better in high IILs concentration. This discovery might allow greater use of IIL-treated biomass for the production of biofuels, as it shows one powerful method of increasing the tolerance of biofuel-producing yeast to toxic IILs.

So this is indeed a case where looking at the “standing genetic variation” of a species has helped discover new and useful biotechnological functions in yeast, and also shown us that resistance (to IILs at least) is NOT futile, and may indeed help us make yeast more efficient at making more biofuels!

Resistance might be futile if you’re up against the Borg, but at least yeast can resist IILs!

by Barbara Dunn, Ph.D. and Kevin MacPherson, M.S.

Categories: Research Spotlight

Tags: lignocellulosic biomass, biofuels, variation

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