The Functional Genome

Question 1

What are two examples of next generation sequencing?

Answer 1

We have:

• Whole Exome Sequencing (WES), which is used to capture the sequence of the coding region of the genome.
• Whole Genome Sequencing (WGS), which captures the whole thing (it is not always necessary)

They are rapid modern methods for high throughput DNA sequencing
They aim to identify potential disease-causing genetic variants: personalised medicine.

Question 2

Describe candidate gene filtering using WES.

Answer 2

WES data is subjected to a prioritisation filtering protocol.

During this process, we make multiple assumptions:

• we remove any variants that are common in the database, so we assume that the mutation is rare
• we also assume that the people who have the variant also have the disease
• we also assume that the disease is being caused by a change in the protein rather than a change elsewhere (e.g. promoter sequence)

15-20,000 coding SNPs are reduced to one or several candidate genes. They are checked for co-segregation (if family members have it as well) and validated by Sanger sequencing.

Question 3

The filtered WES variants do not proven causality. We still need further functional evidence.

List some of that evidence.

Answer 3

• tissue/cell expression: see if the gene is actually expressed in that cell type
• detection of protein in patient samples?
• how does change affect protein behaviour?
• how does the change affect cell or development of tissues
• identification of the molecular mechanism of action: common pathways
• development of in vitro and in vivo models for dysfunction of GOI
• knockdown or overexpression affects phenotype?

Question 4

Describe cell culture techniques.

Answer 4

It is the removal of cells from an animal and their subsequent growth in favourable conditions.
It provides a cheap, rapid and reproducible model for
studying the normal physiology and biochemistry of cells.

Primary cells have finite divisions but can immortalised to provide a continuous source.
It’s a good alternative to using animal models, reducing the numbers of animals being used in research, as there are less restrictions on this technique.

Many tissue specific cell lines are commercially available.

Question 5

How do we study gene knockdown?

Answer 5

We study it using RNAi (interference) mediated gene silencing. This can be achieved using two RNAs:

• shRNA (short hairpin RNA)
• siRNA (short interfering RNA)

Question 5

How do we study gene knockdown?

Answer 5

We study it using RNAi (interference) mediated gene silencing. This can be achieved using two RNAs:

• ShRNA (short hairpin RNA)
• SiRNA (short interfering RNA)

Question 6

What is the difference between the siRNA and shRNA techniques?

Answer 6

The difference between shRNA and siRNA is how they’re introduced into the cell.

SiRNA is similar to shRNA; it is chemically synthesised, but it is not vector-based. We can simply transfect it into the cell, skipping out on the transcription phase.

Question 6

Describe short hairpin RNA (ShRNA).

Answer 6

It’s based on endogenous microRNA gene silencing. It’s modified to include GOI complementary sequence

It’s packaged in a DNA plasmid, and its expression is
controlled by an RNA Polymerase III promoter

It exits the nucleus, gets cleaved by a
nuclease called Dicer (found in the cytoplasm). The cleaved segments bind to the RNA induced
silencing complex (RISC) and direct
the cleavage and degradation of the complementary mRNA.

Question 7

What is the difference between the siRNA and shRNA techniques?

Answer 7

The difference between shRNA and siRNA is how they’re introduced into the cell.

Question 8

How can you find out where your GOI’s encoded protein is localised?

Answer 8

You can use antibody staining:

• for the protein of interest
• or for a downstream target

You can also transfect cells with GFP-tagged GOI (in a CMV promoter).

Question 9

Expand on animals in research.

Answer 9

Ideally, we wouldn’t use animals in research. Up to 90% of research uses non-animal methods.
However, the cells behave differently in vitro to in vivo.

Most of the medicines we have today come from animal research. They contributed to 70% of the Nobel prizes.

This is research scientists seek to alleviate pain and suffering for these animals in the experiments, so it has rigorous HO monitoring.

Question 10

Expand on mice as models for human genetic diseases.

Answer 10

• they have an accelerated lifespan (1 yr = 30 human years)
• they’re mammals, so they’re genetically similar
  to humans
• lots of mouse strains and models already exist
• modern genomic engineering has allowed for precise
  mutation to recreate a disease
• it’s deemed more ethical than using
  larger animals/non-human
  primate/humans
• they’re small, reproduce quickly, and are relatively easy to handle and transport

Question 11

Expand on animals in research.

Answer 11

Ideally, we wouldn’t use animals in research. Up to 90% of research uses non-animal methods.
However, the cells behave differently in vitro to in vivo.

Most of the medicines we have today come from animal research. They contributed to 70% of the Nobel prizes.

This is research scientists seek to alleviate pain and suffering, but it needs rigorous HO monitoring.

Question 12

List some reasons as to why zebrafish are a good model for human genetic disease.

Answer 12

• you can add drugs to their water
• they’re an inch in length (so don’t take up space)
• you can take their cells out and implant them into another organisms to see if their fate is determined
• they develop ex-utero, so you can monitor their develop microscopically
• they’re easy to genetically manipulate
• lay eggs on a weekly basis

Question 13

How would you make a mutant mouse?

Answer 13

1) Put lox sites on either sides of the exons, or within the introns of your GOI
2) You have another mouse with Cre-recombinase under the control of a ubiquitously expressing promoter or a tissue-specific promoter
3) You reintroduce ES cells into the mouse (into the cell mass), which will then proliferate and be put into a donor mother, then grow up.
4) You hope some of the mutations enter the germ line, and you select for those that have and develop a stable, mutant transgenic mouse.

Question 14

List some reasons as to why zebrafish are a good model for human genetic disease.

Answer 14

• you can add drugs to their water
• they’re an inch in length (so don’t take up space)
• you can take their cells out and implant them into another organisms to see if their fate is determined
• they develop ex-utero, so you can monitor their develop microscopically
• they’re easy to genetically manipulate
• lay eggs on a weekly basis, so their life cycle is very short

Question 15

When analysing mutations, what are the two ways in which you can do it?

Answer 15

• FORWARD GENETICS (phenotype-based): when you try to find the genetic cause of a phenotype
• REVERSE GENETICS (genotype-based): when you try to find the phenotypic consequence of a genotype change