Genomics and Epigenomics Flashcards
What is rare disease
It affects less than 1 in 2000 people
Typically single gene - can be monogenic, syndromes, or the genetic cause unknown
Give examples of monogenic rare diseases
Cystic fibrosis, phenylketonuria and sickle-cell disease
Give examples of syndromic rare diseases
Down syndrome – trisomy 21
Turner syndrome – monosomy X
DiGeorge syndrome – 22q11 deletion
What is common disease
Affects are more than one in 2000 people
Typically they are complex genetic diseases involving genetic and environmental factors
Come on non-genetic diseases such as bacteria infection may still involve genetics such as in susceptibility and resistance e.g. Covid 19 and ABO locus
Give examples of common non-infectious paediatric diseases
Obesity
Allergic disorders such as hayfever eczema asthma food allergies
Mental health disorders such as anxiety, eating, ADHD, schizophrenia
Learning disabilities
What are some examples of genome variations
SNP Microsatellite Minisatellites Copy number variation Structural variation Chromosomal variants
Describe chromosomal rearrangements
These can be insertions, deletions, inversions and translocations
Unbalanced – localised gene dosage changes
Balance – gene dosage is unaffected but can cause gene disruption or fusion products
An example of this is the chronic myeloid leukaemia BCR-ABL gene located on the Philadelphia chromosome
How are chromosomal rearrangements detected
INSERT ANS
What is are balanced and unbalanced translocations
Unbalanced - localised gene dosage changes
Balanced - gene dosage unaffected but fusion products can occur or it can fall under a different promoter
Example: in chronic myeloid leukaemia, a Philadelphia chromosome contains a BCR-ABL fusion gene, causing constant expression of ABL(a tyrosine kinase gene) causing increased unnecessary thus harmful cellular signalling pathways
What is penetrance and expressivity
Penetrance is when an individual has the disease genotype but do not express symptoms thus does not express a phenotype
Many diseases show age dependent penetrance
Expressivity is the severity of the symptoms and how they can differ person-to-person
What is pleiotropy
A mutation that affects multiple body systems
This is usually seen when the gene affected is involved in early development
What is sex-influence or limited inheritance
This is when there is over representation of a disease in one sex not due to the gene but due to other factors related to sex such as hormones or presence of womb/prostate etc.
What may be a complication caused by presence of de novo mutations when sequencing DNA for genetic diagnosis
De novo mutation may be discarded as the mutation is not found in the parents and may seem like an artefact
Analysis is performed after Mendelian inheritance is investigated
Give an example of a single gene that is associated with multiple disorders
The LMNA gene produces lamin A and C
These are nuclear lamin protein which form the fibrillar network
These are involved in many different disorders including muscular dystrophies
What is heritability
Heritability is the proportion of phenotypic variation due to genotypic variation
What are two ways of measuring heritability
GWAS
Twin studies
What is missing heritability
It is when GWAS results differ from twin studies
What are the possible reasons for missing heritability
GWAS may measure many infrequent or rare SNPs
Each SNP may have variable effect sizes
There may be copy number or structural variations
Epigenomic influence
Or maybe the measurements and investigations were conducted wrong
Give an example of a disease that is rare and common
Obesity and the MC4R gene
Explain how obesity is a rare and common disease and the involvement of the MC4R gene
MC4R is the melanocortin 4 receptor
It responds to alpha melanocyte stimulating hormone which releases anorexigenic signals decrease in appetite
Rare =
Deficiency causes hyperphagia and obesity
Deficiency is autosomal dominant
Common =
Variance in this gene can also contribute to complex obesity
What do you know about DNA methylation
DNA methylation is the main way gene activity is adjusted during life, especially during early development. It is a process by which methyl groups are added to DNA. This suppresses gene transcription. Two of DNA’s four nucleotides, cytosine and adenine, can be methylated.
Regulating tissue-specific gene expression, genomic imprinting, and X chromosome inactivation.
Aging is strongly correlated with changes in DNA methylation. DNA methylation and epigenetic alterations have been directly linked to longevity in a wide array of organisms, ranging in complexity from yeast to humans.
