New & Noteworthy
Proteome-wide abundance data
March 11, 2019
SGD has now incorporated proteome-wide protein abundance data obtained from a comprehensive meta-analysis by Ho et al., 2018. The authors normalized and combined 21 different S. cerevisiae protein abundance datasets—including data from both untreated cells and cells treated with various environmental stressors—to create a unified protein abundance dataset where all values are in the intuitive units of molecules per cell. The original datasets were initially obtained using different methodologies (mass spectrometry, fluorescence microscopy, flow cytometry, and TAP-immunoblot), allowing Ho et al. to evaluate the strengths and weaknesses of these methods in addition to providing the community with a comprehensive reference map of the yeast proteome.
Normalized abundance measurements and associated metadata from untreated and treated cells are displayed in tabular form in the experimental data section of protein-tabbed pages (e.g. CDC28). Several different controlled vocabularies have been employed to standardize the metadata display. In addition, calculated median abundance and median absolute deviation (MAD) values are displayed in the protein section of Locus Summary pages (e.g. PHO85). Two new YeastMine templates have been created to provide access to these data: Gene -> Protein Abundance and Gene -> Median Protein Abundance
Special thanks to Brandon Ho and Grant Brown for generating this comprehensive reference map of protein abundance, and for their help in making this data available to the larger community.
Categories: New Data
Apply Now for the 2019 Yeast Genetics and Genomics Course
March 05, 2019
For almost 50 years, the legendary Yeast Genetics & Genomics course has been taught each summer at Cold Spring Harbor Laboratory. (OK, the name didn’t include “Genomics” in the beginning…). The list of people who have taken the course reads like a Who’s Who of yeast research, including Nobel laureates and many of today’s leading scientists. The application deadline is April 1st, so don’t miss your chance! Find all the details and application form here. This year’s instructors – Grant Brown, Greg Lang, and Elçin Ünal – have designed a course (July 23 – August 12) that provides a comprehensive education in all things yeast, from classical genetics through up-to-the-minute genomics. Students will perform and interpret experiments, learning about things like:
- Finding and Analyzing Yeast Information Using SGD
- Isolation and Characterization of Mutants
- Yeast Transformation, Gene Replacement by PCR, and Construction and Analysis of Gene Fusions
- Tetrad Analysis
- Genome-scale Screens Using Synthetic Genetic Array (SGA) Methodology
- Deep Sequencing Applied to SNP Mapping and Deep Mutational Scanning
- Exploring Synthetic Biology with CRISPR/Cas9-directed Engineering of Biosynthetic Pathways
- Computational Methods for Data Analysis
- Modern Cytological Approaches Including Epitope Tagging and Imaging Yeast Cells Using Fluorescence Microscopy
Techniques have been summarized in a completely updated course manual, which was recently published by CSHL Press.
There’s fierce competition between students at CSHL courses in the Plate Race, a relay in which teams carry stacks of 40 Petri dishes (used, of course).
Scientists who aren’t part of large, well-known yeast labs are especially encouraged to apply – for example, professors and instructors who want to incorporate yeast into their undergraduate genetics classrooms; scientists who want to transition from mathematical, computational, or engineering disciplines into bench science; and researchers from small labs or institutions where it would otherwise be difficult to learn the fundamentals of yeast genetics and genomics. Significant stipends (in the 30-50% range of total fees) are available to individuals expressing a need for financial support and who are selected into the course.
Besides its scientific content, the fun and camaraderie at the course is also legendary. In between all the hard work there are late-night chats at the bar and swimming at the beach. There’s a fierce competition between students at the various CSHL courses in the Plate Race, which is a relay in which teams have to carry stacks of 40 Petri dishes (used, of course). There’s also a sailboat trip, a microscopy contest, and a mysterious “Dr. Evil” lab!
The Yeast Genetics & Genomics Course is loads of fun – don’t miss out!
Categories: Announcements
Register for the 29th International Conference on Yeast Genetics and Molecular Biology (ICYGMB)
January 24, 2019
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
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.
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
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