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The Yeast Orphan Gene Project: Finding a place for ORFans to “GO”

Genomic sequence of model eukaryote Saccharomyces cerevisiae completed in 1996. (12.1 Mb) Despite 16 years of intense research, function of nearly 30% of putative open reading frames (ORFs) remain unknown. In genomics, termed “ORFans” Likely have function specific to fungi.

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The Yeast Orphan Gene Project: Finding a place for ORFans to “GO”

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  1. Genomic sequence of model eukaryote Saccharomyces cerevisiae completed in 1996. (12.1 Mb) Despite 16 years of intense research, function of nearly 30% of putative open reading frames (ORFs) remain unknown. In genomics, termed “ORFans” Likely have function specific to fungi. Potentially important to food and drug industry. The Yeast Orphan Gene Project: Finding a place for ORFans to “GO”

  2. To determine the cellular function of a yeast ORFan gene by: • Reviewing basic gene information at yeastgenome.org • Analyzing data from a comparative RNAseq analysis of the deletion strain and the isogenic wild type strain to look for global changes in mRNA profiles • Grouping genes of similar expression profiles • Using pathway analysis to putatively link the ORFan to a Gene Ontology (GO) function. Module Research Goals https://encrypted-tbn2.gstatic.com/images?q=tbn:ANd9GcQpx-HhripNInzlpjfIepFTmma0q8k-okvJq9_9Uml0SjsssDgPag

  3. Be able to access and use the basic search tools at yeastgenome.org Understand the process of RNAseq analysis from RNA isolation through cDNA construction and sequencing. Be able to load RNAseq data into the Galaxy platform for quality assessment, transcriptome alignment and differential expression analysis. Be able to analyze differentially expressed genes for putative pathway placement. http://craftbeeracademy.com/wp-content/uploads/2012/09/yeast_large_winter.gif Learning goals

  4. Vision and change core competencies 1. ABILITY TO APPLY THE PROCESS OF SCIENCE: 2. ABILITY TO USE QUANTITATIVE REASONING : 3. ABILITY TO USE MODELING AND SIMULATION: 4. ABILITY TO TAP IN TO THE INTERDISCIPLINA RY NATURE OF SCIENCE: www.exploreyeast.com

  5. 1. Ability to apply the process of science • Specifically, the ability to interpret and analyze data • 2. Ability to use quantitative reasoning • Specifically, the understanding and using statistics to analyze data • 3. Ability to use modeling and simulation • Specifically, the use of pathway analysis to assign gene function • 4. Ability to tap into the interdisciplinary nature of science • Specifically, learning and using computational tools. • www.exploreyeast.com Vision and change core competencies

  6. GCAT-SEEK sequencing requirements • Use of IlluminaHiSeq • 10-100 x 106 reads per sample, 50 – 150 nt • Do not need long sequencing runs for RNAseq • Program requirements for data analysis • Standard Mac or PC with internet access • Galaxy account (is this enough computing power for a yeast reference genome?) • Do not need to assemble because Saccharomyces reference genome is available Technology requirements www.mayo.edu

  7. Goals of yeast ORFan project: • organize a consortium of undergraduate researchers and PIs to assign functions to S. cerevisiae ORFans. • pilot project for summer of 2013 • generate updated yeast ORFan list; draft a flow chart outlining process for determining the function of yeast ORFans • begin to work through the drafted process with three selected ORFans • design and begin RNAseq analysis of expression profiles in two ORFan deletion strains. • Full project: Students between consortium schools collaborate as teams to assign a gene ontology (GO) term to a given ORFan. • Ultimately, the yeast orphan gene project aims to use the process of determining ORFan gene function as a tool to gain experience in scientific research, • collaboration and leadership. www.bsse.ethz.ch Module Research Goals

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