Genetics part 3 Flashcards
What are 5 of the genes that cause DC?
- DKC1
- TERT
- TERC
- TINF2
- RTEL1
What is DKC1?
- Dyskeratosis congenita 1
- Encodes the protein called dyskerin
- Core component of telomerase
What is TERT?
The reverse transcriptase component of telomerase
Uses TERC as a template to synthesise telomeric DNA
What is TERC?
RNA component of telomerase
Act as a template for TERT
What is TINF2
A shelterin component
Protecting the telomere
What is RTEL1?
A regulator of telomere elongation
A DNA helicase that resolves D-loops during replication
What is pathophysiology of DC?
- Mutations in DC genes result in defective telomere maintenance
- Defective telomere maintenance results in premature senescence and apoptosis
- Early loss of cells (e.g. stem cells) leads to progressive development of disease features
- This is most pronounced in rapidly dividing tissues, notably the bone marrow
What are BMF syndromes?
Inherited
What is Dyskeratosis congenita?
Clinically and genetically heterogenous BMF syndrome
What are telomeres?
Specialised structures that protects the end of each chromosome
What are three distinct pathways that are defective in the inherited BMF syndromes?
- Fanconi anaemia
- Shwachman Diamond
- Dyskeratosis congenita
Fanconi anaemia
FANC genes
Involved in DNA damage response
Shwachman Diamond
Only 1 gene that causes this disease
Defect is present in the ribosome
Dyskeratosis congenita
Telomere maintenance
TERC, TERT
What is ERCC6L2?
New disease gene
Allelic series in exome sequencing data
What does ERCC6L2 stand for?
excision repair cross-complementation group 6 like 2 gene
Homozygous Arg655*
Red is loss of variant function
Green - missense
What is ERCC6?
DNA binding protein
Transcription coupled excision repair
What does mutation in the ERCC6 cause?
Cockayne syndrome
Not associated with bone marrow failure
What does ERCC6L2 play a role in?
DNA damage response
Mitomycin C
- Causes interstrand cross link
- Key test for people with Fanconi anemia
- Fanconi anaemia very sensitive to this drug
What does Irofulven cause?
Adducts
What is R-loops?
Occurs every time a gene is transcribed
RNA polymerase ploughs along the DNA making RNA and loop back on itself
R loop are dangerous and need to be re-solved
RNA coated with proteins – looked after as soon as it is made
2 loss of function variants in affected individuals
What is DNAJC21
- Disease causing genes
- Spectrum of phenotypes overlapping
- Homozygous - biallelic - both alleles are affected
What is Jjj1?
- Ribosome maturation
2. Involved in ribosome biogenesis
Ribosome biogenesis
- The rDNA locus in the genome – is the DNA that encodes for the ribosomal proteins
- It is repeated massively in vast tracks as we make a lot of ribosomes
- We transcribe the locus and process it and process it down again and get 2 subunits forming
- The large subunit will try to get out of the nucleolus to the cytoplasm
- To do that, it needs accessory proteins, there are a number of enormous accessory proteins involved in getting a ribosome made e.g. 200 proteins involved in ribosome assembly
- They get onto the ribosomes to get it out into the cytoplasm where it is joined to two other proteins which all stick together and cause reaction and kick the red protein back into the cytoplasm
How many ribosomal subunit cross the nuclear pore every minute?
20,000
What is theory of defective ribosome maturation?
Disturbs stem cell function
Also leukaemia promotion
What is SDS (shwackman diamond syndrome) characterised by?
- BMF
- pancreatic insufficiency
- Predisposition to leukaemia
What bis required for the last stage of 60S subunit maturation?
SBDS
What is Dameshek’s riddle?
The hypo-proliferative to hyper-proliferative paradox
What is the yeast orthologue of DNAJC21?
Jjj1
Define Orthologue?
a gene in a different species that evolved from a common ancestral gene
What is the gene in humans related to?
Ancestral gene in yeast
What is Epigenetic effects?
