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Flashcards in Gene interactions Deck (33)
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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
Model cell
Short generation time
Can be frozen
Can be replicated
Basic, biomedical and industrial applications


Describe yeast mitosis

Spindle pole body duplication
Bud emergence
DNA replication
Nuclear migration
Spindle formation
Chromosome segregation
Nuclear division


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



Describe ISA QTL

Pick individual clones (haploid)
Sequence individually


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