mechanisms of mutation and inheritance

general facts

• mutations can occur due to mistakes during genome replication or cell division (e.g. polymerase makes a mistake)

• germline (entire organism carries the mutation, half of the gametes carry mutation)

• somatic (certain affected areas, none of the gametes carry the mutation)

• missense (1+ bases change, causing a change in amino acid)

• polyploidy (extra set of chromosomes)

• aneuploidy (an extra or missing single chromosome)

aneuploidy

• Chromosomes line up during metaphase (only kinetochores on one side of the chromosome attaches to the spindle fibres 

• In anaphase, both sister chromatids go to one side of the cell (nondisjunction) 

• When gametes form one will have 0 chromosome, one will have 2 

  • The cell without any dies, the other can fertilise 

  • If a cell has 3 sets of chromosomes it causes downs syndrome 

splice site mutations

• Splice sites: Exon–intron boundaries needed for pre-mRNA splicing

  • 5′ donor site = GU

  • 3′ acceptor site = AG

• Splice site mutations: DNA changes that disrupt normal splicing

  • Canonical (GU/AG) or nearby regulatory regions

• Abnormal splicing outcomes:

  • Exon skipping

  • Intron retention

  • Cryptic splice site activation

• mRNA consequences:

  • Frameshift or premature stop codon

  • Nonsense-mediated decay (NMD)

• Protein effects:

  • Truncated or absent protein

  • Loss of function (most common)

  • Rare dominant-negative or gain-of-function effects

• Mutation types:

  • 5′ donor → exon skipping/intron retention

  • 3′ acceptor → exon skipping

  • Deep intronic → cryptic splice sites

  • ESE mutations → altered exon recognition

• Disease relevance:

  • ~10–15% of pathogenic variants affect splicing

  • Seen in inherited disorders and cancer

recessive vs dominant mutations

• Both copies of a gene need to be inactivated by mutations for a genetic disease to manifest (recessive) 

• Mutation in one copy is sufficient for a given disease phenotype (dominant) 

• In other cases, the single mutated gene copy may have a 'dominant negative'. This interferes with normal structure as half the protein is mutated 

mendelian (monogeneic inheritance)

• The presence of mutation in a single gene is sufficient for disease phenotype 

locus heterogeneity

• One phenotype can be caused by multiple different mutations 

• Phenotypic rescue can occur (as a normal gene can be passed on from both parents) 

incomplete penetrance

• May not cause disease when otherwise expected 

• Genetic background (variation in other genes) and environment can influence the disease phenotype 

x-linked inheritance

• Male = XY 

• Female = XX 

• Leads to non-standard inheritance patterns 

• Recessive = sex of parent affects whether children can be affected 

• Dominant = more likely 

x inactivation

• Happens in the female early embryo (@200 cells) 

• Can lead to some unexpected outcomes 

  • Normally half normal and half mutated are inactivated 

  • If over half of normal are inactivated = disease 

  • Can then be passed onto future children 

genetic anticipation

• Where 'premutations' are phenotypically benign but are destined to transform into pathological mutations in subsequent generations 

• CGG repeats are transcribed 

  • DNA transferase methylates them (target is long sequences of CGG repeats) 

  • Often full mutation is many repeats (builds up over generations) 

  • For CGG = over 200 repeats = mutation 

mitochondrial inheritance

• MtDNA = small (roughly 37 genes) 

• Inheritance displayed in own patterns 

• Inherited exclusively from mother (matrilineal) 

  • As mitochondria are in egg cell 

• Heteroplasmy complicates inheritance 

  • Bottleneck affect (a small number of mothers mitochondria randomly go into each egg cell) 

  • Different amounts of mutated mitochondria can be found in egg cells 

  • The number of mitochondria increases (more mutated = greater proportion mutated = worse disease 

  • Symptoms in each organ will only manifest if they contain a certain number of mutated mitochondria 

the polygenic/infinitesimal model

• Several mendelian units contribute additively to the end result 

  • Explains reduced recurrence risk amongst siblings (as there are a larger number of risk alleles (all with a smaller affect) needed for disease manifestation 

polygenic threshold model

• Do display a binary character despite polygenic nature 

• There is a polygenic disease threshold (large number of disease alleles) which when reached = disease 

Carter effect

• Some complex genetic diseases also display sex dimorphism 

  • Can be explained with polygenic threshold model 

  • Thought females have a higher disease threshold than males 

heretability and its estimation

• Phenotypic variation in a given population that is due to variation in genetic factors within the population is referred to as 'heritability' 

• It is a population-specific parameter that relates to variance  

• It has classically been estimated via 'twin studies' which aim to estimate the extent to which a particular trait is determined by genetics vs environment 

twin studies

• Monozygotic (genetic study) 

• Dizygotic (environmental study) 

• Some studies consistently suggest that both genetic factors and environment can contribute to complex disease manifestation 

  • Phenotypic variance = heritable genetic variance + environmental variance (broad sense heritability) 

  • Heritability = 2 (concordance rate monozygotic x concordance rate dizygotic) 

• In the classic view of the polygenic model, genetic variants each contribute additively to heritability (narrow-sense heritability) 

• Broad sense/total heritability estimates include contribution from non-additive genetic factors too 

• Such non additive contributions can result from interaction between genetic variants and two types can be defined 

  • Dominant vs epistasis 

dominant vs epistasis

• When there is interaction on one gene loci (dominant) 

• When one loci effects the phenotype of another loci (epistasis) 

• V_G = V_{A (additive)} + V_D(dominant) + V_I(epistasis)  

  • Narrow sense heritability 

somatic mutations in non-cancerous disease

• Mutations/genetic variation occur continually throughout normal growth 

• These are very difficult to detect  

• Can cause non-cancerous diseases 

• The earlier on a mutation happens, the more likely it is to affect a larger proportion of the organism 