Causes a difference in methylation
Regulates gene expression
Mutations, which lead to different severity of clinical phenotypes
- Differences in severity of clinical phenotype e.g. BMD and DMD
- Mutations in which you have changes in the frame of MRNA that will cause catastrophic changes to protein (DMD)
- If the protein stays inframe but becomes either larger or smaller – (BMD)
What does Genome Engineering allow for?
Targeted and specific modification of a genome of living organism
What are the types of targeting methods?
- Zinc finger nucleases
- Talens
- Crispr-Cas9
Repair of double-stranded breaks
- once double strand break is generated - cell attempts to repair it as quickly as possible
- Via non-homologous end joining
- Error-prone technique
- Introduce or delete a few nucleotides
What happens when double-stranded break occurs?
You cannot influence the type of mutation generated
What is another experiment of double-stranded break?
- Provide the cells with a donor template
- Cell uses donor template to manufacture missing sequence to fill gap
- o When the donor template is designed the 5’ and 3’ regions need to be exactly the same sequence as sequence you attempt to target – introduce mutation within the middle
How do you create double-stranded break?
Use zinc finger nucleases
What are zinc finger?
Combined DNA and are the most common DNA binding in eukaroytes
Different versions - Cys (2) his (2) - Cys (2) hiscys Hold a zinc atom Zinc fingers bind 3-4 BP of DNA
Assembling zinc fingers to bind DNA – create targeted double stranded breaks by FOK1
Libraries with zinc fingers – known to bind to triplets of nucleotides
If the right zinc fingers are put together molecularly – bind to particular sequence of choice
The zinc finger itself wont make a double-stranded break – an endonuclease is required
FOK1 molecules are added
FOK1 is endonuclease but it needs to dimerise – 2 fok1 molecules required
Fok1 dimerizes and makes a double stranded break
Problem with zinc finger is that they don’t always bind to their target
Assay: 3 zinc finger together = determines if it binds and a reporter gene
Where do Talens come from?
Pathogens Xanthomonas
What are Xanthomonas?
Transcription factors that bind DNA and drive host genes which are beneficial to Xanthomonas
Talens
- Contains repeat domains – essential for binding
- Transcription factors need to be in the nucleus and contain activation domains
- Contains 34 amino acids – repeated many times
- Amino acids between 12 and 13 which nucleotides of DNA it binds to – called repeat variable di-residues
What do Talens bind and activate?
Host promoters
What are 2 component system of Talens?
- DNA binding domain
2. FokI DNA-cleaving domain
What does Talen enable?
Editing of the genome in specific locations
Determining which variable di-residues bind to different nucleotides
- E.g. histidine and aspartic acid – mainly binds to C
- E.g. asparagine and glycine mainly bind to T
- Make molecule and clone the right repeat domain in sequence
- If you get the right amino acid together in 12 and 13 – target any sequence you would like to bind to
- In Xanthomonas these are transcription factors – so they don’t make a double stranded break
How does Talen clones generate double stranded breaks?
combining (Targeted/specific) DNA binding capability with FOKI endonuclease activity
What is Crispr-Cas9?
- Edit parts of the genome – removing, adding or altering sections of the DNA sequence
- Comes from single cellular organism – Achaea and bacteria
- Used as an adaptive immunity
- Invasion of single cellular organism by phage
What are 2 molecules of Crispr-Cas9?
- Enzyme: Cas 9 – acts as molecular scissors that cut 2 strands of DNA at a specific location in the genome – bits of DNA can then be added or removed
- A piece of RNA called guide RNA (gRNA) – consist of small piece of pre-designed RNA sequence located within a longer RNA scaffold
- Scaffold part bind to DNA
- Pre-designed sequence guides cas9 to the right part of the genome
- The guide RNA is designed to find and bind to a specific sequence in the DNA
- The cas9 follows the guide RNA to the same location in the DNA sequence and makes a cut across both strands of DNA
- At this stage the cell recognises that DNA is damaged and tries to repair it
What is involved in maturing pre-CRISP RNA?
