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Biology 430 > 1st half review > Flashcards

1st half review Flashcards

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1
Q

how can genome size change during evolution of single genus

A

large variation within species– correlation between number of retrotransposons and gene size

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2
Q

How can genomes expand in size?

A
  • amplification of transposons, especially retrotransposons
  • polyploidy (recent)
  • expansion of other non-coding regions
  • large segmental duplications
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3
Q

how can genomes decrease in size?

A
  • recombination that eliminate DNA
    • between repeats or between transposons
  • more deletions relative to insertions
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4
Q

Draw unequal crossing over BTW LTR retrotransposons

A

intra and inter element recombination

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5
Q

Effects of genome size

A
  • variation in distance between genes and gene density
    • due to TEs
  • can vary in different regions of chromosomes
  • can vary in species
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6
Q

cellular effects of genome size increases

A
  • nucleus size
  • cell size
  • duration of cell cycle
  • cell differentiation rate
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7
Q

class 2 TEs

A

DNA elements “cut and paste”

  • transposition through DNA intermediate: element excises and reinserts elsewhere in genome
  • autonomous or non-autonomous elements
    • autonomous - code for transposase
    • non-autonomous – don’t code for transposase
  • terminal inverted repeats
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8
Q

Class 1 elements

A 
RNA elements: retrotransposons
- mRNA intermediate
- usually high copy number
A) LTR retrotransposons
- long terminal repeats in direct orientation
- gag and pol coding regions
- gag= capside like, pol= RT, protease etc.
--Nucleus, RT in cytoplasm, cDNA transport to nucleus
B) non-LTR retrotransposons
- most common in human genomes
- no terminal repeats
- LINEs - autonomous
-SINEs - non-autonomous
--nucleus, priming and RT at target site
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9
Q

Draw DNA, LTR, non-LTR transposons

A

DRAW

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10
Q

effects of TEs that insert into genes

A
  1. insertional mutagenesis
    - insert into exon
    - insert into enhancer
    - insert into repressor
  2. Epigenetic regulation
    - antisense downregulation
    - - inserts into 3’ region and makes antisense RNA to form dsRNA– rna degraded and downregulated
    - epigenetic silencing
    - - metalation of transposon to prevent proliferation
  3. Introduction of new information
    - TEs bring new enhancers/ repressors
    - TEs introduce new splice sites
    - TEs bring new promoter or start site
  4. Transduction!
    - introduce new exon into gene
    - 5’, 3’, or premature polyadenylation
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11
Q

Nested retrotransposons

A
  • transposons often insert into other transposons
    • not selected against
  • each retrotransposon originated later than DNA flanking it
  • can lead to greatly increased distance between genes and to increased genome size
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12
Q

Dating of insertion retroelements

A

for non-nested

  • LTR dating to infer timing
  • LTRs same upon insertion, then diverge
  • LTR divergence level indicates age of insertion
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13
Q

Families of TEs

A
  • phylogenetic analysis of AUTONOMOUS based on ORFs within TEs
  • shows relative TE relatedness
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14
Q

epigenetic silencing of retrotransposons and mechanisms

A 
Transcriptional silencing
- methylation of TE promoters
- chromatin remodeling
Post-transcriptional silencing
- sequence specific RNA degradation
- double stranded RNA, formed by readthrough transcription from neighboring gene
-- inverse of antisense degradation
- siRNAs can target TEs for degradation
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15
Q

paleopolyploidy

A

ancient polyploidy events, more than ~10 mya

  • 2R in vertebrates
  • multiple rounds during flowering plant evolution
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16
Q

paleopolyploidy in vertebrates

A

2 rounds, one before emergence of jawless fish, and one after

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17
Q

fish-specific genome duplication

A

paleopolyploidy

  • many genes present in 2 copies in teleost fish but one copy in other vertebrates
  • pairs in teleost seem to have originated at the same time
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18
Q

how is paleopolyploidy detected

A
  1. find duplicated blocks of genes
  2. estimate relative ages of blocks using synonymous substitutions (Ks)
  3. Analyze degree overlap between adjacent blocks;
    - if overlap = segmental duplications not polyploidy