• Brain is the most susceptible to phenotypic outcome from disease (due to large number of cells) 

 

• Phenotypic characters may not only be determined by heritable genetic variants and environment, but also an individualized genetic variation that each of us pick up during our own development and growth 

• Phenotypic variance (V_P) = Environmental variance (V_E) + Heritable genetic variance (V_G) + ‘Personalised’ genetic variance (V_S) 

somatic mutations in non-cancerous disease p2

 

• Uncontrolled cellular growth can be considered a natural Darwinian process whereby a cell picks up genetic variations that confer selective growth advantages to it and its progeny 

• In a multi-system organism, this can be harmful and thus genetic mechanisms have evolved to supress this Darwinian instinct 

 

• In cancers, such genetic defence mechanisms are inactivated via successive mutations; cancerous cells thus display some common features, including 

  • The ability to replicate indefinitely  

  • The ability to evade apoptosis 

 

• Genetic mutation is thus a central event in tumour formation. Mutations which accelerate the mutation rate itself are thought to be the 'early drivers' of some cancers, e.g. 

  • Mutations that inactivate DNA repair pathways 

  • Mutations that increase the rate of cell division and therefore DNA replication 

cancer stem cells

• Cells that can replicate themselves or undergo differentiation 

• Adult stem cells are found in all organs 

  • To replenish tissue throughout the lifetime of the individual 

  • Replicate indefinitely 

• Cancer stem cells can renew themselves indefinitely  

  • Due to a mutation 

  • Already have the ability to replicate already (stem cells) 

  • If tumour cells are targeted, the tumour will shrink and grow back 

  • If tumour stem cells are targeted, the tumour can degenerate 

oncogenes

• When activated in a certain way will drive cancerous formation 

• This activation involves a somatically occurring 'gain of function' mutation, and this only needs to occur in one copy of the gene 

• Associated cancers usually occur sporadically with no family history 

• Can amplify a gene/change gene function 

• e.g. abl/bcr gene 

  • Combine 

  • Cause uncontrolled hemopoietic cell division 

  • Leads to leukaemia 

tumour supressor genes

• These usually carry out some function that supresses tumour formation 

• Their biallelic inactivation contributes to tumorigenesis 

• Associated cancers much more commonly display a family history 

• Can occur sporadically more rarely 

• Knudson's two-hit hypothesis 

  • A mutation occurs in a somatic cell 

  • A mutation occurs in a single cell 

  • A mutation occurs in the same single cell = tumour 

  • If already likely to have one mutation = much more susceptible (only need to have one mutation) 

breast cancer and fanconi’s anaemia

• BRCA1 and BRRCA2 are the major human breast cancer susceptibility genes 

• If a mutant copy of the genes if inherited, the risk of breast cancer jumps to 60/45% by 70yrs 

• The genes encode proteins for efficient repair of damaged DNA 

• Fanconi's anaemia is a congenital condition associated with bone marrow failure, developmental abnormalities present at birth and an increased risk of leukaemia 

• Biallelic mutations in any one of several genes can cause FA 

• It was found that biallelic mutations in BRCA2 can also cause FA 

  • Heterozygous BRCA2 inherited from parents + mutation as an adult = breast cancer 

  • Homozygous defective BRCA2 inherited from parent = FA 

non-homologous end joining

• Purpose:

  • Repairs DNA double-strand breaks (DSBs)

• When it occurs:

  • Active throughout the cell cycle (G0, G1, S, G2)

  • Primary DSB repair pathway in G1

• Key feature:

  • Does NOT require a homologous DNA template

• Major repair pathway for:

  • Ionizing radiation-induced damage

  • Programmed DSBs

• Essential for:

  • V(D)J recombination (immune system diversity)

process of non homologous end joining

• Break recognition:

  • Ku70/Ku80 heterodimer binds to DNA ends

• Recruitment:

  • Ku recruits DNA-PKcs → forms DNA-PK complex

• End processing:

  • DNA ends may be trimmed or filled in

  • Enzymes involved:

    • Artemis (nuclease)

    • DNA polymerases μ and λ

• Ligation:

  • DNA ends joined by:

    • DNA ligase IV

    • XRCC4

    • XLF (Cernunnos)

homologous recombination

• Purpose:

  • Repairs DNA double-strand breaks (DSBs) accurately

• When it occurs:

  • Mainly during S and G2 phases

  • Requires a homologous DNA template (sister chromatid)

• Key feature:

  • High-fidelity repair (error-free)

• Repairs:

  • Replication-associated DSBs

  • Collapsed replication forks

• Maintains:

  • Genomic stability

• Essential for:

  • Meiosis (crossing over)

process of homologous recombination

• DSB recognition & resection:

  • MRN complex (MRE11-RAD50-NBS1) detects break

  • 5′ ends resected → creates 3′ single-stranded DNA (ssDNA)

• Strand protection:

  • RPA binds ssDNA to prevent degradation

• Strand invasion:

  • RAD51 replaces RPA

  • RAD51-ssDNA filament invades homologous duplex DNA

• DNA synthesis:

  • DNA polymerase extends invading strand using template

• Resolution:

  • Holiday junctions resolved → intact DNA restored

von hippel-lindau syndrome

• VHL is characterised by fatigue, poor motor-coordination and vision impairment 

• One mutated copy of the VHL gene is sufficient for symptoms to manifest 

  • HIF alpha cannot be degraded (due to mutation) 

  • Binds to HIF beta 

  • Causes hypoxia induced gene expression 

• If somatic inactivation of the second VHL copy occurs, then this leads to tumours in the vasculature that supplies various systems/organs