What causes Fragile X?
Severity of dz correlates w/ # of CGG repeats on the FMR1 gene on the X chromosome. MC inherited form of mental retardation. Expansion from pre- to full mutation only occurs through female meiosis.
Results from XYY?
47XYY, masculine men, tall, Alien 3 syndrome
What is Klinefelters?
47XXY-hypogonadism, tall in stature, weak bones, may be infertile
What occurs with histone methylation (chromatin stage regulation)?
Target sites of histone methylation are the Cytidine residues which exist as a dinucleotide. CG(CpG)
Areas rich with CpG are known as CpG islands
Methylation of Cytidine down regulates transcription
What occurs with histone acetylation (chromatin stage regulation)?
Addition of an acetyl group
DNA is stopped from getting further condensed
Active transcription is thus encouraged
Describe other types of histone methylation.
Addition of other groups to lysines and arginines
Methylation stimulates transcription
Demethylation inhibits gene transcription at that region
What do histones do?
They are proteins found in nuclei that package and order DNA into nucleosomes- chief protein component of chromatin- the spools around which DNA winds.
Describe the purpose of exons and introns.
Exons: Sequences appear in mature transcript (and can be shuffled) (meaning- they are translated into mRNA coding regions and are joined to form contiguous coding sequences)
Introns: DNA bases that are non coding and are removed through RNA splicing. They are found between exons.
How do we regulate transcription?
Promoters (CCATT and TATA boxes)
Exon Shuffling
Enhancers (transcription factors bind enhancer regions)
How do we regulate RNA transport?
Via nuclear transport, in which entry and exit of large molecules from the nucleus is tightly controlled by nuclear pore complexes (NPCs).
–Exportins: actively transport RNA into cytoplasm, can be inhibited by blocking their attachment.
How do we regulate translation?
- Addition of 5’cap/3’poly tail
- Removal of introns (non-coding)
- Splicing exons. Different combinations cause different proteins with different functions.
When the poly(A)-binding protein (PABP) interacts with the translation initiation factor bringing the 5’ and 3’ ends of the mRNA together translation is enhanced.
In what sex do we see fragile x syndrome?
Males
What are proto-oncogenes?
Normal genes that are involved in synthesis of receptors and messenger systems, and involved in nuclear transcription.
Oncogenes cause cancer by affecting what?
Cell growth and differentiation:
Encode proteins
Stimulate cell cycle
Create more active protein
Tumor suppressor genes require what level of mutation for cancer to develop?
Two hit process (both alleles must be mutated)
If oncogenes take 2 hits do they produce more or less protein?
???
Oncogenes need “one hit” to become active, no idea about what happens with two hits (both alleles mutated)
Where are the locations of modifications marked in epigenomic maps?
Locations are marked above BP sequences: altering, activating, repressing, ending/undwinding and opening/closing sequences
How does proximity interplay with gene linkage?
Genes are said to be linked when they occur in close proximity to one another on the same chromosome.
Tend to be inherited together and less likely to be cross-linked.
DNA polymorphism: RFLP
Restriction Fragment Length Polymorphisms:
Refers to differences in homologous DNA sequences resulting from the presence or absence of restriction enzyme sites.
Can be visualized on Southern blot, as DNA fragments of varying lengths are produced when the DNA is chomped up by a restriction enzyme.
DNA polymorphism: VNTR
Variable Number of Tandem Repeats:
Variation in specific region of chromosome dt differences in number of basepair repeats, ranging from 20-70 bases –> minisatellites.
The repeat is flanked on both sides by a restriction site.
Fragile X
Huntington
DNA polymorphism: STRP
Short Tandem Repeat Polymorphisms:
Variation dt differences in in number of basepair repeats, only 2-6 bases long –> microsatellites.
Can be amplified with a PCR.
Used in paternity testing, forensic cases, gene mapping.
DNA polymorphism: SNP
Single nucleotide polymorphism:
A single difference in a nucleotide sequence.
Typed by PCR or DNA probe chips.
Why are VNTRs valuable to us?
DNA profiling.
VNTRs loci are very similar between closely related humans, but unrelated individuals are extremely unlikely to have the same VNTRs.
What is amniocentesis? When is it performed?
What percentage do we associate with fetal risk for the procedure?
