M6-Lecture1

Question 1

Gene mutations can be classified in two major ways:

2-3% of liveborn infants have a genetic disease

Answer 1

Hereditary/germline mutations

Acquired (or somatic) mutations: occur at some time during a person’s life (or embryo) and are present only in certain cells, not in every cell in the body.
Not passed on to offspring.

Question 2

Causes of mutations are both endogenous and exogenous

Question 3

generally arise during cell division. They can be numeric, involving the number of chromosomes, or structural, involving the atypical configuration of one or more chromosomes.

Answer 3

Deletions, translocations, duplication, inversion

Question 4

Abnormal number of chromosomes.
Disturb the delicate balance of gene products.
Most are lethal

Answer 4

Aneuploidy

Question 5

Viable trisomies are restricted to only a few human chromosomes

The only ones are:

Answer 5

trisomy 21 (Down syndrome), trisomy 18 (Edwards syndrome), and trisomy 13 (Patau syndrome

Question 6

Monosomies are missing one chromosome. Cells seem to be particularly sensitive to the loss of a chromosome, because the only viable humanmonosomyinvolves the X chromosome.

Answer 6

So, while missing an X chromosome is a serious condition in females (like in Turner syndrome), it’s fatal for males.

Question 7

Most aneuploidies arise from errors in meiosis, especially in maternal meiosis I

Question 8

Trisomy 16 accounts for 16% of first-trimester spontaneous abortions

1.5% of pregnancies

Question 9

Types of genetic damage - DNA:

Silent
Nonsense
Misense

Answer 9

Silent Mutation: This is a change in the DNA sequence that does not alter the amino acid sequence of the protein, so it has no effect on the protein’s function. This occurs due to the redundancy of the genetic code (multiple codons can code for the same amino acid).
Nonsense Mutation: This mutation changes a codon to a stop codon, prematurely terminating protein synthesis. This usually results in a shortened, nonfunctional protein.
Missense Mutation: This is when a change in the DNA sequence results in the substitution of one amino acid for another in the protein. Depending on the location and nature of the substitution, this can alter the protein’s function or structure, potentially causing disease.

Question 10

A frameshift mutation - caused by a deletion or insertion in a DNA sequence that shifts the way the sequence is read.

Answer 10

This can occur due to insertions or deletions that are not in multiples of three nucleotides, causing the codons (three-nucleotide sequences) to be read incorrectly.

Question 11

Types of Genetic Alterations - Genes

Answer 11

Insertion: A segment of DNA is added into a gene, potentially causing a frameshift or disrupting protein function.

Deletion: A portion of DNA is removed from a gene, which can lead to a frameshift mutation or loss of gene function.

Duplication: A segment of DNA is repeated, resulting in extra copies that can cause overexpression of proteins.

Inversion: A portion of DNA is reversed within a gene, potentially disrupting its normal function.

Transposition: A segment of DNA moves from one part of the genome to another, potentially causing mutations or altering gene expression.

Intron/exon inclusions and
exclusions: Changes in RNA splicing that include or exclude certain exons or introns can result in altered or nonfunctional proteins.

Mutations in regulatory regions: Alterations in promoter or enhancer regions of genes can disrupt gene expression, leading to diseases or abnormal protein levels.

Question 12

Insertion and deletion can lead to frameshift mutations if the number of nucleotides added or removed is not a multiple of three.

Other alterations like duplication, inversion, and transposition typically do not cause frameshift mutations in the same way, but they can still impact gene function and protein production in other ways.

Question 13

occur when a sequence of three nucleotides (trinucleotide) is repeated multiple times in a gene. These repeats can expand in number, leading to disruptions in gene function (chromosome stability, gene expression, & protein function) and often causing genetic diseases.

Types of genetic damage:

Answer 13

Trinucleotide-repeat mutations

Question 14

Trinucleotide repeats typically cause diseases like Huntington’s disease, Fragile X syndrome, Fragile X tremor ataxia and myotonic dystrophy, Friedreich ataxia

Answer 14

Not always a mutation in the gene itself

Question 15

The majority are thought to be genetic, directly caused bychanges in genes or chromosomes.