TracrRNA
What are 3 molecules important for binding of CRISPR cas9?
- CRISPR RNA
- TracrRNA
- Cas9
DNA sequence requirements for CRISP-cas9
- CRISP RNA is complementary to the sequence you want to target
- NGG – protospacers – the sequence you are trying to target in the genome
- Protospacers adjacent motif – important sequence for the complex
- For Cas9 to bind to the complex – need particular sequence called NGG
- Any nucleotide followed by two G
- To target sequence by CRISP RNA – NGG has to be adjacent
How do we get TALEN/CRISPR- Cas9 reagents into the cell?
• Viral method
• Lipid transfection
- Lipid binds to the DNA
- By endocytosis you get all the RNA into the cell
Electroporation
- Mix the cells with DNA or RNA – use current to get the macromolecules in
- Optimization is required because high current is used – destroy the cell whereas if you don’t use enough – nothing can happen
- After the molecules are introduced into the cell – make clonal line – dilute the cells
Assessing how efficient the genome engineering tools are
- Assay used
- Introduce CRISPR-cas9 or talen into cells- by non-homologous end joining you will get introduction of mutations (small deletions/small insertions)
- Pool of different mutations in this dish
- T7E1 detects little mismatches in DNA and it can cleave
- See cleavage products on agarose gels when you separate these
- Some cells will have mutations but they may be different mutations (small BP insertion 1,3) and some will be wild type
- After a few days you isolate the genomic DNA from the cells, so you have a mixture
- And you do PCR amplification with primers which flank the region your targeting
- When you do PCR you have some molecules which have a mutation at a location ur tryna target and some will be wild type
The higher intensity of these cleavage products
the better your reagent works
Detection of mutations in closes after genome engineering
- Clonal lines of cells
- Non-homologous end joining – PCR – flank region you are trying to target
- Larger deletions are detected on an agarose gel
- Do PCR run on agarose gel – smaller products
- Resolution of gels aren’t great – wont see a difference
- DNA sequencing done – determine if mutation is present or not
Off-target effect
o Mutation that occurs when the reagent doesn’t bind to regions, bind elsewhere in the genome and cause mutation there
o For talen – 1% mutations somewhere
o CRISPR-CAS9 – up to 77%
o The differences in percentage is because for talens you need 2 fok1 molecules to dimerise – chance of this happening elsewhere in the genome is low
o Zinc finger nucleases
- Adv.: eliminates risk of random genome integration of expression plasmid DNA
- Lowers cytotoxicity
- Higher efficiency
- Expanded range of cell types
- Eliminated the need to use different promoters for ZNF expression
- Dis: off-target effect
o Talens
- Adv.: all DNA sequences can be targeted
- The cloning of construction of DNA molecules with TALEN repeats is more cumbersome
- Highly repetitive nature of TALEN- coding sequence creates barrier to their delivery – viral vectors
- Dis: only single site at one time
- Designing construct is time consuming and are not cost-effective
- Sensitive to target DNA methylation
o CRISPR-CAS9
- Adv.: highly specific
- Highly efficient
- Simultaneous targeting of multiple sites
- Dis: target selection limited by requirement of PAM sequence
- Off target effects
Mitochondrial disease treatment
• Technique to remove the disease causing mitochondria by producing 3 parent babies
• Genomic engineering techniques
- Correct pathogenic mtDNA mutations in vivo in the mouse
• Mutation: TRNA is affected
• Mouse model: leads to cardiomyopathy
• Mitochondrial zinc finger nucleases are used to target this mutation
• Zinc fingers that specifically target these sequences
• Types of zinc fingers
- Wtm1: will always bind
- Mtm25: won’t bind if its wild type
• Ta – mutation – bind and caused double stranded break
• Degradation of mtDNA – double stranded break
• Change the ratio from wild type to mutated mtDNA
• >60% mutated mtDNA – see a phenotype
• Push the percentage down below threshold – stop the disease from happening
• Injected 2 zinc finger nucleases construct into the tail vein of mice
• Then used adeno-associated virus – specifically targets the heart – change the ratio
