Lecture 5

Question 1

What is a genome? What are its two components?

Answer 1

A genome is all the genetic material (DNA) present in a particular organism. It includes

• coding and non-coding DNA
• nuclear and organelle genomes

Question 2

What is a transcriptome?

Answer 2

A transcriptome is all RNA coded by the genome

Question 3

What is a proteome?

Answer 3

a proteome is all proteins coded by the genome

Question 4

How many protein coding genes are in the mammalian genome? How many RNA & mRNA do the produce? how many proteins/spots in total and per gene does this yield?

Answer 4

~21,000 protein coding genes
~70,000-100,000 RNA due to alternative start, stop or splicing
~45,000 coding mRNA
~5 proteins per gene
~100,000 proteins total

Question 5

How many genes on average does a single tissue express?

Answer 5

30-40%

Question 6

how many different cell types with different compliment mRNA and proteins are there in animals?

Answer 6

~252

Question 7

What does genomics investigate in genomes?

Answer 7

Construction of genetic and physical maps

Identification of structural and functional components of the genome (genes and noncoding DNA)

Question 8

Explain using the google maps example how genetic mapping and mapping by genome sequence are different?

Answer 8

If you are trying to get to ANNU:

• A map of TO will give you a low resolution result, allowing you to see a lot of markers and can be used to get to a general place (genetic map)
• A map of campus will give you a high resolution result, and you can easily find the building (high resolution physical map)

Question 9

What is the importance/purpose of accurate and different maps?

Answer 9

• Maps provide the likely order of genes/markers along a chromosome
• A single map is usually not sufficient

Question 10

What is mapping?

Answer 10

Any method used for determining the location of, and relative distances between, genes on a chromosome

Question 11

What are two examples of low resolution maps? Using the google maps example what do they allow us to do?

Answer 11

Genetic and cytogenetic

allow you to drive from one city to another

Question 12

What are three examples of High resolution maps? Using the google maps example what do they allow us to do?

Answer 12

radiation hybrid, BAC clones and sequencing

allows you to find specific street in the city

Question 13

What is an examples of an Ultra resolution map? Using the google maps example what do they allow us to do?

Answer 13

Complete DNA sequence of the genome

allows you to find a specific house in the city

Question 14

What two things can a genome map be based on?

Answer 14

indirect and direct estimates of the distance between two markers

Question 15

What are two things you could use for an indirect estimate? What map types are they associated with?

Answer 15

Recombination rate for genetic linkage maps

Radiation induced fragmentation for radiation hybrid maps

Question 16

What can you use for a direct estimate? what map types is this associated with (3)?

Answer 16

Physical distances for all of cytogenic, BAC clones and sequencing maps

Question 17

What is a genetic linkage map?

Answer 17

A map of the relative positions of the genetic loci/DNA markers along the chromosome, determined based on recombination frequency between markers

Question 18

How is distance measured for genetic linkage maps? what recombination frequency usually corresponds with 1cM?

Answer 18

Distance is measured in morgans or centimorgans

1cM=1% recombination frequency

Question 19

Generally, 1cM=1% recombination frequency. How is this different across species? Give two examples of species in Mb (million basepairs)

Answer 19

This may correspond to different physical distances in different species, of even different places on the same chromosome.
~0.5Mb in Drosophila
~1Mb in human and bovine

Question 20

Who produced the first genetic map? When? What was it based on?

Answer 20

Alfred Sturtevant, 1913
Based on noticeable phenotypic observations and allelic segregation on the physical characteristics of flies such as eye colour, body colour, wing length, etc.

Question 21

What can serve as mapping markers?

Answer 21

Any inherited physical or molecular characteristic that differs among individuals and is easily detectable has potential

Question 22

What are the three important features of a marker?

Answer 22

Polymorphism (different forms within a population)
Frequency (closer to equal frequency = more info)
Ease and cost of detection (eg microsatellites are too expensive vs. SNPs)

Question 23

Give three examples of DNA based markers for DNA sequence polymorphism

Answer 23

Single Nucleotide Polymorphism (SNPs)
Insertions and Deletions (Indel)
Restriction fragment length polymorphism (RFLP)(old)

Question 24

Give an example of a DNA based markers for DNA length variation

Answer 24

Microsatellite - parentage test and genetic diversity studies

Question 25

What are microsatellites?

