Gene Duplication

Question 1

types of gene duplication

Answer 1

• tandem- individual genes
• segmental
• chromosome duplication
• whole genome duplication

Question 2

Tandem duplicates

Answer 2

found in clusters of 2 or more members, usually 2-6/cluster

• sometimes clusters interrupted by non-related gene
• • due to recombination effect
• 14-17% of genes in human genome
• (+) correlation with recombination rate
• usually formed by unequal crossing over
• if promoter gene not duplicated – altered gene regulation or pseudogene
• can undergo recombination– concerted evolution

Question 3

unequal crossing over

Answer 3

mechanism for gene duplication

- can result in extra copy of gene

Question 4

retroposition

Answer 4

mRNA revere transcribed to cDNA which is randomly inserted into genome
- parental gene can reside in different chromosome

Question 5

segmental duplication

Answer 5

1kb to over 200kb

• 5% of human genome, on all chromosomes
• duplicative transpositions of small portions of a chromosome
• common in pericentromeric and subtelomeric regions
• identified by computational methods and by fluorescent in situ hybridization

Question 6

pericentromeric regions

Answer 6

Situated near, or on each side of, the centromere of a chromosome

Question 7

subtelomeric regions

Answer 7

Subtelomeres are segments of DNA between telomeric caps and chromatin

Question 8

Dispersed duplications

Answer 8

generated by retroposition or DNA transposition after gene formation

Question 9

Retroposed duplications

Answer 9

generated by retroposition

some have regulatory elements some become pseudogenes

Question 10

fates of gene duplication

Answer 10

• one copy lost or loses function= pseudogenes
• both copies retain original function
• neofunctionalization or regulatory neofunctionalization
• subfuntionalization

Question 11

neofunctionalization

Answer 11

one copy of duplicated gene gains new function or expression pattern
- can also be regulatory neofunctionalization – new expression pattern

Question 12

subfunctionalization

Answer 12

original function or expression pattern is divided among duplicates
- regulatory: change in expression pattern

Question 13

Pseudogenes

Answer 13

common in eukaryote genomes
- derived from functional genes but nonfunctional
-rapid rate of substitutions/ INDELs
- evolve neutrally
- useful for evaluating neutral substitution rate
- eventually deleted or sequence becomes unrecognizable
Features:
- lack of transcription or premature stop codon
- or INDEL that disrupts reading frame
- incorrect splicing

Question 14

selection on duplicated genes

Answer 14

positive (KA/KS >1)

• selection promotes fixation of advantageous alleles
• increased sequence divergence
• example pathogen receptors

purifying selection (KA/KS <1)

• selection prevents fixation of deleterious allele
• results in LESS sequence divergence
• ka/ks close to 0= strong
• close to 1=weak or relaxed purifying selection

concerted evolution
- duplicates remain similar in sequence because of crossing over

Question 15

gene families

Answer 15

formed by gene and genome duplication

• consists of paralogs
• can range in size, up to 100s of members
• ex MADS-box, cytochrome p450 etc
• relationships within families can be deduced by phylogenetic analyses

Question 16

what can be inferred from ancestral expression pattern and function

Answer 16

neofunctionalization or subfunctionalization

Question 17

how to evaluate rates of sequence evolution

Answer 17

rates of non-synomous to synomous genes (Ka/Ks ratios)

Question 18

How can genes undergo neofunctionalization

Answer 18

• mutations in amino acid sequences or structural changes in sequences (INDELs)

if regulatory neofunctionalization
- with or without changes in function of protein coding genes

Question 19

retroposition

Answer 19

mRNA is reverse transcribed to cDNA and inserted into genome randomly