Authors compared the heart with the ear
determined % of wild type mtDNA with mutated mtDNA in heart and earo Since the virus only targets the heart – expected to change the ratio only at the heart
o Virus will bind to mutated DNA in heart – double stranded break – degradation of mutated DNA
o First control: use without zinc finger nuclease – compare heart and ear - % of mutated DNA is around 0
o Second control: one zinc finger nuclease – similar quantities between heart and ear
o Put both in increasing concentration of viral vector – see an effect
Pronuclear transfer technique
o Technique that uses cells
o Lady who has mitochondrial disease
o Aim: prevent transmitting the mutated mitochondria
o Use oocyte of a donor female without disease
o Fertilize both oocytes with sperm from the father
o Remove the pronuclei from donor
o Insert pronuclei from parents into donor egg
o You have genomic DNA from the parent but mtDNA from donor
o By IVF – get a baby without mitochondrial disease
Spindle transfer technique
o Before the oocytes are fertilized
o Remove genetic material from the donor
o Insert the genetic material from lady who can transmit the mitochondrial disease
o Fertilize it with sperm from the father
o IVF: get lady pregnant and deliver baby
- Too early to determine if the methods are completely safe
- Some carry over of mutated mitochondria (2% reported) – affect future generations – effect female to the donor
- Technique approved by house of common
- UK license granted last year
- Law has been passed in London to create baby via pro nuclear transfer technique and not spindle transfer technique
The use of TALEN to create haemophilia A model
• Mutation in factor 8 can give rise to haemophilia A
• Factor 8 has region in intron 1 which is identical to a sequence which is 140,000 BP over to this side
• Recombination between these two
• Net effect
- Exon 1 of the gene with all the regulatory element pointing in one direction
- Exon 2 with non-regulatory elements and the rest of gene pointing in other direction
• Severe phenotype – no factor 8 produced
• Inversion – refer it back to wild type
• Number of different talen reagents - which one is best to use for inversion
• T7E1 assay
• In control – don’t see smaller products – cleavage with T7E1
• Talen 1 – good – 33% mutations incorporated
• Talen 3 is very bad – don’t see affect any of these smaller products
Talen-mediated inversion of F8 locus in IPSC
o Wild type line + some controls
o Control from patient
o Had double strand break
o Talen is identical – regions are identical in sequence
o To make double strand break in both – make inversion
Use PCR:
o Wild type intron 1 – have homolog 1, consist of primers 1F and 1R
- 140,000 bp you have 2F and 2R in homolog 2
o Inversion: primer 2R sits opposite 1R and 1F is opposite 2F
o By using PCR reaction – you can tell if you’ve managed to get this inversion
o First line of PCR → looking with primer 1F and 1R
o Wild type situation: amplify band o In patient where 1F and 1R are both pointing in the same direction and are 140,000 bp apart – never going to amplify the PCR product here – the line is empty
o 1R-2R – flipped over when we have this inversion
o Patient in junction 1: primer 1R and 2R are used – amplify the PCR product
REVERSIONS of the F8 gene inversion
o Take one of the inversion clones and reverted it back to a normal gene
o Used same talen
o Can flip it back to normal
o Homolog 1 – 1F and 1R – wild type give you a PCR product
o The patient and inversion clone’s don’t
o Cells are hematopoietic lineages and can be isolated – returned relatively easily
o All processes conducted at a clinical grade
o Off-target effects have to be controlled for
CRISPR-CAS9 – restore Dystrophin function in DMD:
o Mutations in dystrophin can lead to BMD and DMD
o Mutation in exon 44
o Goes out of frame and you get a stop codon – lead to DMD
- REMOVE splice acceptor from exon 45, get splicing from 43-46 – the protein goes back into frame – shorter protein
- Creating reading frame shifts – add extra nucleotide to exon 45 – back into frame – it can be 1 bp or multiple
- Knocking exon 44 in front of exon 45 – restore the whole of the protein donor template required -
- This is intron-exon boundary