Polyploidy if: large duplicated, non-overlapping regions, with genes of similar ages

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19
Q

evolution after paleopolyploidy

A
  • organism returns to diploid state by chromosomal structural changes, (rearrangements and fusions)
  • many duplicated genes lost
  • duplicated genes that are retained often diverge in expression patterns
  • one copy may experience relaxation of purifying selection or occasionally positive selection
  • retained duplicated undergo subcellular relocalization
  • neo or sub functionalization can occur
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20
Q

evolutionary and ecological significance of polyploidy

A
  • novel phenotypes
  • speciation— mechanism of instant speciation
  • ecological diversification
    • often can colonize new habitats
  • new alleles for gene evolution because all genes are duplicated
  • major effects on genome evolution
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21
Q

polyploidy in plants

A

prominent and ongoing in plants

  • many crop plants are polyploids
    ex. canola, cotton, bread, strawberry
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22
Q

polyploidy in animals

A

not as common as in plants

  • some polyploidy fish, amphibians and insects, but rare in mammals, NOT IN BIRDS
  • ancient polyploidy in vertebrate evolution
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23
Q

mechanisms of polyploidy formation

A

-union of unreduced (2N) gametes: produces tetraploid
- union of one reduced and one unreduced gamete:
= triploid
– usually inviable, ex. seedless watermelon
- experimentally induced by colchicine treatment
– microtubule inhibitor that prevents cell division

24
Q

polyploidy and gene evolution

A
  • gene loss immediately and over time
  • chromosomal rearrangements
  • changes in DNA methylation and histone modifications
  • neo and sub functionalization
25
Q

gene expression changes in polyploidy

A
  • up or down regulation of expression compared to parents
  • silencing of one or both homeologs
  • possible mechanisms include DNA methylation, histone modifications (methylation and deacetylation)
  • can be organ specific or in response to stress conditions
26
Q

types of gene duplications

A

tandem
segmental
chromosomal
whole genome

27
Q

tandem duplicates

A

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
28
Q

mechanisms for gene duplication

A

unequal crossing over

retroposition

29
Q

segmental duplications

A

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
30
Q

dispersed duplications

A

generated by retroposition or DNA transposition after gene formation

31
Q

retroposed duplications

A

generated by retroposition

some have regulatory elements some become pseudogenes

32
Q

fates of duplicated genes

A
  1. one copy lost or looses function/expression
    - pseudogene
  2. both copies retain original function
    - can be redundant
  3. one copy gains new function
    - neofunctionalization
    - expression pattern: regulatory neofunctionalization
  4. subfunctionalization
33
Q

pseudogenes

A

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

34
Q

types of selection acting on duplicated genes

A

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
35
Q

Chloroplast genomes and phylogenetics

A

entire genomes are sequenced
- illumina sequencing

  • DNA is being tagged and sequenced simultaneously = Barcoding— cost effective
  • disadvantage- only half lineage so wont represent original phylogeny
36
Q

non-functional gene transfer to nucleus

A

Mitochondria/chloroplast gene transfer to nucleus

  • integrates but non-functional
  • happens frequently
  • gene fragment, single gene, multi-gene region
  • many mito and chloroplast pseudogenes in the nuclear genome
37
Q

functional gene transfer to nucleus

A

integrated and functional gene that creates product or RNA

  • In plants BUT NOT animals
  • transfer often occurs by RNA intermediate
    • proven by no introns
    • direct DNA wouldn’t have correct aa sequence due to c to u RNA editing
  • needs to acquire RNA targeting sequence
    • from other genes or de novo
  • needs regulatory elements for nucleus expression
  • Original mito or chloroplast copy is still expressed until nuclear copy becomes functional
38
Q

plant vs animal mitochondrial genomes

A
  • size
  • -Plants: wide range, around 400kb
    • animals: 14-17kb
  • number of genes
    • P: up to 40 protein coding
  • -A: 13 protein coding
  • gene order in the circular genome
  • -P: not conserved
  • -A: conserved
  • introns
  • -P: many
  • -A: NONE
  • intergenic regions
  • -P: large
  • -A: little
  • rate of nucleotide substitutions
  • -P: very low
  • -A: very high
39
Q

