5. Eukaryotic genomes Flashcards
What is the general hierarchy of genome size in organisms?
Viruses < bacteria < eukaryotes
What are the smallest/largest genome prokaryotes?
Smallest: endosymbionts that live intracellularly - ex: Wolbachia - male killer
Largest: randomly large - eukaryote-sized
What are the reasons why eukryote genomes should be larger than prokaryote?
Eukaryote genomes should be larger because:
- eukaryotic cells bigger
- eukaryotic cells more complex - specialised - many different cell types
- eukaryotic cell division/reproduction more complex
What is the sizde of a home genome?
~ 3.6 Gb
What is C-value?
C-value - the amount of DNA (in weight pg) found in a haploid nucleus - for diploids need to divide by 2 to find C-value
C -> constant because: comparing haploid, in weight
1 pg of DNA = 965 Mb
What is used to measure the size of a genome?
C-value - measured in weight -> Mb inferred
What are the older/current mechanisms used to measure genome size?
Older:
- Feulgen staining: staining nucleus -> densitometry of fixed cells
- Fluorescence-actiavted cell sorting (FACS): using DAPi / PI / Hoechst staining - intercalates in between strands - compare dye intensity to a standard of known genome size
Current: sequencing and genome assembly - estimated from k-mer frequency
What is the k-mer genome measuring unit?
k-mer - unique subsequence of a particular lentgh in a genome - k corresponding to the length of the fragment
Can use k-mer distribution to estimate the genome size - N=(L-K)-1 -> at large numbers approximate to N=~L
where N=# of possible k-mers, L=length, K=k-mer size
Describe the organism of the smallest eukaryotic genome?
Smallest eukaryotic genome - endosymbiont algae - doesn’t need as many genes because used host cells
Describe the smallest free-living organism genome
Smallest genome of a free-living organism - plant parasitic fungi
Describe the smallest photosynthetic eukaryotic genome
Marine algae - carbon fixing
Describe the smallest genome animal
Smallest genome animal - plant parasitic nematode
Describe the largest genome single-celled eukaryote
Single-celled dinoflagellate
Describe largest genome animal
Fish - 43Gb - compared to 3.5Gb human
Describe the largest genome plant
140 Gb - compared to 3.5Gb human
Guessed largest ever genome
Explain C-value paradox
C-value paradox - complexity of eukaryotic organism can’t be predicted from genome size - gene content doesn’t relate to organism complexity
True only for lower range complexity in general: eukaryotes > bacteria > viruses
Why are eukaryotic genomes larger than prokaryotic?
Eukaryotic genomes more complex because of:
- expression regulation - complex promoters
- on average encoded proteins are longer
- presence of introns
Eukaryotic gene structure:
What are the costs of increasing genome size?
If genome size bigger - costs:
- bigger cells
- slower cell division rate
- slower growth rate
What are the benefits of large genomes to salamanders?
Salamanders -very large genomes - biphasic - two different stages: juvenile in water env - adult on dry land - rapid metamorphosis (transition)
As genome increases what components increase and what don’t along with it?
Increase %: intron proportion, intergenic regions
Decrease %: exons proportion - exon numbers remain constant - become a lower part of the genome as genome size increases
Explain what is intergentic DNA
Intergenic DNA - non-coding sequences in betweeen genes - interspersed repeats - mostly mobile elements ex: TEs
What kind of mobile elements can be intergenic DNA?
What are the types of TEs in eukaryotes?
TEs types:
Class I: retrotransposons / “Copy & Paste” / RNA->DNA
Class II: transposons / “Cut & paste” / DNA
What are the types of jumping genes in eukaryotes?
[insert diagram from MOG prep paper notes]
How are eukaryotic genomes organised?
Eukaryotes have linear chromosomes - 1-several hundred can be in a genome - all eukaryotes also have organellar genomes (mt, chlrp)
Is chromosome number directly related to genome size?
No, chromosome number doesn’t correspond to genome size
Between closely related organisms - genomes can greatly differ but chromosome number usually not - diff chromosome numbers are a barrier for interbreeding
How does chromosome number change?
Chromosome number can change:
- defects in chromosome segregation - ex in polyploidy - common in plants because selfing is possible
What are the two phenomena widely associated with chromosomal number changes (aneuploidy) in humans?
- miscarriage
- cancer
Explain the structure of a linear chromosome
- telomeres (long arrays of simple sequences)
- subtelomeric region
- centromeres
- chromosome arms (p, q)
Explain centromeres in chromosomes
Centromeres - primary constriction - where kinetochore forms - connects to mitotic spindle
Centromere sequence: high proportion of repetitive DNA - flanked by pericentric heterochromatin - silenced epigenetically - centromeres can move along chromosome
Explain telomeres ins chromosomes
Telomeres - at chromosome ends - long arrays of repetitive sequence - protect chromosomes from:
- ds DNA repair- fuse with other chromosomes
- shortening
Telomeres have ss DNA segement at the ends - 3’ overhang - caused by RNA primer removal in DNA replication - ‘end replication problem’
What is the function of telomerase?
Telomere ‘end-replication problem’ - to protect the 3’ end is repair by telomerase:
- reverse transcriptase (RNA->DNA) - using a short RNA template lengthens the telomere
- expressed in germline cells + stem cells
- often activated in cancers - allows constant replication
Why somatic cells line can’t be cultured indefinitely?
Because in each division telomeres shortened - will end at one point
How can a chromosome number change?
Chromosome can fuse or break
Explain Robertsonian translocation
Robertsonian translocation: combines two arms
Explain Robertsonian translocation
Robertsonian: genetic exchange between non-homologous acrocentric chromosomes - centric fusion
=> two chromosomes form one large fused chromosome -> depending on gamete which is used for fertilization - effect size (diff final gametes)
Because p arm so small - main genes in q - if p lost => still balanced translocation
What allows malaria to evade human immune system?
Malaria - Plasmodium flaciparum - evades immune system by:
- adhering to vascular endothelium
- variable antigenic proteins - hypervariable gene families at subtelomeric regions - specialised function in parasitism
How does antigenic variation arise in malaria (parasites)?
Antigenic variation results from:
- amplification of gene families - variable copies
- high rates of subtelomeric recombination
- modulated expression of gene silencing
- ability to switch mutually exclusive expression of individual genes - makes it very parasitic - good at evading host immune system
How is Trypanosoma brucei genome arranged for it to evade host immune system?
T. brucei causes sleeping sickness - 11 large, 10 medium and 100s of mini chromosomes - subtelomeres contain repeats of gene families:
- variable surface antigen genes (VSG) - one VSG expressed at a time - regularly switched between expression sites changing its surface coat
- expression site associated genes (ESAG) - involved with host interaction
