5. Eukaryotic genomes Flashcards by Barbora Buc

What is the general hierarchy of genome size in organisms?

Viruses < bacteria < eukaryotes

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What are the smallest/largest genome prokaryotes?

Smallest: endosymbionts that live intracellularly - ex: Wolbachia - male killer

Largest: randomly large - eukaryote-sized

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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

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What is the sizde of a home genome?

~ 3.6 Gb

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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

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What is used to measure the size of a genome?

C-value - measured in weight -> Mb inferred

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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

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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

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Describe the organism of the smallest eukaryotic genome?

Smallest eukaryotic genome - endosymbiont algae - doesn’t need as many genes because used host cells

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Describe the smallest free-living organism genome

Smallest genome of a free-living organism - plant parasitic fungi

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Describe the smallest photosynthetic eukaryotic genome

Marine algae - carbon fixing

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Describe the smallest genome animal

Smallest genome animal - plant parasitic nematode

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Describe the largest genome single-celled eukaryote

Single-celled dinoflagellate

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Describe largest genome animal

Fish - 43Gb - compared to 3.5Gb human

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Describe the largest genome plant

140 Gb - compared to 3.5Gb human

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Guessed largest ever genome

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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