Gene interactions Flashcards
What is annotation?
The determination in total genome sequence of the open reading frames encoding proteins and determination of mRNA transcripts, introns and exons from sequenced genomes.
What is the process of genome annotation?
Determining ORFs and identify the start, stop, and promoter sequences
Assign transcriptosome
Determine numbers and types of regulatory RNAs
Assigning function to genomic sequences
Determine transiently heritable epigenetic modifications that affect gene expression
What is epigenetics?
Heritable changes to DNA expression and its associated proteins that alter gene expression without altering the DNA sequence
What is Gene ontology?
Genes being meaningfully grouped by three categories of likeness
Biological process
Molecular function
Cellular component
Why do we study yeast?
Yeast genetics tools are superior to other organisms and one can use it as a model to understand basic cell biology and develop relevant hypotheses to test in more complex organisms.
What are the characteristics of S. cerevisiae?
Simplest eukaryote Fungus Model cell Short generation time Phototroph Can be frozen Can be replicated Basic, biomedical and industrial applications
Describe yeast mitosis
Start Spindle pole body duplication Bud emergence DNA replication Nuclear migration Spindle formation Chromosome segregation Nuclear division Cytokinesis Growth
What is epistasis?
Where the phenotype gets more than the sum of the parts of contributing genes
Measurement of epistasis between genes allows characterisation of functional genetic interaction networks
What is synthetic lethality?
An epistatic phenomenon in which pairs of individually nonessential genes interact to cause double mutant inviability
What is an additive interaction?
1 - (1st growth reduction x 2nd growth reduction) = total growth reduction
What is an aggravating interaction?
Negatively epistatic
The double mutant fitness is lower than the additive expected which implies separate but compensatory pathways
What is an alleviating interaction?
Positively epistatic
Fitness is greater than expected but the interaction is in the same pathway or complex
What does synthetic lethality reveal?
Functional redundancy
Occurs in compensating pathways producing some essential protein or complementing components of a complex process
What is synthetic genetic array?
A method to construct non-essential deletion mutant pairs
Describe the process of SGA
Mating and diploid selection in histidine auxotrophs
When grown in medium containing histidine, diploids survive, haploids killed
Sporulate diploids by replicating onto plates with minimal nutrients
Two mating types
Select haploids by growing in Histidine minus medium
Double mutant haploids selected in presence of kan and nat (select for query and dma gene mutants)
Name 3 features of genetic interactions
Functional unit of the cell
Resultant integration of the network acting in concert within the cell
Local networks enriched for genes that share the phenotype of the query gene
What happens when we replace a query gene with a small molecule inhibitor?
SMI and mutant array may give the same syntheticly lethal profile as query mutant and mutant array
Describe the advantages that chemical genetics make have over mutations
SMIs are quicker
SMIs are reversible can can be titrated
SMIs allow study of essential gene interactions
What are we looking for in forward chemical genetics?
An unknown protein target
What are we looking for in reverse chemical genetics?
An SMI that will bind to a known protein
What is competition growth assay?
Pooling of deletion mutants into one flask and the growth of the mutants in the presence or absence of the drug
Barcodes are amplified
They are hybridised to microarrays
Barcodes identified
What does QTL stand for?
Quantitative Trait Loci
What does QTL analysis provide?
A way to map function directly to marker positions on genomes which may allow mapping of a function to a genome sequence
Name 3 principles of QTL mapping
A quantitative trait may comprise a number of QTL though one QTL is the result of only one gene (locus)
Trait variance in a population will be greater if there are a number of contributing QTL loci
QTL contributing to a quantitative trait may be on the same or different linkage group
What is a LOD score?
A method to test the significance of linkage to a marker
How could you determine QTL?
Candidate gene association
Positional cloning
Narrowing down regions with further backcrossing
Linkage disequilibrium mapping
Name the three types of QTL analysis
Linkage analysis
Fine mapping
Candidate prioritisation and testing
Describe X-QTL
Generation of segregating populations of a very large size
Selection based phenotyping of these popultions to recover large number of progeny with extreme trait values
Quantitative measurement of pooled allele frequencies across the genome
Describe eQTL
Identifies loci that control transcript levels
Tests the linkage between variation in expression and genetic polymorphisms
The only considerable difference between QTL and eQTL is eQTL studies can involve a million or more expression microtraits
The final steps in defining DNA variants that cause variation in traits are usually difficult and require a second round of experimentation
Can be cis or trans (local or distant)
Name the three QTL mapping methods
ISA
BSA
RHS
Describe ISA QTL
Pick individual clones (haploid)
Sequence individually
Map
Describe BSA QTL
Pool clones (haploid)
Add control to flask A
Add selective pressure to flask B
Sequence the pool
Describe RHS QTL
Construct deletion strains (diploid)
Pool strains
Add control and selective pressure
Hybridize