A test used for prenatal genetic diagnosis.
Amniotic fluid sample take at 16 weeks gestation.
Risk of fetal demise is 0.5%.
BRCA1 is expressed where? What does it do?
BRCA1 gene is located on q arm of chromosome 17.
It produces breast cancer type 1 susceptibility protein, which repairs or destroys double-strand breaks in DNA.
If BRCA1 is mutated, increases breast cancer risk.
People with BRCA1 and 2 mutations have what condition?
Hereditary breast-ovarian cancer syndrome.
What has contributed to failure of gene therapy?
- Short lived: pts would need many rounds of gene therapy.
- Immune Response: risk of stimulating the immune system when introducing any foreign material into the body, esp with multiple rounds.
- Viral vectors can cause toxicity, immune and inflammatory response, etc., and may recover ability to cause disease.
- Multigene disorders: most diseases are due to combined effects of variations in many genes.
What is RNAi? What can it be used for? What is its importance in human evolution related to parasites and viruses?
- Interference RNA: inhibits gene expression or translation by neutralizing targeted mRNA.
- Moderates the activity of genes.
- Important role in defending cells against parasitic and viral nucleotide sequences.
- Passes down to subsequent generations, therefore DNA is not the only form of inheritance.
(Is also important to us because it can be used to shut down each gene in a cell which allows us to identify the component necessary for a particular cellular process or an event such as cell division (knock down studies). This is used to test the effect of mutated genes.)
Gene control regulation and expression can be manipulated in which stages?
- Chromatin stage: histone (compact DNA) methylation and acetylation.
- Transcriptional stage: promoters, exon shuffling.
- Translational stage: RNA transport.
- Post-translational control into cytoplasm.
- Post-translational modification: folding, cutting, phosphorylation
What is populationgenetics?
The study of allele frequency distribution under the influence of the four main evolutionary processes: o Natural selection o Genetic drift o Mutation o Gene flow Allele frequency change = Evolution
What types of processes influence evolution?
- Natural selection: increasing the frequencies of alleles that promote survival or fertility and reduce the frequency of alleles that cause disease
- Genetic drift: A change in allele frequency in a population due to random chance. MB beneficial, neutral or detrimental
- Mutation: 70% are harmful. The founder effect is when novel genes are produced through duplication and mutation of an ancestral gene.
- Gene flow: Exchange of genes between populations- usu of the same species. Populations that live near each other often have similar gene frequency.
What is Hardy-Weinberg? Why do we care?
Hardy-Weinberg equilibrium: allele/genotype frequency remains constant in the absence of influence (how variation is maintained in Mendelian genetics).
Important because it explains how variation is maintained in a Mendelian population.
What karyotypes do we see in Turner Syndrome?
45X, 46XX, 47XXX
• Is the only monosomy consistent with life (bc it is not autosomal)
• Results in short stature, ovarian dysgenesis.
Know the rates of breast cancer for women with BRCA1 mutation at different ages.
BRCA mutation (unspecified): o BCa by age 50: up to 50% o BCa by age 70: up to 87% o 2nd BCA by Age 70: up to 64% o OCa by age 70: 44%
Female BRCA1 mutation:
o BCa by age 70: 57-87%
o OCa by age 70: 39-40%
What happens if you are homozygous for BRCA2?
Fanconi anemia.
Most develop AML, with 90% rate of bone marrow failure by age 40.
For women with BRCA2, what is the breast and ovarian cancer risk stratification?
Female BRCA2 mutation:
o BCa by age 70: 45-84%
o OCa by age 70: 11-18%
o OCa (lifetime): 25%
Female BRCA1 or BRCA2 carriers:
o BCa by age 90: up to 60%
For males with BRCA2 what is their prostate and BC risk?
- PrCa by age 65: 15%
* BCa by age 70: 6.8%
Individuals with BRCA1 or 2 have increased risk for what other types of cancers?
BRCA1: fallopian tube, prostate CA
Both: leukemia, lymphoma, melanoma, pancreas, gallbladder, bile duct, stomach CA
Pancreatic, ovarian, liver and testicular CA testing markers?
- Pancreatic: CA 19-9
- Ovarian: CA 125
- Liver: AFP
- Testicular: Beta-HCG