Mostly children are affected

Answer 15

Rare diseases

Question 16

issues with rare diseases:

Answer 16

Misdiagnosis
Unnecessary surgeries
Social isolation
Financial hardship
Lack of treatment options
Early death

Question 17

FORGE (Finding of Rare Disease Genes) Canada used next generation sequencing to identify mutations

Question 18

A human mosaic mutation occurs when a genetic mutation happens during embryonic development, leading to a subset of cells in the body carrying the mutation, while others do not.

Answer 18

True

Question 19

Identical twin studies show that autism ishighly heritable

Answer 19

If one has autism, 70%-80% chance the other will have it too.

40% for fraternal twins

Question 20

Factors such as in utero exposure toa maternal immune responseor complications during birth, may work with genetic factors (play major role) to produce autism or intensify its traits.

Answer 20

Maybe 100 genes strongly linked to autism.

Many are important for communication between neurons or control the expression of other genes

Question 21

The concordance rates in monozygotic twins are 70% for autism and 90% for ASD, whereas the concordance rates in dizygotic twins are 5% and 10%.

Question 22

Spontaneous copy number changes are more frequent in patients with ASD than in unaffected individuals

Question 23

Most mutations in persons with autism were deletions

Answer 23

Also duplication

Question 24

Although de novo mutations arise from changes in the egg or sperm of parents during formation of embryo, they are not considered inherited because they occur for the first time in the offspring, rather than being passed down from the parents’ genetic material.

Answer 24

Mosaic mutations in both parents:
Both the mother and the father can have mosaic mutations, where some of their cells have genetic changes that aren’t present in every cell of their body. These mutations can be passed on to their children.

• Father’s mutations: In older fathers, mutations accumulate in sperm cells due to repeated spermatogenic divisions (the process by which sperm is produced), increasing the risk of passing on genetic mutations.
• Mother’s mutations: In older mothers, oocyte aging (the aging of egg cells) leads to chromosomal abnormalities and increased risk of mutations being passed on through the egg.

Offspring’s post-zygotic mosaic mutations: After fertilization, some mutations may arise in the zygote (the fertilized egg) during the early cell divisions, leading to post-zygotic mosaicism, where some cells of the child carry the mutation, but not all cells do.

De novo mutations: These are new mutations that arise in the offspring, which were not inherited from either parent, but are the result of mutations in the egg or sperm or mutations that occurred in the early stages of development.

Question 25

Age: Parental age is a risk factor for germline mutations and an important cause of genetic disease

Question 26

Maternal age effect

Answer 26

Less frequent than paternal mutations

Rate of maternal de novo point mutations increases with age (rate of accumulation is slower than paternal)

The mechanism of the maternal age effect cannot be that of genome replication as seen with paternal age.

meiotic gene conversions (where genetic information is exchanged between chromosomes) and meiotic crossovers (where chromosomes exchange genetic material during egg formation) are more frequent in older women, possibly contributing to the maternal age effect.

CpG sites (DNA regions where a cytosine nucleotide is followed by a guanine nucleotide) are less likely to mutate in the maternal allele compared to the paternal allele. This might be linked to differences in DNA methylation patterns, where males tend to have higher methylation of CpG sites, potentially protecting the paternal genome from mutations.

Question 27

Down syndrome higher with maternal age

Or trisomy 21 or aneuploidy

Question 28

he paternal age effect refers to the increased risk of genetic diseases in offspring due to mutations in sperm cells, which occur more frequently as men age. The genome replication hypothesis suggests that as men continuously produce sperm through many cell divisions, the DNA copying process becomes less precise, leading to a higher rate of de novo mutations (DNM) in their offspring.

Question 29

between advanced paternal age at conception and adverse neurodevelopmental outcomes in offspring (autism and schizophrenia).