Heteroplasmy

A

some mitochondrial genomes in a cell are normal and some are mutant
- need a threshold to cause disease

40
Q

Cyto-nuclear interactions

A

cross-talk btw mitochondrial gene expression and nuclear gene expression so complexes can form
mitochondria do not encode Transcription factors

  • some TF regulate both mito and nuclear genes
  • some TF regulate other TF that regulate mito genes
  • also: TFA–> TFB –> Mitochondrial genes
    and TFA–> nuclear encoded mitochondrial genes
41
Q

codon usage bias

A

certain codon preferentially used to code for aa

  • varies by organism
  • can select against nucleotide changes at silent sites
  • not all silent sites are neutral evolving
42
Q

origin of new genes

A

gene duplication

  • retro-position
  • exon shuffling
  • integration of transposable elements
  • gene fusion
  • gene fission
  • de novo
  • horizontal or lateral gene transfer
  • change in subcellular localizations
43
Q

Why is animal mtDNA a desirable molecule for phylogenetic studies

A
  • maternally inheritance
  • no recombination
  • conserved and less conserved regions
  • high mutation rates to compare individuals in a population and within species
44
Q

why do mtDNA being multi-copy per cell facilitate phylogenetic studies

A
  • multiple copies makes amplification easier
  • lack of recombination makes tracing lineages easier
  • – universal primers
45
Q

How is maternal transmission of mtDNA accomplished

A

male mtDNA in sperm destroyed

- pre and post fertilization

46
Q

Hydrophobicity of Mitochondrial proteins

A

hypothesis: long hydrophobic proteins with hydrophobic TMDs are targets for ER by binding SRP
alternate hyp: hydrophobic segments of mt proteins prevent import across the mitochondrial membrane

47
Q

what can be inferred from ancestral expression pattern and function

A

neofunctionalization or sub-functionalization

48
Q

how to evaluate rates of sequence evolution

A

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

  • higher ratio = positive selection
  • less than one= purifying
49
Q

How can genes undergo neofunctionalization

A
  • mutations in amino acid sequences or structural changes in sequences (INDELs)
    if regulatory neofunctionalization
  • with or without changes in function of protein coding genes
50
Q

short term consequences of polyploidy

A

gene silencing + loss of redundant genes/sequences

  • chromosome exchanges resulting in loss or doubling in sequences + genome wide rewiring
  • subfunctionalization or neofunctionalization
51
Q

Biased fractionalization

A

the non-random or biased loss of ancestral genes following allopolyploidy
- more loss from one sister genome compared to other

52
Q

genome dominance in context of polyploidy

A

genome wide homology expression bias

- 2 subgroups - more genes from one group expressed than other = genome dominance of expressed subgroup

53
Q

how can small RNAs and TEs affect expression levels of homeologs and result in one homeolog having lower expression

A

can silence one homeolog as they are silenced by epigenetic modifications, when insert next to a gene can silence that gene
- density of TEs is higher in regions adjacent to homologs that exhibit lower expression

54
Q

how does selection and genetic drift act on distribution of TEs

A

strong deleterious rapidly removed

- no effect on function/fitness - may reach fixation

55
Q

TE balance btw expression and repression

A

expression should be sufficient to promote amplification but not so much that leads to fitness disadvantage for host

56
Q

how can TEs add exons to genes

A

transduction (addition of exons)

- cryptic splice sites which can cause alternative splicing

Biology 430 (16 decks)

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