What is histone modification
Occurs at the C and N terminal tails
This includes acetylation, methylation, phosphorylation, ubiquitination
Example = H3K4ME3
What enzymes are involved in histone modification
Writers Histone acetyltransferase (HAT1) - targets lysine residues reducing the charge and opening up the DNA Histone methyltransferase (HMT1) - represses OR activates
Erasers Histone deacetylase (HDAC1) Histone demethylase (KDM1)
Readers
Bromodomain and extra terminal proteins -BRD2
Chromodomain proteins - CBX1
What do you know about the 3D interaction of nucleosomes
They form topologically associated domains (TAD) which create chromosomal loops
These can be separated into two compartments – A and B
A = early replicating / active chromatin
B = late replicating / inactive chromatin
This helps in regulation by bringing silences or enhances in contact with the promoters
Cohesion and CTCF separate and compartmentalise these loops preventing cross reaction
What do you know about X-inactivation
Regulated by X inactivation centre (Xic)
lncRNA Xist is transcribed from here which spreads and coats the X chromosome in cis
Xist recruits various chromatin modifying enzymes like polycomb = heterochromatin, chromosome compaction (Barr body) and gene repression
Random inactivation - Mosaic like
What do you know about genomic imprinting
Process by which one parental allele is silenced according to its parental origin
Conflict hypothesis
Paternally expressed genes = promote growth
Maternally expressed genes = supress growth
Describe how enhancers are involved in Alzheimer’s disease
30% of SNP’s are associated with enhancers
95% of these enhancers are involved in TADs associated with amyloid beta clearance, synaptic transmission, and immune response
What is the transcriptome and epitranscriptome
Transcriptome - all RNA transcribed from DNA
Epitranscriptome - all RNA transcribed that is involved in gene expression
What are some examples of RNA involved in the epitranscriptome
LncRNA - X-inactivation miRNA siRNA tRF - tRNA related fragments piRNA- piwi-interacting DNA
These are involved in gene expression regulation, anti-viral activity, regulation of the proliferation and differentiation
How do miRNAs work
They are transcribed and processed by Drosha-DGCR8 into pre-miRNA and then further processed by Dicer
It binds upstream of the ORF to stop translation or cleavage of mRNA
What are siRNAs and what are their drawbacks
They are short RNA which are also processed by Dicer and incorporated into RISC
Off target effect – it tolerates mismatches and can silence multiple genes
Efficacy – less than 20% induce 90% silencing
Delivery – Rapidly degraded nucleases/excreted by the kidneys, the half life is from 15 mins to 1 hour
Immune response – it is naturally part of the innate immune system and can induce interferon expression
Can RNA be methylated and how is it detected
Like DNA,RNA can be methylated
Different NGS methods can be used and mass spectrometry
What is pharmacoepigenetics and how is it used
These are drugs which take advantage of the epigenetic genome
This includes understanding and taking advantage of epigenetic regulation which can impact ADME and disease gene to improve drug efficacy
Also drugs may be involved in correction of epigenetic markers
Describe the epigenetics of cancer
In cancer there is a global DNA methylation alteration
Hyper methylation of tumour suppressors
Hypo methylation of tumour activators
Also epigenetic enzymes are often mutated
This includes DNMT3A and TET, and histone enzymes
Give examples of pharmacoepigenetic drugs
DNA methyltransferase inhibitors
Histone deacetylase inhibitors
Histone methyltransferase inhibitors
miRNA - cancer, heart failure, hepatitis C infection, scar tissue
siRNA - mainly targets diseases of the eye, some cancers, scars
Describe how enhancers are involved in Alzheimer’s disease
30% of SNP’s are associated with enhancers
95% of these enhancers are involved in TADs associated with amyloid beta clearance, synaptic transmission, and immune response
What is the transcriptome and epitranscriptome
Transcriptome - all RNA transcribed from DNA
Epitranscriptome - all RNA transcribed that is involved in gene expression
What are some examples of RNA involved in the epitranscriptome
LncRNA - X-inactivation miRNA siRNA tRF - tRNA related fragments piRNA- piwi-interacting RNA
These are involved in gene expression regulation, anti-viral activity, regulation of the proliferation and differentiation
How do miRNAs work
They are transcribed and processed by Drosha-DGCR8 into pre-miRNA and then further processed by Dicer
It binds upstream of the ORF to stop translation or cleavage of mRNA
What are siRNAs and what are their drawbacks
They are short RNA which are also processed by Dicer and incorporated into RISC
Off target effect – it tolerates mismatches and can silence multiple genes
Efficacy – less than 20% induce 90% silencing
Delivery – Rapidly degraded nucleases/excreted by the kidneys, the half life is from 15 mins to 1 hour
Immune response – it is naturally part of the innate immune system and can induce interferon expression
How can RNA methylation be tested for
Some NGS methods
Mass spectrometry
What is pharmacoepigenetics and how is it used
These are drugs which take advantage of the epigenetic genome
This includes understanding and taking advantage of epigenetic regulation which can impact ADME and disease gene to improve drug efficacy
Also drugs may be involved in correction of epigenetic markers
Describe the epigenetics of cancer
In cancer there is a global DNA methylation alteration
Hyper methylation of tumour suppressors
Hypo methylation of tumour activators
Also epigenetic enzymes are often mutated
This includes DNMT3A and TET, and histone enzymes
Give examples of pharmacoepigenetic drugs
DNA methyltransferase inhibitors
Histone deacetylase inhibitors
Histone methyltransferase inhibitors
miRNA - cancer, heart failure, hepatitis C infection, scar tissue
siRNA - mainly targets diseases of the eye, some cancers, scars
What test can find insertions and deletions, and what can find inversions and translocations
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