Midterm 2 - Notes 3 (Part 2) Flashcards
What are modules?
Any functionally discrete portion of a locus
What are 3 examples of modules?
- Cis regulatory element
- Protein domain (exon)
- Alternative splice site
What does redundancy imply?
That both genes have the same function
- cant be maintained over long evolutionary period
What is the most common fate of duplication?
Loss of function
- degeneration of a copy (can occur after of during duplication)
Sub-functionalization
Is a neutral mutation process in which each paralog retains a subset of its original ancestral gene
- degeneration of different modules in each copy (LOF)
- different functions are maintained after duplication
What do the duplicated genes in sub-functionalization do?
Together they fulfill the function of the original gene
- maintaining (purifying) selection acts on both copies
- allows for further specialization of functions
What is assumed in sub-functionalization?
Original gene contains multiple functions
What kind of selection does sub-functionalization use?
Purifying selection
Purifying selection
Is the selective removal of alleles that are deleterious
- selective pressures to maintain existing functions
Neo-functionalization
Is the perspective that all integration is the result of past integration
- evolution of new modules in one copy (one copy stays the same)
- the other copy acquires a new function
When may neo-functionalization occur?
Either during or after duplication
What kind of selection does neo-functionalization use?
Positive selection
Positive selection
Is the process by which new advantageous genetic variants sweep a population
How does neo-functionalization get a new gene copy?
Through translocation
Genome mining
Refers to deriving various information about the organism based on genome analysis
Sequence analysis
Is the process of subjecting a DNA, RNA or peptide sequence to nay of a wide range of analytical methods to understand its features, functions, structure or evolution
Expression profiling
Is the measurement of the activity of thousands of genes at once, to create a global picture of cellular function
What is intronnless and example of?
Hallmark
What were the steps for the retro-copies experiment? (6)
- Started off with a collection of all protein coding sequences (not the introns), including pseudogenes
- included known function of protein function sequences and suto regions - Used a set of mRNA sequences and performed a similar search against complete human genomes
- Found 4 hits without gaps
- This gave them a collection of all intronless genes in the human genome which would be candidates for retro copies
- this means that not all intronless genes are retro copies (which is why they looked further) - Took the candidates and did a similar sequence search but included the introns in the search
- looked fro additional hits that had gaps (at least 50% similar –> paralog) - Found 3,951 putatuve retro-copies
- of these, 705 (18%) were intact (the rest were pseudogenes
What does it mean if they found no gaps in their hit?
That no introns were in the sequence
- because introns creates gaps
What did it mean when they found intact sequence? (2)
- No premature stop codons
2. No frame shift mutations
Ks
Silent sites
Silent sites
Not changing encoded amino acids
- change DNA sequence though (but not the function)
Why should silent mutations accumulate over evolution?
Because they are under no selection and should accumulate over time based on mutation rate