Question 30

Selfish mutations in sperm

Answer 30

Sperm cells are produced when stem cells called spermatogonia divide, to produce sperm and one stem cell

But mutations can make stem cells divide abnormally (like producing two stem cells)

Overtime, #s of mutants or selfish stem cells and sperm increase

Question 31

A cancer-like process in the testicles may explain why brain disorders like autism andschizophreniaare so common

As well as parental lifestyle (eating, ageing, endocrine disrupting chemicals, affect sperm/seminal plasma quality) lead to effect on embryo reprogramming and fetal growth.

Question 32

Causes of genetic damage

Answer 32

Ionising radiation
– ethylnitrosourea (ENU) and other chemicals - Benzo(a)pyrene
– Smoking
– Air pollution/Smog
– Folic acid deficiency
– Chemotherapy drugs

Question 33

Polyaromatic hydrocarbons (PAH)

Answer 33

Natural and anthropogenic sources

They are well-recognized as carcinogenic, teratogenic and genotoxic compounds

Question 34

Minisatellites are highly unstable, largely noncoding, genetic elements that are used to demonstrate that environmental factors can affect germline mutation rates. Consist of sequences with 10- to >100-bp repeat units

Answer 34

They have a highermutationrate than other areas of DNA

Question 35

The presence of mutations was subsequently related to general lifestyle factors, including paternal smoking before the partner became pregnant.

Question 36

BaP and ENU increase microsatellite mutation frequencies in sperm

Question 37

Chemically induced germline mutations can be detected through analysis of highly unstable tandem repeat DNA.

Answer 37

BaP is a male germ cell mutagen that broadly impacts tandem repeat DNA

Question 38

Dividing sperm will be more sensitive to the effects of BaP.

Question 39

Chemical exposures can cause mutations in microsatellites, and by analyzing multiple loci, researchers can more reliably determine if a chemical is inducing genetic mutations.

Question 40

Pregnant mice were exposed to BaP during fetal organogenesis, and offspring tissues (brain, liver, bone marrow, ovaries, testis, and sperm) were examined at 10 weeks to assess the effects of transplacental exposure.

Question 41

in utero exposure to BaP affects male offspring reproductive parameters

Question 42

In UteroExposure to Benzo[a]pyrene Induces Ovarian Mutations at Doses that Deplete Ovarian Follicles in Mice

Question 43

BaP effect in reproductive tissues

Answer 43

Developing tissues are highly susceptible

affects sperm development and function.

oogenesis may even be more sensitive to these effects than spermatogenesis

impact on health and disease risk across generations

Question 44

is an inheritance process independent of the classical Mendelian inheritance.

It is an epigenetic process that involves DNA methylation and histone methylation without altering thegeneticsequence.

Genetic imprinting is a process where certain genes are expressed depending on whether they are inherited from the mother or the father, with one allele being silenced in a parent-specific manner.

Answer 44

Genomic imprinting

Question 45

GI

Answer 45

In mammals, a small proportion (<1%) of genes are imprinted, meaning that gene expression occurs from only one allele.

Imprinted genes tend to be organized in clusters

Two major clusters of imprinted genes have been identified in humans, one on the short (p) arm ofchromosome 11
another on the long (q) arm ofchromosome 15.

Question 46

is a type of asexual reproduction in which offspring are produced from an unfertilized egg, meaning no sperm is involved. In some species, the egg develops into a complete organism without genetic input from a male.

Answer 46

Parthenogenesis

does not naturally occur in mammals because genetic imprinting requires contributions from both the mother and father for proper gene expression, and a single-parent offspring lacks this necessary genetic diversity.

If only one parent provides genetic material (as in parthenogenesis, where there’s no fertilization), the offspring only has one set of imprinted genes. Without a contribution from both parents, there’s an imbalance in the expression of these imprinted genes. Some of them won’t be activated, and the others won’t be silenced properly, which disrupts the development process.

Genetic imprinting requires contributions from both parents for the right genes to be activated or silenced. Without this, like in parthenogenesis, the imprinted genes don’t function as they should, making normal development impossible in mammals.

In genetic imprinting, certain genes are either activated or inactivated depending on whether they are inherited from the mother or the father, and this process is essential for normal development.