Answer 25

Short tandem repeats defined by a variable number of repetitions of 2-3 nucleotide base pairs within a sequence.

Question 26

With microsatellites, is the number of repeats consistent across species?

Answer 26

No, it may differ between animals.

Question 27

Give three characteristics of microsatellites.

Answer 27

- Multiallelic - can have many alleles/repetitions in pop'n - Codominant - separates the homozygous from heterozygous alleles - Low throughput

Question 28

What are SNPs?

Answer 28

Single nucleotide polymorphisms are individual point mutations or substitutions of a single nucleotide that do not change the overall length of the DNA sequqnce in that region.

Question 29

What are three characteristics of SNPs?

Answer 29

- SNPs occur at a high frequency throughout the genome. - Usually Biallelic - Codominant

Question 30

Why is sequencing considered the gold standard?

Answer 30

Because it allows both detection of new SNPs and genotyping of known SNPs.

Question 31

Is sequencing low throughput or high throughput?

Answer 31

Low Throughput

Question 32

List 10 SNP genotyping techniques.

Answer 32

``` Hybridization Primer extension Oligonucleotide Ligation Nuclease Cleavage DNA conformation Gel Separation Array Mass Spectrometry Plate reader Chromatography ```

Question 33

What are the disadvantages of genetic maps?

Answer 33

- Starting genetic maps is easier than finishing them - Difficult to produce high resolution maps due to small sample sizes and inability to increase recombination rate (to detect 1% recomb. need to examine >100 offspring) - Variation between genetic and physical distances

Question 34

What are two differences between physical maps and genetic maps?

Answer 34

Physical maps: measured in bp and based on physical distances between markers Genetic maps: measured in cM and based on recombination frequency between markers

Question 35

Briefly explain FISH.

Answer 35

Fluorescent in situ Hybridization | - a DNA probe is labelled with a fluorescent dye and hybridized to the homologous region on a chromosome

Question 36

What are 4 characteristics of Cytogenic Maps?

Answer 36

- Low resolution - Direct physical distances between markers - Alignment of different types of maps - comparative mapping across different species

Question 37

Explain Radiation Hybrid mapping.

Answer 37

- In vitro radiation-induced chromosome fragmentation and cell fusions to create panels of cells in which fragments of DNA from the irradiated cells become integrated into the chromosomes of the host cells

Question 38

What does RH mapping allow us to do?

Answer 38

Allows for rapid increase in the amount of genomic information to produce a high resolution map with gene based markers and integrate different maps

Question 39

How does RH mapping calculate distance?

Answer 39

RH mapping uses frequency of co-segregation of two DNA markers to calculate distance between markers. the closer two markers are, the less chance they will be broken by radiation and segregate into different cells.

Question 40

What are 4 advantages of RH maps?

Answer 40

- unique ability to map polymorphic markers (microsatellites, SNPs) and non-polymorphic markers (or genes) - Integration of maps (genetic linkage and physical) based on different markers - Ability to adjust mapping resolution by changing the radiation dosage (low or high resolution maps; provides distance measure between markers with direct correlation to physical distance (1cR~2-13kbp) - Allows creation of comparative maps between different species (pig/mouse)

Question 41

What are comparative maps?

Answer 41

Comparative maps are a powerful approach for the expansion of gene maps of less analyzed genomes by transfer of information from well analyzed genomes.

Question 42

How do comparative maps work?

Answer 42

The genomic address for a gene from a map poor species can be transferred to a corresponding region of a map rick species. It is based on gene synteny between two species.

Question 43

how can comparative maps be produced?

Answer 43

using cytogenic approach (chromosome painting) or RH mapping

Question 44

What is gene synteny?

Answer 44

the concept that orthologous genes often show conserved gene order

Question 45

Why do we sequence genomes?

Answer 45

to produce a complete catalog/blueprint of the organism for: - Rapid identification of genes and proteins - identifiaction of regulatory and structural elements of the genome - transcriptome, proteome analysis - Comparative genetics (evolution, comparing species)