Unit 4 (Lessons 26-27)

Gregor Mendel and William Bateson

• Gregor=founder

• William=champion

What are Mendel’s 3 Laws?

1. Law of segregation

2. law of independent assortment

3. law of dominance

Law of Segregation

• 2 copies of each genetic factor segregate during gamete formation, ensures each parent’s offspring obtains one factor

• Predict probabilities of inheritance

Law of Independent Assortment

• segregation of alleles at one locus is independent of segregation of alleles at another locus

Law of Dominance

• one allele dominates the other

why is the law of independent assortment an assumption rather than a law?

• basic unit of transmission is the chromosome and genes on chromosome that are close together do not actually assort independently

• this creates linked genes

How many chrossovers per chromosome in meiosis?

• a finite number

Recombination Frequency (RF)

• measure of how often genetic crossover occurs between 2 loci during meiosis

• =(recombinant/total chromosomes)*100

• Genes with independent assortment have RF= 50%

• 1% RF= 1m.u. (1 centiMorgan)

how do genetic companies build genealogies?

• tracking how chunks of alleles are inherited through generational time

• leads to haplotypes

Explain the concept of “Identical By Descent”

• certain chunks of DNA don’t recombine very often (b/c they are linked) so they are inherited in blocks

• genotyping SNPs all along chromosome lets you infer relationships between distantly related people

how does “Identical By Descent” compare to “Identical By Choice”?

• minimum segment size thresholds were built into the matching algorithm

• false matches can still appear!

Neomorphic

• GOF but completely new function

Hypermorphic

• GOF with higher activity levels

Amorphic

• LOF but complete loss of function

Hypomorphic

• LOF but only partially decreases function, still works to certain extent

How do we know if 2 genes interact genetically? (as opposed to physical interaction of products)

• by counting phenotypic classes among offspring of Dihybrid Cross (AaBb x AaBb)

• expected ratios are 9:3:3:1

What are 4 types of gene interactions with inheritance?

1. Redundancy- 2 genes make same product

2. Additivity- 2 genes generate 1 phenotype (ex: amount of pigment adds to darker shades)

3. Epistasis- 1 gene masks phenotype of another (AKA Gatekeeper effect)

4. Modification- 1 gene changes how another gene behaves (but doesn’t have its own phenotype) (AKA called modifiers)

What role do Epistasis and Redundancy play in SMA (Spinal Muscular Atrophy)?

1. Epistasis: SMN1=Gatekeeper, master gene and is 100% functional in normal conditions

2. Redundancy: SMN2=Backup gene, duplicate in case SMN1 is broken, which then follows the logic of additivity

Explain genetics behind SMA (spinal muscular atrophy)

• null mutant (complete LOF) causes embryonic lethality

• SMA zone=hympomorphic state

• 2 thresholds=more than 1 SMN function

NOD2

• encodes intracellular “sensor” that detects small molecules associated with bacterial pathogens and activates the immune response

• when lost or reduced, bacteria overgrow and inflammation results

• mutations in NOD2 not completely penetrant

What does penetrant mean with reference to disease?

• everyone with mutation develops the disease

What are the “DNA markers” that allowed scientists to fine map locus and identify causal gene?

SNPs (Single nucleotide polymorphisms)

• main difference between people

• places in genome where one person has one bp and a different person has another

• AKA SNPs are a type of genetic mutation that creates different alleles

• to qualify as SNP, base change has to be found in at least 1% of human population

• most SNP differences have no effect

True or false: any disease-causing mutation has many neutral SNPs linked to them

true!

Define haplotype

• particular combination of DNA variants in a region of chromosome

• usually containing many linked SNPs

• frequency of haplotypes varies in different human populations, reflecting different more recent common ancestors

How would a missense mutation in an SNP in Haplotype 1 affect gene?

• mutation would be associated with the other SNPs in Haplotype 1

• AKA it is inherited by descendants

How can haplotypes be used to map disease causing mutations among multiple families with affected and unaffected individuals?

• look for linked SNPs

• look for haplotypes shared by affected individuals and NOT found in unaffected individuals

• Shared haplotype likely contains disease mutation

• Ex: TERT mutation in melanoma

When determining which haplotype is associated with a disease causing mutation, scientists found that only a fraction is more common, how did they determine if it actually caused the mutation?

• calculated the likelihood ratio

• AKA likelihood that it is ore frequent in the disease than expected by chance.

• use logarithm score to yield simple number and set boundaries

What percent of people with Crohn’s disease have a first-degree relative with the disorder?

• 15%

Pleiotropy

• one gene influences multiple traits

What % of disease-associated SNPs are located in gene coding sequences and have the potential to disrupt splicing or alter function of encoded proteins?

5%

• Remaining 95% of disease-associated SNPs located in non-coding DNA sequences that make up 98% of genome

Forward Genetics

• Mutagenesis

• Mapping-by-sequencing

• used to identify genetic basis responsible for observed phenotype, mapping done to identify underlying gene

Reverse Genetics

• Ectopic expression

• gene silencing

• gene sequence is known but function is unknown

• Gene then “knocked out” and phenotype is observed, then transgenic rescue or ectopic expression

How are “Knock-out” mice made?

• animal cells have less homologous recombination, must select for it

• totipotency is not common so transgenes injected into eggs, embryos, or embryonic stem cells to give rise to gametes

• develops genetic chimera

How are “knock outs” made in embryonic stem cells?

• by homologous recombination

How are embryonic stem cells incorporated into mice?

How does CRISPR-Cas9 work as a gene editing tool?

• naturally in bacteria to produce sgRNA

• Natural bacterial immune system, leads to adaptation then expression then interference

• utilizes guide RNA (crRNA), tracrRNA (helps Cas9 bind) and PAM

What is PAM?

• Protospacer Adjacent Motif

• short DNA sequence (2-3 bases) sits right next to target sequence

After you’ve made your knockout gene and analyzed the phenotype, how do you prove the observed phenotype is due to the mutation and not some genetic background effect?

• complementation

• Non-complementation

What is genetic copmlementation?

• 2 recessive mutants used as evidence that two genes operate within common pathway and not on different genes

• Shows that defect generated is fixed by expression of transgene

• If genes complement one another then they are in different genes

• Fail to complement=same gene

What are histone PTMs?

• histone post-translational modifications

• chemical alterations to histone proteins (mostly on N-terminus)

• AKA acetylation and methylation