Question 47

To achieve parent-specific gene expression, epigenetic marks like differently methylated regions (DMRs) are used. One type of DMR is methylated during gametogenesis (germline DMR), and the other becomes methylated after fertilization (somatic DMR).

Question 48

In mammals, epigenetic reprogramming occurs during gametogenesis and early embryogenesis, where parental imprints are erased and new imprints reflecting the embryo’s sex are established. These imprints are passed on to daughter cells but must be reset in each generation to ensure proper parent-specific gene expression.

Question 49

children conceived with assisted reproductive technology (ART), have a greater risk of having imprinting disorders.

Question 50

is the tissue where imprinted genes are most highly expressed

Answer 50

The brain

Question 51

Human diseases involving genomic imprinting includeAngelman syndrome,Prader–Willi syndrome and Beckwith-Wiedemann Syndrome

Answer 51

See diagram

Question 52

is caused by a deletion on the paternal chromosome 15q11-13, leading to symptoms like poor muscle tone, developmental delay, cognitive impairment, hypogonadism, and obesity after weaning. About 25% of cases result from maternal uniparental disomy (UPD) of chromosome 15.

Answer 52

Prader-Willi syndrome (PWS)

Question 53

is caused by a deletion on the maternal chromosome 15q11-13, leading to delayed development, speech and balance issues, intellectual disability, and a characteristic happy, excitable personality. Seizures are also common.

Answer 53

Angelman syndrome (AS)

Question 54

The Y chromosome contains few genes (∼70) and is present only in males, while the X chromosome contains many genes (∼900–1500)

To relieve these imbalances two mechanisms

Answer 54

X upregulation of expressed genes in males and females, and
X inactivation or silencing of one X chromosome in females.

Question 55

TheSRYgeneprovides instructions for making a protein called the sex-determining region Y protein. This protein is involved in male-typical sex development

Question 56

X-chromosome inactivation occurs randomly for one of the two X chromosomes in female cells during development.

Answer 56

Occurs when RNA transcribed from theXistgene on the X chromosome from which it is expressed spreads to coat the whole X chromosome.

Question 57

During X-inactivation, Xist RNA coats and silences the inactive X chromosome (Xi), while Tsix is silenced. If Xist is deleted or truncated, X-inactivation fails, which is lethal for female embryos.

Question 58

About 12% of X-linked genes in humans escape X-inactivation and remain active on the inactive X chromosome (Xi), while another 15% show variable expression across individuals and tissues. These escape regions lack repressive histone marks and have hypomethylated CpG regions.

Question 59

having two X chromosomes leads to improved blood pressure regulation and an increase in the capacity to blunt the effects of brain injuries.

Also developing autoimmune

b/c certain X-linked genes involved in immune response susceptible to reactivation.

Question 60

is a unique technology that enables geneticists and medical researchers to edit parts of the genomeby removing, adding or altering sections of the DNAsequence.

Answer 60

CRISPR-Cas9

Question 61

The CRISPR-Cas9 technique, based on a bacterial defense system, is crucial in biotechnology and medicine, with applications in creating new medicines, genetically modified organisms, and controlling pathogens. It also shows potential for treating genetic diseases and cancer but remains controversial for human germline modification.

Question 62

Delivering CRISPR/Cas9 to mature cells is challenging, with viral vectors being the most common but not 100% efficient or accurate, leading to potential off-target edits. While somatic cells can be edited, germline editing (editing gametes or embryos) could affect future generations and raise ethical concerns, including the potential for enhancing traits rather than just treating diseases.

Question 63

In a case where the mother is healthy and the father is HIV-infected, CRISPR was used to deactivate the CCR5 gene in embryos created through IVF. The CCR5 gene normally allows the HIV virus to enter cells, so deactivating it could reduce the risk of infection. Some people with a homozygous defect in CCR5 are naturally resistant to HIV.

Question 64

The CRISPR edits made in the embryos were not thoroughly tested, and the effects are unknown, raising concerns about unintended consequences. The editing was also not 100% efficient, leading to mosaicism in the embryos. Moreover, the procedure addressed no clear medical need, making the decision unjustifiable.