Lecture 5 Flashcards
What is a genome? What are its two components?
A genome is all the genetic material (DNA) present in a particular organism. It includes
- coding and non-coding DNA
- nuclear and organelle genomes
What is a transcriptome?
A transcriptome is all RNA coded by the genome
What is a proteome?
a proteome is all proteins coded by the genome
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?
~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
How many genes on average does a single tissue express?
30-40%
how many different cell types with different compliment mRNA and proteins are there in animals?
~252
What does genomics investigate in genomes?
Construction of genetic and physical maps
Identification of structural and functional components of the genome (genes and noncoding DNA)
Explain using the google maps example how genetic mapping and mapping by genome sequence are different?
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)
What is the importance/purpose of accurate and different maps?
- Maps provide the likely order of genes/markers along a chromosome
- A single map is usually not sufficient
What is mapping?
Any method used for determining the location of, and relative distances between, genes on a chromosome
What are two examples of low resolution maps? Using the google maps example what do they allow us to do?
Genetic and cytogenetic
allow you to drive from one city to another
What are three examples of High resolution maps? Using the google maps example what do they allow us to do?
radiation hybrid, BAC clones and sequencing
allows you to find specific street in the city
What is an examples of an Ultra resolution map? Using the google maps example what do they allow us to do?
Complete DNA sequence of the genome
allows you to find a specific house in the city
What two things can a genome map be based on?
indirect and direct estimates of the distance between two markers
What are two things you could use for an indirect estimate? What map types are they associated with?
Recombination rate for genetic linkage maps
Radiation induced fragmentation for radiation hybrid maps
What can you use for a direct estimate? what map types is this associated with (3)?
Physical distances for all of cytogenic, BAC clones and sequencing maps
What is a genetic linkage map?
A map of the relative positions of the genetic loci/DNA markers along the chromosome, determined based on recombination frequency between markers
How is distance measured for genetic linkage maps? what recombination frequency usually corresponds with 1cM?
Distance is measured in morgans or centimorgans
1cM=1% recombination frequency
Generally, 1cM=1% recombination frequency. How is this different across species? Give two examples of species in Mb (million basepairs)
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
Who produced the first genetic map? When? What was it based on?
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.
What can serve as mapping markers?
Any inherited physical or molecular characteristic that differs among individuals and is easily detectable has potential
What are the three important features of a marker?
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)
Give three examples of DNA based markers for DNA sequence polymorphism
Single Nucleotide Polymorphism (SNPs)
Insertions and Deletions (Indel)
Restriction fragment length polymorphism (RFLP)(old)
Give an example of a DNA based markers for DNA length variation
Microsatellite - parentage test and genetic diversity studies
What are microsatellites?
Short tandem repeats defined by a variable number of repetitions of 2-3 nucleotide base pairs within a sequence.
With microsatellites, is the number of repeats consistent across species?
No, it may differ between animals.
Give three characteristics of microsatellites.
- Multiallelic - can have many alleles/repetitions in pop’n
- Codominant - separates the homozygous from heterozygous alleles
- Low throughput
What are SNPs?
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.
What are three characteristics of SNPs?
- SNPs occur at a high frequency throughout the genome.
- Usually Biallelic
- Codominant
Why is sequencing considered the gold standard?
Because it allows both detection of new SNPs and genotyping of known SNPs.
Is sequencing low throughput or high throughput?
Low Throughput
List 10 SNP genotyping techniques.
Hybridization Primer extension Oligonucleotide Ligation Nuclease Cleavage DNA conformation Gel Separation Array Mass Spectrometry Plate reader Chromatography
What are the disadvantages of genetic maps?
- 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
What are two differences between physical maps and genetic maps?
Physical maps: measured in bp and based on physical distances between markers
Genetic maps: measured in cM and based on recombination frequency between markers
Briefly explain FISH.
Fluorescent in situ Hybridization
- a DNA probe is labelled with a fluorescent dye and hybridized to the homologous region on a chromosome
What are 4 characteristics of Cytogenic Maps?
- Low resolution
- Direct physical distances between markers
- Alignment of different types of maps
- comparative mapping across different species
Explain Radiation Hybrid mapping.
- 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
What does RH mapping allow us to do?
Allows for rapid increase in the amount of genomic information to produce a high resolution map with gene based markers and integrate different maps
How does RH mapping calculate distance?
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.
What are 4 advantages of RH maps?
- 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)
What are comparative maps?
Comparative maps are a powerful approach for the expansion of gene maps of less analyzed genomes by transfer of information from well analyzed genomes.
How do comparative maps work?
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.
how can comparative maps be produced?
using cytogenic approach (chromosome painting) or RH mapping
What is gene synteny?
the concept that orthologous genes often show conserved gene order
Why do we sequence genomes?
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)
